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PDBsum entry 5p21

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protein ligands metals links
Oncogene protein PDB id
5p21
Jmol
Contents
Protein chain
166 a.a. *
Ligands
GNP
Metals
_MG
Waters ×211
* Residue conservation analysis
PDB id:
5p21
Name: Oncogene protein
Title: Refined crystal structure of the triphosphate conformation of h-ras p21 at 1.35 angstroms resolution: implications for the mechanism of gtp hydrolysis
Structure: C-h-ras p21 protein. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
1.35Å     R-factor:   0.196    
Authors: E.F.Pai,A.Wittinghofer,W.Kabsch
Key ref: E.F.Pai et al. (1990). Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J, 9, 2351-2359. PubMed id: 2196171
Date:
30-Apr-90     Release date:   15-Jan-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
166 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     signal transduction   3 terms 
  Biochemical function     GTP binding     1 term  

 

 
EMBO J 9:2351-2359 (1990)
PubMed id: 2196171  
 
 
Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis.
E.F.Pai, U.Krengel, G.A.Petsko, R.S.Goody, W.Kabsch, A.Wittinghofer.
 
  ABSTRACT  
 
The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail. For the stretch of amino acid residues 61-65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma-phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in-line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3pxn
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PDB codes: 3sbd 3sbe 3th5
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PDB codes: 3kxi 3kxk 3kxl
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PDB codes: 3k8y 3k9n 3lbh 3lbi 3lbn
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PDB code: 2w6d
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PDB codes: 3e7w 3e7x
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17599776 J.Milić, R.Seidel, C.F.Becker, R.S.Goody, and M.Engelhard (2008).
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18386081 J.Petersen, C.J.Mitchell, K.Fisher, and D.J.Lowe (2008).
Structural basis for VO(2+)-inhibition of nitrogenase activity: (B) pH-sensitive inner-sphere rearrangements in the 1H-environment of the metal coordination site of the nitrogenase Fe-protein identified by ENDOR spectroscopy.
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PDB codes: 3bb1 3bb3 3bb4
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PDB code: 3def
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Cofactor dependent conformational switching of GTPases.
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PDB code: 2cjw
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Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations.
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17385754 C.Kötting, A.Kallenbach, Y.Suveyzdis, C.Eichholz, and K.Gerwert (2007).
Surface change of Ras enabling effector binding monitored in real time at atomic resolution.
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  Mol Cell Biol, 27, 3695-3707.  
17320764 M.Sethuraman, N.Clavreul, H.Huang, M.E.McComb, C.E.Costello, and R.A.Cohen (2007).
Quantification of oxidative posttranslational modifications of cysteine thiols of p21ras associated with redox modulation of activity using isotope-coded affinity tags and mass spectrometry.
  Free Radic Biol Med, 42, 823-829.  
17302736 M.Spoerner, A.Nuehs, C.Herrmann, G.Steiner, and H.R.Kalbitzer (2007).
Slow conformational dynamics of the guanine nucleotide-binding protein Ras complexed with the GTP analogue GTPgammaS.
  FEBS J, 274, 1419-1433.  
16866878 A.Yanuar, S.Sakurai, K.Kitano, and T.Hakoshima (2006).
Crystal structure of human Rad GTPase of the RGK-family.
  Genes Cells, 11, 961-968.
PDB code: 2dpx
16531227 B.Ford, V.Hornak, H.Kleinman, and N.Nassar (2006).
Structure of a transient intermediate for GTP hydrolysis by ras.
  Structure, 14, 427-436.
PDB codes: 1zvq 1zw6
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Mutation of Gly51 to serine in the P-loop of Lactobacillus casei folylpolyglutamate synthetase abolishes activity by altering the conformation of two adjacent loops.
  Acta Crystallogr D Biol Crystallogr, 62, 548-558.
PDB codes: 2gc5 2gc6 2gca 2gcb
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Germline missense mutations affecting KRAS Isoform B are associated with a severe Noonan syndrome phenotype.
  Am J Hum Genet, 79, 129-135.  
16541253 C.Oswald, I.B.Holland, and L.Schmitt (2006).
The motor domains of ABC-transporters. What can structures tell us?
  Naunyn Schmiedebergs Arch Pharmacol, 372, 385-399.  
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The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study.
  Proteins, 63, 65-77.  
16489751 P.D.Adams, and R.E.Oswald (2006).
Solution structure of an oncogenic mutant of Cdc42Hs.
  Biochemistry, 45, 2577-2583.
PDB code: 2ase
16139957 B.B.Friday, and A.A.Adjei (2005).
K-ras as a target for cancer therapy.
  Biochim Biophys Acta, 1756, 127-144.  
15878843 B.Ford, K.Skowronek, S.Boykevisch, D.Bar-Sagi, and N.Nassar (2005).
Structure of the G60A mutant of Ras: implications for the dominant negative effect.
  J Biol Chem, 280, 25697-25705.  
16277747 C.Bekpen, J.P.Hunn, C.Rohde, I.Parvanova, L.Guethlein, D.M.Dunn, E.Glowalla, M.Leptin, and J.C.Howard (2005).
The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage.
  Genome Biol, 6, R92.  
15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
  Proteins, 59, 580-591.  
15889648 E.J.Milner-White, and M.J.Russell (2005).
Sites for phosphates and iron-sulfur thiolates in the first membranes: 3 to 6 residue anion-binding motifs (nests).
  Orig Life Evol Biosph, 35, 19-27.  
15778967 F.Noé, F.Ille, J.C.Smith, and S.Fischer (2005).
Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21.
  Proteins, 59, 534-544.  
15889153 J.Zaitseva, S.Jenewein, T.Jumpertz, I.B.Holland, and L.Schmitt (2005).
H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB.
  EMBO J, 24, 1901-1910.
PDB code: 1xef
15777481 M.Rossbach, O.Daumke, C.Klinger, A.Wittinghofer, and M.Kaufmann (2005).
Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold.
  BMC Struct Biol, 5, 7.
PDB code: 1ye8
16235217 M.Spoerner, T.F.Prisner, M.Bennati, M.M.Hertel, N.Weiden, T.Schweins, and H.R.Kalbitzer (2005).
Conformational states of human H-Ras detected by high-field EPR, ENDOR, and 31P NMR spectroscopy.
  Magn Reson Chem, 43, S74-S83.  
15994326 M.Ye, F.Shima, S.Muraoka, J.Liao, H.Okamoto, M.Yamamoto, A.Tamura, N.Yagi, T.Ueki, and T.Kataoka (2005).
Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases.
  J Biol Chem, 280, 31267-31275.
PDB codes: 1x1r 1x1s
15998249 R.E.Shackelford, A.N.Heinloth, S.C.Heard, and R.S.Paules (2005).
Cellular and molecular targets of protein S-glutathiolation.
  Antioxid Redox Signal, 7, 940-950.  
16118217 S.D.Auerbach, and K.A.Johnson (2005).
Kinetic effects of kinesin switch I and switch II mutations.
  J Biol Chem, 280, 37061-37068.  
15728574 Y.Yu, S.Li, X.Xu, Y.Li, K.Guan, E.Arnold, and J.Ding (2005).
Structural basis for the unique biological function of small GTPase RHEB.
  J Biol Chem, 280, 17093-17100.
PDB codes: 1xtq 1xtr 1xts
15789417 Z.Y.Friedman, and Y.Devary (2005).
Dissection of the GTPase mechanism of Ras protein by MD analysis of Ras mutants.
  Proteins, 59, 528-533.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
14997535 A.Shurki, and A.Warshel (2004).
Why does the Ras switch "break" by oncogenic mutations?
  Proteins, 55, 1.  
15653425 E.J.Helmreich (2004).
Structural flexibility of small GTPases. Can it explain their functional versatility?
  Biol Chem, 385, 1121-1136.  
14977045 E.W.Becker (2004).
Relevance of the kinetic equilibrium of forces to the control of the cell cycle by Ras proteins.
  Biol Chem, 385, 41-47.  
15040446 G.J.Praefcke, and H.T.McMahon (2004).
The dynamin superfamily: universal membrane tubulation and fission molecules?
  Nat Rev Mol Cell Biol, 5, 133-147.  
14648622 H.Gohlke, and D.A.Case (2004).
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
  J Comput Chem, 25, 238-250.  
15211515 H.Gohlke, L.A.Kuhn, and D.A.Case (2004).
Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
  Proteins, 56, 322-337.  
15507210 H.Sondermann, S.M.Soisson, S.Boykevisch, S.S.Yang, D.Bar-Sagi, and J.Kuriyan (2004).
Structural analysis of autoinhibition in the Ras activator Son of sevenless.
  Cell, 119, 393-405.
PDB codes: 1xd2 1xd4 1xdv
15234971 J.H.Cleator, R.Ravenell, D.T.Kurtz, and J.D.Hildebrandt (2004).
A dominant negative Galphas mutant that prevents thyroid-stimulating hormone receptor activation of cAMP production and inositol 1,4,5-trisphosphate turnover: competition by different G proteins for activation by a common receptor.
  J Biol Chem, 279, 36601-36607.  
15150238 M.Kurz, B.Dalrymple, G.Wijffels, and K.Kongsuwan (2004).
Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein.
  J Bacteriol, 186, 3508-3515.  
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Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
  J Biol Chem, 279, 42907-42915.
PDB codes: 1rn8 1rnj 1seh 1syl
14696184 P.J.Focia, H.Alam, T.Lu, U.D.Ramirez, and D.M.Freymann (2004).
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.
  Proteins, 54, 222-230.
PDB code: 1o87
15292263 P.P.Chakrabarti, Y.Suveyzdis, A.Wittinghofer, and K.Gerwert (2004).
Fourier transform infrared spectroscopy on the Rap.RapGAP reaction, GTPase activation without an arginine finger.
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14962108 P.Wolf, H.Kreimer-Erlacher, H.Seidl, B.Bäck, H.P.Soyer, and H.Kerl (2004).
The ultraviolet fingerprint dominates the mutational spectrum of the p53 and Ha-ras genes in psoralen + ultraviolet A keratoses from psoriasis patients.
  J Invest Dermatol, 122, 190-200.  
15178760 X.Du, G.E.Black, P.Lecchi, F.P.Abramson, and S.R.Sprang (2004).
Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state.
  Proc Natl Acad Sci U S A, 101, 8858-8863.  
14701738 Y.Ward, B.Spinelli, M.J.Quon, H.Chen, S.R.Ikeda, and K.Kelly (2004).
Phosphorylation of critical serine residues in Gem separates cytoskeletal reorganization from down-regulation of calcium channel activity.
  Mol Cell Biol, 24, 651-661.  
14557620 A.K.Kar, and P.Roy (2003).
Defining the structure-function relationships of bluetongue virus helicase protein VP6.
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12869548 A.P.Tabancay, C.L.Gau, I.M.Machado, E.J.Uhlmann, D.H.Gutmann, L.Guo, and F.Tamanoi (2003).
Identification of dominant negative mutants of Rheb GTPase and their use to implicate the involvement of human Rheb in the activation of p70S6K.
  J Biol Chem, 278, 39921-39930.  
12837776 A.Teplyakov, G.Obmolova, S.Y.Chu, J.Toedt, E.Eisenstein, A.J.Howard, and G.L.Gilliland (2003).
Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid.
  J Bacteriol, 185, 4031-4037.
PDB code: 1jal
12433916 G.Zhu, J.Liu, S.Terzyan, P.Zhai, G.Li, and X.C.Zhang (2003).
High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop.
  J Biol Chem, 278, 2452-2460.
PDB codes: 1n6h 1n6i 1n6k 1n6l 1n6n 1n6o 1n6p 1n6r
14674766 J.B.Créchet, R.H.Cool, E.Jacquet, and J.Y.Lallemand (2003).
Characterization of Saccharomyces cerevisiae Ras1p and chimaeric constructs of Ras proteins reveals the hypervariable region and farnesylation as critical elements in the adenylyl cyclase signaling pathway.
  Biochemistry, 42, 14903-14912.  
12399457 J.M.Manganello, J.S.Huang, T.Kozasa, T.A.Voyno-Yasenetskaya, and G.C.Le Breton (2003).
Protein kinase A-mediated phosphorylation of the Galpha13 switch I region alters the Galphabetagamma13-G protein-coupled receptor complex and inhibits Rho activation.
  J Biol Chem, 278, 124-130.  
12759365 K.R.Legate, and D.W.Andrews (2003).
The beta-subunit of the signal recognition particle receptor is a novel GTP-binding protein without intrinsic GTPase activity.
  J Biol Chem, 278, 27712-27720.  
12910454 L.Oliveira, P.B.Paiva, A.C.Paiva, and G.Vriend (2003).
Identification of functionally conserved residues with the use of entropy-variability plots.
  Proteins, 52, 544-552.  
14556626 M.Geyer, C.Wilde, J.Selzer, K.Aktories, and H.R.Kalbitzer (2003).
Glucosylation of Ras by Clostridium sordellii lethal toxin: consequences for effector loop conformations observed by NMR spectroscopy.
  Biochemistry, 42, 11951-11959.  
12910458 S.B.Pandit, and N.Srinivasan (2003).
Survey for g-proteins in the prokaryotic genomes: prediction of functional roles based on classification.
  Proteins, 52, 585-597.  
12663860 S.O.Shan, and P.Walter (2003).
Induced nucleotide specificity in a GTPase.
  Proc Natl Acad Sci U S A, 100, 4480-4485.  
12732734 S.Vorobiev, B.Strokopytov, D.G.Drubin, C.Frieden, S.Ono, J.Condeelis, P.A.Rubenstein, and S.C.Almo (2003).
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
  Proc Natl Acad Sci U S A, 100, 5760-5765.
PDB codes: 1d4x 1nlv 1nm1 1nmd 1yag
12642594 T.L.Baker, H.Zheng, J.Walker, J.L.Coloff, and J.E.Buss (2003).
Distinct rates of palmitate turnover on membrane-bound cellular and oncogenic H-ras.
  J Biol Chem, 278, 19292-19300.  
11909951 A.Carr-Schmid, C.Pfund, E.A.Craig, and T.G.Kinzy (2002).
Novel G-protein complex whose requirement is linked to the translational status of the cell.
  Mol Cell Biol, 22, 2564-2574.  
12213964 B.E.Hall, D.Bar-Sagi, and N.Nassar (2002).
The structural basis for the transition from Ras-GTP to Ras-GDP.
  Proc Natl Acad Sci U S A, 99, 12138-12142.
PDB codes: 1lf0 1lf5
11782421 D.A.Hattendorf, and S.L.Lindquist (2002).
Cooperative kinetics of both Hsp104 ATPase domains and interdomain communication revealed by AAA sensor-1 mutants.
  EMBO J, 21, 12-21.  
12220175 D.M.Daigle, L.Rossi, A.M.Berghuis, L.Aravind, E.V.Koonin, and E.D.Brown (2002).
YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics.
  Biochemistry, 41, 11109-11117.  
12009891 H.Garavini, K.Riento, J.P.Phelan, M.S.McAlister, A.J.Ridley, and N.H.Keep (2002).
Crystal structure of the core domain of RhoE/Rnd3: a constitutively activated small G protein.
  Biochemistry, 41, 6303-6310.
PDB code: 1gwn
12429851 H.Onishi, T.Ohki, N.Mochizuki, and M.F.Morales (2002).
Early stages of energy transduction by myosin: roles of Arg in switch I, of Glu in switch II, and of the salt-bridge between them.
  Proc Natl Acad Sci U S A, 99, 15339-15344.  
11904419 I.Kosztin, R.Bruinsma, P.O'Lague, and K.Schulten (2002).
Mechanical force generation by G proteins.
  Proc Natl Acad Sci U S A, 99, 3575-3580.  
12403627 J.Petersen, K.Fisher, C.J.Mitchell, and D.J.Lowe (2002).
Multiple inequivalent metal-nucleotide coordination environments in the presence of the VO2+-inhibited nitrogenase iron protein: pH-dependent structural rearrangements at the nucleotide binding site.
  Biochemistry, 41, 13253-13263.  
11888286 K.J.Polach, and O.C.Uhlenbeck (2002).
Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA.
  Biochemistry, 41, 3693-3702.  
11889037 K.L.Rossman, D.K.Worthylake, J.T.Snyder, D.P.Siderovski, S.L.Campbell, and J.Sondek (2002).
A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange.
  EMBO J, 21, 1315-1326.
PDB codes: 1kz7 1kzg
12510823 K.N.Cho, and K.I.Lee (2002).
Chemistry and biology of Ras farnesyltransferase.
  Arch Pharm Res, 25, 759-769.  
12235385 M.S.Mitchell, S.Matsuzaki, S.Imai, and V.B.Rao (2002).
Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases.
  Nucleic Acids Res, 30, 4009-4021.  
12412043 M.Y.Peng, H.J.Wen, L.J.Shih, C.M.Kuo, and S.P.Hwang (2002).
Myosin heavy chain expression in cranial, pectoral fin, and tail muscle regions of zebrafish embryos.
  Mol Reprod Dev, 63, 422-429.  
11939594 O.V.Tsodikov, M.T.Record, and Y.V.Sergeev (2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
  J Comput Chem, 23, 600-609.  
12383797 S.Sever (2002).
Dynamin and endocytosis.
  Curr Opin Cell Biol, 14, 463-467.  
  11359919 A.S.Gladfelter, J.J.Moskow, T.R.Zyla, and D.J.Lew (2001).
Isolation and characterization of effector-loop mutants of CDC42 in yeast.
  Mol Biol Cell, 12, 1239-1255.  
11574532 A.Saka, M.Abe, H.Okano, M.Minemura, H.Qadota, T.Utsugi, A.Mino, K.Tanaka, Y.Takai, and Y.Ohya (2001).
Complementing yeast rho1 mutation groups with distinct functional defects.
  J Biol Chem, 276, 46165-46171.  
11251813 B.Lin, J.M.Skidmore, A.Bhatt, S.M.Pfeffer, L.Pawloski, and J.R.Maddock (2001).
Alanine scan mutagenesis of the switch I domain of the Caulobacter crescentus CgtA protein reveals critical amino acids required for in vivo function.
  Mol Microbiol, 39, 924-934.  
11258917 C.Allin, and K.Gerwert (2001).
Ras catalyzes GTP hydrolysis by shifting negative charges from gamma- to beta-phosphate as revealed by time-resolved FTIR difference spectroscopy.
  Biochemistry, 40, 3037-3046.  
11438727 C.Allin, M.R.Ahmadian, A.Wittinghofer, and K.Gerwert (2001).
Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time.
  Proc Natl Acad Sci U S A, 98, 7754-7759.  
11551790 C.Geourjon, C.Orelle, E.Steinfels, C.Blanchet, G.Deléage, A.Di Pietro, and J.M.Jault (2001).
A common mechanism for ATP hydrolysis in ABC transporter and helicase superfamilies.
  Trends Biochem Sci, 26, 539-544.  
11483774 C.L.Tai, W.C.Pan, S.H.Liaw, U.C.Yang, L.H.Hwang, and D.S.Chen (2001).
Structure-based mutational analysis of the hepatitis C virus NS3 helicase.
  J Virol, 75, 8289-8297.  
11340663 G.M.Langdon, M.A.Jiménez, C.G.Genzor, S.Maldonado, J.Sancho, and M.Rico (2001).
Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxin-like family.
  Proteins, 43, 476-488.  
11689422 H.H.Niemann, M.L.Knetsch, A.Scherer, D.J.Manstein, and F.J.Kull (2001).
Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms.
  EMBO J, 20, 5813-5821.
PDB codes: 1jwy 1jx2
11547572 H.Kreimer-Erlacher, H.Seidl, B.Bäck, H.Kerl, and P.Wolf (2001).
High mutation frequency at Ha-ras exons 1-4 in squamous cell carcinomas from PUVA-treated psoriasis patients.
  Photochem Photobiol, 74, 323-330.  
11371635 H.Resat, T.P.Straatsma, D.A.Dixon, and J.H.Miller (2001).
The arginine finger of RasGAP helps Gln-61 align the nucleophilic water in GAP-stimulated hydrolysis of GTP.
  Proc Natl Acad Sci U S A, 98, 6033-6038.  
11296216 I.Hayashi, T.Oyama, and K.Morikawa (2001).
Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus.
  EMBO J, 20, 1819-1828.
PDB codes: 1g3q 1g3r
11738594 K.D.Corbett, and T.Alber (2001).
The many faces of Ras: recognition of small GTP-binding proteins.
  Trends Biochem Sci, 26, 710-716.  
11709168 K.Scheffzek, P.Grünewald, S.Wohlgemuth, W.Kabsch, H.Tu, M.Wigler, A.Wittinghofer, and C.Herrmann (2001).
The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast.
  Structure, 9, 1043-1050.
PDB code: 1k8r
11320243 M.Spoerner, C.Herrmann, I.R.Vetter, H.R.Kalbitzer, and A.Wittinghofer (2001).
Dynamic properties of the Ras switch I region and its importance for binding to effectors.
  Proc Natl Acad Sci U S A, 98, 4944-4949.
PDB code: 1iaq
11494598 M.Tsuda (2001).
[Molecular science of the living organism: the case of G-proteins]
  Yakugaku Zasshi, 121, 523-534.  
11721009 N.Futatsugi, and M.Tsuda (2001).
Molecular dynamics simulations of Gly-12-->Val mutant of p21(ras): dynamic inhibition mechanism.
  Biophys J, 81, 3483-3488.  
11566135 S.Padmanabhan, and D.M.Freymann (2001).
The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
  Structure, 9, 859-867.
PDB codes: 1jpj 1jpn
11746677 T.A.Soares, J.H.Miller, and T.P.Straatsma (2001).
Revisiting the structural flexibility of the complex p21(ras)-GTP: the catalytic conformation of the molecular switch II.
  Proteins, 45, 297-312.  
11222280 T.J.Minehardt, R.Cooke, E.Pate, and P.A.Kollman (2001).
Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd.
  Biophys J, 80, 1151-1168.  
11258916 Z.Zhu, J.J.Dumas, S.E.Lietzke, and D.G.Lambright (2001).
A helical turn motif in Mss4 is a critical determinant of Rab binding and nucleotide release.
  Biochemistry, 40, 3027-3036.
PDB code: 1hxr
10644379 A.A.Kolykhalov, K.Mihalik, S.M.Feinstone, and C.M.Rice (2000).
Hepatitis C virus-encoded enzymatic activities and conserved RNA elements in the 3' nontranslated region are essential for virus replication in vivo.
  J Virol, 74, 2046-2051.  
  11071909 A.Echard, F.J.Opdam, H.J.de Leeuw, F.Jollivet, P.Savelkoul, W.Hendriks, J.Voorberg, B.Goud, and J.A.Fransen (2000).
Alternative splicing of the human Rab6A gene generates two close but functionally different isoforms.
  Mol Biol Cell, 11, 3819-3833.  
  10739258 A.Sillen, J.F.Díaz, and Y.Engelborghs (2000).
A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data.
  Protein Sci, 9, 158-169.  
10676968 B.Prakash, G.J.Praefcke, L.Renault, A.Wittinghofer, and C.Herrmann (2000).
Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins.
  Nature, 403, 567-571.
PDB code: 1dg3
10970849 B.Prakash, L.Renault, G.J.Praefcke, C.Herrmann, and A.Wittinghofer (2000).
Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
  EMBO J, 19, 4555-4564.
PDB code: 1f5n
11188692 C.T.Farrar, J.Ma, D.J.Singel, and C.J.Halkides (2000).
Structural changes induced in p21Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular-dynamics simulation.
  Structure, 8, 1279-1287.  
10944329 D.Chattopadhyay, G.Langsley, M.Carson, R.Recacha, L.DeLucas, and C.Smith (2000).
Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form.
  Acta Crystallogr D Biol Crystallogr, 56, 937-944.
PDB code: 1d5c
10747784 D.Gizachew, W.Guo, K.K.Chohan, M.J.Sutcliffe, and R.E.Oswald (2000).
Structure of the complex of Cdc42Hs with a peptide derived from P-21 activated kinase.
  Biochemistry, 39, 3963-3971.
PDB code: 1ees
10692337 F.von Germar, A.Barth, and W.Mäntele (2000).
Structural changes of the sarcoplasmic reticulum Ca(2+)-ATPase upon nucleotide binding studied by fourier transform infrared spectroscopy.
  Biophys J, 78, 1531-1540.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10844644 H.Iwasaki, Y.W.Han, T.Okamoto, T.Ohnishi, M.Yoshikawa, K.Yamada, H.Toh, H.Daiyasu, T.Ogura, and H.Shinagawa (2000).
Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for holliday junction branch migration.
  Mol Microbiol, 36, 528-538.  
  10716188 J.F.Díaz, M.M.Escalona, S.Kuppens, and Y.Engelborghs (2000).
Role of the switch II region in the conformational transition of activation of Ha-ras-p21.
  Protein Sci, 9, 361-368.  
11029431 J.R.Walker, C.Hervas, J.D.Ross, A.Blinkova, M.J.Walbridge, E.J.Pumarega, M.O.Park, and H.R.Neely (2000).
Escherichia coli DNA polymerase III tau- and gamma-subunit conserved residues required for activity in vivo and in vitro.
  J Bacteriol, 182, 6106-6113.  
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
10625475 M.A.Joyce, M.E.Fraser, M.N.James, W.A.Bridger, and W.T.Wolodko (2000).
ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
  Biochemistry, 39, 17-25.
PDB codes: 1cqi 1cqj
11044135 M.S.Marín, R.Casais, J.M.Alonso, and F.Parra (2000).
ATP binding and ATPase activities associated with recombinant rabbit hemorrhagic disease virus 2C-like polypeptide.
  J Virol, 74, 10846-10851.  
11121079 S.P.Dinesh-Kumar, W.H.Tham, and B.J.Baker (2000).
Structure-function analysis of the tobacco mosaic virus resistance gene N.
  Proc Natl Acad Sci U S A, 97, 14789-14794.  
10618446 T.Nishiwaki, H.Iwasaki, M.Ishiura, and T.Kondo (2000).
Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria.
  Proc Natl Acad Sci U S A, 97, 495-499.  
  10739241 W.Dall'Acqua, and P.Carter (2000).
Substrate-assisted catalysis: molecular basis and biological significance.
  Protein Sci, 9, 1-9.  
10722686 X.Du, H.Frei, and S.H.Kim (2000).
The mechanism of GTP hydrolysis by Ras probed by Fourier transform infrared spectroscopy.
  J Biol Chem, 275, 8492-8500.  
10574788 A.J.Scheidig, C.Burmester, and R.S.Goody (1999).
The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins.
  Structure, 7, 1311-1324.
PDB codes: 1ctq 1qra
  9882335 A.Martins, C.H.Gross, and S.Shuman (1999).
Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase I, a DNA-dependent ATPase of the DExH box family.
  J Virol, 73, 1302-1308.  
  10482526 B.Lin, K.L.Covalle, and J.R.Maddock (1999).
The Caulobacter crescentus CgtA protein displays unusual guanine nucleotide binding and exchange properties.
  J Bacteriol, 181, 5825-5832.  
10387103 B.Turk, R.Awad, E.V.Usova, I.Björk, and S.Eriksson (1999).
A pre-steady-state kinetic analysis of substrate binding to human recombinant deoxycytidine kinase: a model for nucleoside kinase action.
  Biochemistry, 38, 8555-8561.  
10025402 C.Ostermeier, and A.T.Brunger (1999).
Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A.
  Cell, 96, 363-374.
PDB code: 1zbd
  10101168 D.DeRyckere, C.L.Smith, and G.S.Martin (1999).
The role of nucleotide binding and hydrolysis in the function of the fission yeast cdc18(+) gene product.
  Genetics, 151, 1445-1457.  
10358003 D.E.Coleman, and S.R.Sprang (1999).
Structure of Gialpha1.GppNHp, autoinhibition in a galpha protein-substrate complex.
  J Biol Chem, 274, 16669-16672.
PDB code: 1cip
10398103 F.Al-Mulla, E.J.Milner-White, J.J.Going, and G.D.Birnie (1999).
Structural differences between valine-12 and aspartate-12 Ras proteins may modify carcinoma aggression.
  J Pathol, 187, 433-438.  
10531505 G.Montoya, K.te Kaat, R.Moll, G.Schäfer, and I.Sinning (1999).
Crystallization and preliminary x-ray diffraction studies on the conserved GTPase domain of the signal recognition particle from Acidianus ambivalens.
  Acta Crystallogr D Biol Crystallogr, 55, 1949-1951.  
10089426 G.Schmees, K.Höner zu Bentrup, E.Schneider, D.Vinzenz, and U.Ermler (1999).
Crystallization and preliminary X-ray analysis of the bacterial ATP-binding-cassette (ABC) protein MalK.
  Acta Crystallogr D Biol Crystallogr, 55, 285-286.  
10371466 H.LeVine (1999).
Structural features of heterotrimeric G-protein-coupled receptors and their modulatory proteins.
  Mol Neurobiol, 19, 111-149.  
10585400 H.Prinz, A.Lavie, A.J.Scheidig, O.Spangenberg, and M.Konrad (1999).
Binding of nucleotides to guanylate kinase, p21(ras), and nucleoside-diphosphate kinase studied by nano-electrospray mass spectrometry.
  J Biol Chem, 274, 35337-35342.  
10367892 I.R.Vetter, A.Arndt, U.Kutay, D.Görlich, and A.Wittinghofer (1999).
Structural view of the Ran-Importin beta interaction at 2.3 A resolution.
  Cell, 97, 635-646.
PDB code: 1ibr
  10419963 I.Rombel, P.Peters-Wendisch, A.Mesecar, T.Thorgeirsson, Y.K.Shin, and S.Kustu (1999).
MgATP binding and hydrolysis determinants of NtrC, a bacterial enhancer-binding protein.
  J Bacteriol, 181, 4628-4638.  
10542052 I.Rubio, U.Wittig, C.Meyer, R.Heinze, D.Kadereit, H.Waldmann, J.Downward, and R.Wetzker (1999).
Farnesylation of Ras is important for the interaction with phosphoinositide 3-kinase gamma.
  Eur J Biochem, 266, 70-82.  
10494851 J.Müller, A.Marx, S.Sack, Y.H.Song, and E.Mandelkow (1999).
The structure of the nucleotide-binding site of kinesin.
  Biol Chem, 380, 981-992.  
10077621 K.Drotschmann, A.B.Clark, H.T.Tran, M.A.Resnick, D.A.Gordenin, and T.A.Kunkel (1999).
Mutator phenotypes of yeast strains heterozygous for mutations in the MSH2 gene.
  Proc Natl Acad Sci U S A, 96, 2970-2975.  
  10211824 M.G.Rudolph, A.Wittinghofer, and I.R.Vetter (1999).
Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: two different nucleotide states in one crystal.
  Protein Sci, 8, 778-787.
PDB code: 1a4r
  10595559 M.Gruen, C.Becker, A.Beste, J.Reinstein, A.J.Scheidig, and R.S.Goody (1999).
2'Halo-ATP and -GTP analogues: rational phasing tools for protein crystallography.
  Protein Sci, 8, 2524-2528.  
10359839 M.R.Ahmadian, T.Zor, D.Vogt, W.Kabsch, Z.Selinger, A.Wittinghofer, and K.Scheffzek (1999).
Guanosine triphosphatase stimulation of oncogenic Ras mutants.
  Proc Natl Acad Sci U S A, 96, 7065-7070.
PDB codes: 1clu 1rvd
10213614 M.Shirouzu, K.Hashimoto, A.Kikuchi, and S.Yokoyama (1999).
Double-mutant analysis of the interaction of Ras with the Ras-binding domain of RGL.
  Biochemistry, 38, 5103-5110.  
10585950 N.Futatsugi, M.Hata, T.Hoshino, and M.Tsuda (1999).
Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21.
  Biophys J, 77, 3287-3292.  
10196191 N.van den Berghe, R.H.Cool, and A.Wittinghofer (1999).
Discriminatory residues in Ras and Rap for guanine nucleotide exchange factor recognition.
  J Biol Chem, 274, 11078-11085.  
10518715 P.M.Jones, and A.M.George (1999).
Subunit interactions in ABC transporters: towards a functional architecture.
  FEMS Microbiol Lett, 179, 187-202.  
  10493587 S.Kuppens, J.F.Díaz, and Y.Engelborghs (1999).
Characterization of the hinges of the effector loop in the reaction pathway of the activation of ras-proteins. Kinetics of binding of beryllium trifluoride to V29G and I36G mutants of Ha-ras-p21.
  Protein Sci, 8, 1860-1866.  
10347200 T.Kambara, T.E.Rhodes, R.Ikebe, M.Yamada, H.D.White, and M.Ikebe (1999).
Functional significance of the conserved residues in the flexible hinge region of the myosin motor domain.
  J Biol Chem, 274, 16400-16406.  
10381206 T.T.Rohn, L.K.Nelson, A.R.Davis, and M.T.Quinn (1999).
Inhibition of GTP binding to Rac2 by peroxynitrite: potential role for tyrosine modification.
  Free Radic Biol Med, 26, 1321-1331.  
10318792 T.Zhou, and B.P.Rosen (1999).
Asp45 is a Mg2+ ligand in the ArsA ATPase.
  J Biol Chem, 274, 13854-13858.  
10085114 V.Nancy, R.M.Wolthuis, M.F.de Tand, I.Janoueix-Lerosey, J.L.Bos, and J.de Gunzburg (1999).
Identification and characterization of potential effector molecules of the Ras-related GTPase Rap2.
  J Biol Chem, 274, 8737-8745.  
10411886 X.Chen, D.L.Court, and X.Ji (1999).
Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif.
  Proc Natl Acad Sci U S A, 96, 8396-8401.
PDB code: 1ega
  9565765 A.Chahdi, L.Daeffler, J.P.Gies, and Y.Landry (1998).
Drugs interacting with G protein alpha subunits: selectivity and perspectives.
  Fundam Clin Pharmacol, 12, 121-132.  
9868372 A.E.Stellwagen, and N.L.Craig (1998).
Mobile DNA elements: controlling transposition with ATP-dependent molecular switches.
  Trends Biochem Sci, 23, 486-490.  
9858774 A.K.Sinha, U.V.Pathre, and P.V.Sane (1998).
Essential histidyl residues at the active site(s) of sucrose-phosphate synthase from Prosopis juliflora.
  Biochim Biophys Acta, 1388, 397-404.  
9531558 C.D.Nobes, I.Lauritzen, M.G.Mattei, S.Paris, A.Hall, and P.Chardin (1998).
A new member of the Rho family, Rnd1, promotes disassembly of actin filament structures and loss of cell adhesion.
  J Cell Biol, 141, 187-197.  
  9573237 C.H.Gross, and S.Shuman (1998).
The nucleoside triphosphatase and helicase activities of vaccinia virus NPH-II are essential for virus replication.
  J Virol, 72, 4729-4736.  
9632667 C.Herrmann, M.R.Ahmadian, F.Hofmann, and I.Just (1998).
Functional consequences of monoglucosylation of Ha-Ras at effector domain amino acid threonine 35.
  J Biol Chem, 273, 16134-16139.  
  9447979 C.J.Richardson, S.Jones, R.J.Litt, and N.Segev (1998).
GTP hydrolysis is not important for Ypt1 GTPase function in vesicular transport.
  Mol Cell Biol, 18, 827-838.  
9843427 C.L.Strickland, W.T.Windsor, R.Syto, L.Wang, R.Bond, Z.Wu, J.Schwartz, H.V.Le, L.S.Beese, and P.C.Weber (1998).
Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue.
  Biochemistry, 37, 16601-16611.
PDB code: 1qbq
9727495 C.U.Lenzen, D.Steinmann, S.W.Whiteheart, and W.I.Weis (1998).
Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein.
  Cell, 94, 525-536.
PDB code: 1d2n
9422720 C.Zeng, A.E.Aleshin, G.Chen, R.B.Honzatko, and H.J.Fromm (1998).
The roles of glycine residues in the ATP binding site of human brain hexokinase.
  J Biol Chem, 273, 700-704.  
9772163 D.E.Coleman, and S.R.Sprang (1998).
Crystal structures of the G protein Gi alpha 1 complexed with GDP and Mg2+: a crystallographic titration experiment.
  Biochemistry, 37, 14376-14385.
PDB code: 1bof
9920408 D.J.Gawler (1998).
Points of convergence between Ca2+ and Ras signalling pathways.
  Biochim Biophys Acta, 1448, 171-182.  
9786946 D.Otsuga, B.R.Keegan, E.Brisch, J.W.Thatcher, G.J.Hermann, W.Bleazard, and J.M.Shaw (1998).
The dynamin-related GTPase, Dnm1p, controls mitochondrial morphology in yeast.
  J Cell Biol, 143, 333-349.  
9642255 E.H.Bursey, and B.K.Burgess (1998).
Characterization of a variant iron protein of nitrogenase that is impaired in its ability to adopt the MgATP-induced conformational change.
  J Biol Chem, 273, 16927-16934.  
9521782 F.J.van de Loo, and M.E.Salvucci (1998).
Involvement of two aspartate residues of Rubisco activase in coordination of the ATP gamma-phosphate and subunit cooperativity.
  Biochemistry, 37, 4621-4625.  
9786948 G.J.Hermann, J.W.Thatcher, J.P.Mills, K.G.Hales, M.T.Fuller, J.Nunnari, and J.M.Shaw (1998).
Mitochondrial fusion in yeast requires the transmembrane GTPase Fzo1p.
  J Cell Biol, 143, 359-373.  
9576910 H.Käck, K.J.Gibson, Y.Lindqvist, and G.Schneider (1998).
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
  Proc Natl Acad Sci U S A, 95, 5495-5500.
PDB codes: 1a82 1dak
  9611193 H.R.Hotz, and B.Schwer (1998).
Mutational analysis of the yeast DEAH-box splicing factor Prp16.
  Genetics, 149, 807-815.  
9843365 I.I.Mathews, M.D.Erion, and S.E.Ealick (1998).
Structure of human adenosine kinase at 1.5 A resolution.
  Biochemistry, 37, 15607-15620.
PDB code: 1bx4
  9437002 J.H.Overmeyer, A.L.Wilson, R.A.Erdman, and W.A.Maltese (1998).
The putative "switch 2" domain of the Ras-related GTPase, Rab1B, plays an essential role in the interaction with Rab escort protein.
  Mol Biol Cell, 9, 223-235.  
9693007 J.H.Wang, D.G.Xiao, H.Deng, M.R.Webb, and R.Callender (1998).
Raman difference studies of GDP and GTP binding to c-Harvey ras.
  Biochemistry, 37, 11106-11116.  
9706381 J.H.Wang, D.G.Xiao, H.Deng, R.Callender, and M.R.Webb (1998).
Vibrational study of phosphate modes in GDP and GTP and their interaction with magnesium in aqueous solution.
  Biospectroscopy, 4, 219-227.  
9506981 J.Li, and B.P.Rosen (1998).
Steric limitations in the interaction of the ATP binding domains of the ArsA ATPase.
  J Biol Chem, 273, 6796-6800.  
9778364 J.Zhang, and C.R.Matthews (1998).
Ligand binding is the principal determinant of stability for the p21(H)-ras protein.
  Biochemistry, 37, 14881-14890.  
9778365 J.Zhang, and C.R.Matthews (1998).
The role of ligand binding in the kinetic folding mechanism of human p21(H-ras) protein.
  Biochemistry, 37, 14891-14899.  
9668072 K.Fujisawa, P.Madaule, T.Ishizaki, G.Watanabe, H.Bito, Y.Saito, A.Hall, and S.Narumiya (1998).
Different regions of Rho determine Rho-selective binding of different classes of Rho target molecules.
  J Biol Chem, 273, 18943-18949.  
9545299 K.Ihara, S.Muraguchi, M.Kato, T.Shimizu, M.Shirakawa, S.Kuroda, K.Kaibuchi, and T.Hakoshima (1998).
Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue.
  J Biol Chem, 273, 9656-9666.
PDB code: 1a2b
9553053 K.Liu, and G.Li (1998).
Catalytic domain of the p120 Ras GAP binds to RAb5 and stimulates its GTPase activity.
  J Biol Chem, 273, 10087-10090.  
9765257 K.M.Picha, and S.S.Patel (1998).
Bacteriophage T7 DNA helicase binds dTTP, forms hexamers, and binds DNA in the absence of Mg2+. The presence of dTTP is sufficient for hexamer formation and DNA binding.
  J Biol Chem, 273, 27315-27319.  
9697416 K.Scheffzek, M.R.Ahmadian, and A.Wittinghofer (1998).
GTPase-activating proteins: helping hands to complement an active site.
  Trends Biochem Sci, 23, 257-262.  
9687500 K.Scheffzek, M.R.Ahmadian, L.Wiesmüller, W.Kabsch, P.Stege, F.Schmitz, and A.Wittinghofer (1998).
Structural analysis of the GAP-related domain from neurofibromin and its implications.
  EMBO J, 17, 4313-4327.
PDB code: 1nf1
9628477 L.Huang, F.Hofer, G.S.Martin, and S.H.Kim (1998).
Structural basis for the interaction of Ras with RalGDS.
  Nat Struct Biol, 5, 422-426.
PDB code: 1lfd
9553071 M.Ohnishi, Y.Yamawaki-Kataoka, K.Kariya, M.Tamada, C.D.Hu, and T.Kataoka (1998).
Selective inhibition of Ras interaction with its particular effector by synthetic peptides corresponding to the Ras effector region.
  J Biol Chem, 273, 10210-10215.  
9736628 M.Yamauchi, and T.A.Baker (1998).
An ATP-ADP switch in MuB controls progression of the Mu transposition pathway.
  EMBO J, 17, 5509-5518.  
9446556 N.Vitale, J.Moss, and M.Vaughan (1998).
Molecular characterization of the GTPase-activating domain of ADP-ribosylation factor domain protein 1 (ARD1).
  J Biol Chem, 273, 2553-2560.  
9687372 R.Liddington, and L.Bankston (1998).
The integrin I domain: crystals, metals and related artefacts.
  Structure, 6, 937-938.  
9649435 S.Béraud-Dufour, S.Robineau, P.Chardin, S.Paris, M.Chabre, J.Cherfils, and B.Antonny (1998).
A glutamic finger in the guanine nucleotide exchange factor ARNO displaces Mg2+ and the beta-phosphate to destabilize GDP on ARF1.
  EMBO J, 17, 3651-3659.  
9472039 S.H.Lillie, and S.S.Brown (1998).
Smy1p, a kinesin-related protein that does not require microtubules.
  J Cell Biol, 140, 873-883.  
9631293 S.J.Gamblin, and S.J.Smerdon (1998).
GTPase-activating proteins and their complexes.
  Curr Opin Struct Biol, 8, 195-201.  
9857203 T.Pape, W.Wintermeyer, and M.V.Rodnina (1998).
Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome.
  EMBO J, 17, 7490-7497.  
9665734 V.Cepus, A.J.Scheidig, R.S.Goody, and K.Gerwert (1998).
Time-resolved FTIR studies of the GTPase reaction of H-ras p21 reveal a key role for the beta-phosphate.
  Biochemistry, 37, 10263-10271.  
9618466 X.Sun, A.L.Bognar, E.N.Baker, and C.A.Smith (1998).
Structural homologies with ATP- and folate-binding enzymes in the crystal structure of folylpolyglutamate synthetase.
  Proc Natl Acad Sci U S A, 95, 6647-6652.
PDB code: 1fgs
9043664 A.G.Taveras, S.W.Remiszewski, R.J.Doll, D.Cesarz, E.C.Huang, P.Kirschmeier, B.N.Pramanik, M.E.Snow, Y.S.Wang, J.D.del Rosario, B.Vibulbhan, B.B.Bauer, J.E.Brown, D.Carr, J.Catino, C.A.Evans, V.Girijavallabhan, L.Heimark, L.James, S.Liberles, C.Nash, L.Perkins, M.M.Senior, A.Tsarbopoulos, and S.E.Webber (1997).
Ras oncoprotein inhibitors: the discovery of potent, ras nucleotide exchange inhibitors and the structural determination of a drug-protein complex.
  Bioorg Med Chem, 5, 125-133.  
9208093 A.K.Ganguly, B.N.Pramanik, E.C.Huang, S.Liberles, L.Heimark, Y.H.Liu, A.Tsarbopoulos, R.J.Doll, A.G.Taveras, S.Remiszewski, M.E.Snow, Y.S.Wang, B.Vibulbhan, D.Cesarz, J.E.Brown, J.del Rosario, L.James, P.Kirschmeier, and V.Girijavallabhan (1997).
Detection and structural characterization of ras oncoprotein-inhibitors complexes by electrospray mass spectrometry.
  Bioorg Med Chem, 5, 817-820.  
9363942 B.Guenther, R.Onrust, A.Sali, M.O'Donnell, and J.Kuriyan (1997).
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
  Cell, 91, 335-345.
PDB code: 1a5t
9309221 C.T.Farrar, C.J.Halkides, and D.J.Singel (1997).
The frozen solution structure of p21 ras determined by ESEEM spectroscopy reveals weak coordination of Thr35 to the active site metal ion.
  Structure, 5, 1055-1066.  
9305899 D.G.Winkler, J.C.Johnson, J.A.Cooper, and A.B.Vojtek (1997).
Identification and characterization of mutations in Ha-Ras that selectively decrease binding to cRaf-1.
  J Biol Chem, 272, 24402-24409.  
  9371600 D.W.Kim, J.Kim, Y.Gwack, J.H.Han, and J.Choe (1997).
Mutational analysis of the hepatitis C virus RNA helicase.
  J Virol, 71, 9400-9409.  
9384563 G.Auerbach, R.Huber, M.Grättinger, K.Zaiss, H.Schurig, R.Jaenicke, and U.Jacob (1997).
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
  Structure, 5, 1475-1483.
PDB code: 1vpe
9218784 J.A.Bertrand, G.Auger, E.Fanchon, L.Martin, D.Blanot, J.van Heijenoort, and O.Dideberg (1997).
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
  EMBO J, 16, 3416-3425.
PDB codes: 1e0d 1uag
9312017 J.Cherfils, J.Ménétrey, G.Le Bras, I.Janoueix-Lerosey, J.de Gunzburg, J.R.Garel, and I.Auzat (1997).
Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.
  EMBO J, 16, 5582-5591.
PDB codes: 1kao 2rap
9287316 J.F.Díaz, A.Sillen, and Y.Engelborghs (1997).
Equilibrium and kinetic study of the conformational transition toward the active state of p21Ha-ras, induced by the binding of BeF3- to the GDP-bound state, in the absence of GTPase-activating proteins.
  J Biol Chem, 272, 23138-23143.  
9220962 J.L.Feltham, V.Dötsch, S.Raza, D.Manor, R.A.Cerione, M.J.Sutcliffe, G.Wagner, and R.E.Oswald (1997).
Definition of the switch surface in the solution structure of Cdc42Hs.
  Biochemistry, 36, 8755-8766.
PDB code: 1aje
9342335 J.Ma, and M.Karplus (1997).
Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.
  Proc Natl Acad Sci U S A, 94, 11905-11910.  
9125526 J.S.Hu, and A.G.Redfield (1997).
Conformational and dynamic differences between N-ras P21 bound to GTPgammaS and to GMPPNP as studied by NMR.
  Biochemistry, 36, 5045-5052.  
9230308 K.G.Hales, and M.T.Fuller (1997).
Developmentally regulated mitochondrial fusion mediated by a conserved, novel, predicted GTPase.
  Cell, 90, 121-129.  
9144171 L.Han, D.Wong, A.Dhaka, D.Afar, M.White, W.Xie, H.Herschman, O.Witte, and J.Colicelli (1997).
Protein binding and signaling properties of RIN1 suggest a unique effector function.
  Proc Natl Acad Sci U S A, 94, 4954-4959.  
9178102 M.A.Paulik, L.L.Hamacher, D.P.Yarnall, C.J.Simmons, L.Maianu, R.E.Pratley, W.T.Garvey, D.K.Burns, and J.M.Lenhard (1997).
Identification of Rad's effector-binding domain, intracellular localization, and analysis of expression in Pima Indians.
  J Cell Biochem, 65, 527-541.  
9434896 M.Geyer, and A.Wittinghofer (1997).
GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins.
  Curr Opin Struct Biol, 7, 786-792.  
9302994 M.Geyer, C.Herrmann, S.Wohlgemuth, A.Wittinghofer, and H.R.Kalbitzer (1997).
Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling.
  Nat Struct Biol, 4, 694-699.
PDB code: 2rgf
9033596 M.Hirshberg, R.W.Stockley, G.Dodson, and M.R.Webb (1997).
The crystal structure of human rac1, a member of the rho-family complexed with a GTP analogue.
  Nat Struct Biol, 4, 147-152.
PDB code: 1mh1
9166776 P.M.Cullis, A.Maxwell, and D.P.Weiner (1997).
Exploiting nucleotide thiophosphates to probe mechanistic aspects of Escherichia coli DNA gyrase.
  Biochemistry, 36, 6059-6068.  
9115993 R.Misselwitz, K.Welfe, C.Krafft, C.O.Gualerzi, and H.Welfle (1997).
Translational initiation factor IF2 from Bacillus stearothermophilus: a spectroscopic and microcalorimetric study of the C-domain.
  Biochemistry, 36, 3170-3178.  
9312016 S.R.Hubbard (1997).
Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog.
  EMBO J, 16, 5572-5581.
PDB code: 1ir3
9242920 S.R.Sprang (1997).
G protein mechanisms: insights from structural analysis.
  Annu Rev Biochem, 66, 639-678.  
9434906 S.R.Sprang (1997).
G proteins, effectors and GAPs: structure and mechanism.
  Curr Opin Struct Biol, 7, 849-856.  
9396812 T.H.Chang, L.J.Latus, Z.Liu, and J.M.Abbott (1997).
Genetic interactions of conserved regions in the DEAD-box protein Prp28p.
  Nucleic Acids Res, 25, 5033-5040.  
9150458 T.Sugimori, D.L.Griffith, and M.A.Arnaout (1997).
Emerging paradigms of integrin ligand binding and activation.
  Kidney Int, 51, 1454-1462.  
9012677 X.Xu, Y.Wang, D.C.Barry, S.J.Chanock, and G.M.Bokoch (1997).
Guanine nucleotide binding properties of Rac2 mutant proteins and analysis of the responsiveness to guanine nucleotide dissociation stimulator.
  Biochemistry, 36, 626-632.  
9230043 Y.Ito, K.Yamasaki, J.Iwahara, T.Terada, A.Kamiya, M.Shirouzu, Y.Muto, G.Kawai, S.Yokoyama, E.D.Laue, M.Wälchli, T.Shibata, S.Nishimura, and T.Miyazawa (1997).
Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
  Biochemistry, 36, 9109-9119.
PDB code: 1aa9
9174410 Y.Qian, S.M.Sebti, and A.D.Hamilton (1997).
Farnesyltransferase as a target for anticancer drug design.
  Biopolymers, 43, 25-41.  
  8670851 A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, and K.S.Wilson (1996).
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
  EMBO J, 15, 3487-3497.
PDB codes: 1dek 1del
8824275 B.E.Crute, A.F.Lewis, Z.Wu, J.H.Bushweller, and N.A.Speck (1996).
Biochemical and biophysical properties of the core-binding factor alpha2 (AML1) DNA-binding domain.
  J Biol Chem, 271, 26251-26260.  
8810926 B.F.Bellew, C.J.Halkides, G.J.Gerfen, R.G.Griffin, and D.J.Singel (1996).
High frequency (139.5 GHz) electron paramagnetic resonance characterization of Mn(II)-H2(17)O interactions in GDP and GTP forms of p21 ras.
  Biochemistry, 35, 12186-12193.  
8663109 B.W.Poland, Z.Hou, C.Bruns, H.J.Fromm, and R.B.Honzatko (1996).
Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli.
  J Biol Chem, 271, 15407-15413.
PDB codes: 1hon 1hoo 1hop
8805587 C.A.Hasemann, E.S.Istvan, K.Uyeda, and J.Deisenhofer (1996).
The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies.
  Structure, 4, 1017-1029.
PDB code: 1bif
8785318 C.A.Smith, and I.Rayment (1996).
Active site comparisons highlight structural similarities between myosin and other P-loop proteins.
  Biophys J, 70, 1590-1602.  
8805593 C.D.Mol, J.M.Harris, E.M.McIntosh, and J.A.Tainer (1996).
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
  Structure, 4, 1077-1092.
PDB codes: 1q5h 1q5u
8810927 C.J.Halkides, B.F.Bellew, G.J.Gerfen, C.T.Farrar, P.H.Carter, B.Ruo, D.A.Evans, R.G.Griffin, and D.J.Singel (1996).
High frequency (139.5 GHz) electron paramagnetic resonance spectroscopy of the GTP form of p21 ras with selective 17O labeling of threonine.
  Biochemistry, 35, 12194-12200.  
8791426 C.J.Marshall (1996).
Ras effectors.
  Curr Opin Cell Biol, 8, 197-204.  
8805521 C.W.Müller, G.J.Schlauderer, J.Reinstein, and G.E.Schulz (1996).
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.
  Structure, 4, 147-156.
PDB code: 4ake
8662741 E.M.Zera, D.P.Molloy, J.K.Angleson, J.B.Lamture, T.G.Wensel, and J.A.Malinski (1996).
Low affinity interactions of GDPbetaS and ribose- or phosphoryl-substituted GTP analogues with the heterotrimeric G protein, transducin.
  J Biol Chem, 271, 12925-12931.  
  8978702 E.Vorstenbosch, T.Pape, M.V.Rodnina, B.Kraal, and W.Wintermeyer (1996).
The G222D mutation in elongation factor Tu inhibits the codon-induced conformational changes leading to GTPase activation on the ribosome.
  EMBO J, 15, 6766-6774.  
8842197 F.G.Díaz Baños, J.Bordas, J.Lowy, and A.Svensson (1996).
Small segmental rearrangements in the myosin head can explain force generation in muscle.
  Biophys J, 71, 576-589.  
8756317 F.McCormick (1996).
Ras biology in atomic detail.
  Nat Struct Biol, 3, 653-655.  
8702776 G.A.Taylor, M.Jeffers, D.A.Largaespada, N.A.Jenkins, N.G.Copeland, and G.F.Woude (1996).
Identification of a novel GTPase, the inducibly expressed GTPase, that accumulates in response to interferon gamma.
  J Biol Chem, 271, 20399-20405.  
  8892948 G.Kadaré, C.David, and A.L.Haenni (1996).
ATPase, GTPase, and RNA binding activities associated with the 206-kilodalton protein of turnip yellow mosaic virus.
  J Virol, 70, 8169-8174.  
8783394 H.Nakamura (1996).
Roles of electrostatic interaction in proteins.
  Q Rev Biophys, 29, 1.  
8662632 H.Shen, A.Sosa-Peinado, and D.M.Mueller (1996).
Intragenic suppressors of P-loop mutations in the beta-subunit of the mitochondrial ATPase in the yeast Saccharomyces cerevisiae.
  J Biol Chem, 271, 11844-11851.  
8626575 I.Just, J.Selzer, F.Hofmann, G.A.Green, and K.Aktories (1996).
Inactivation of Ras by Clostridium sordellii lethal toxin-catalyzed glucosylation.
  J Biol Chem, 271, 10149-10153.  
8740369 I.Muegge, T.Schweins, R.Langen, and A.Warshel (1996).
Electrostatic control of GTP and GDP binding in the oncoprotein p21ras.
  Structure, 4, 475-489.  
8702787 I.Simon, M.Zerial, and R.S.Goody (1996).
Kinetics of interaction of Rab5 and Rab7 with nucleotides and magnesium ions.
  J Biol Chem, 271, 20470-20478.  
8662740 J.A.Malinski, E.M.Zera, J.K.Angleson, and T.G.Wensel (1996).
High affinity interactions of GTPgammaS with the heterotrimeric G protein, transducin. Evidence at high and low protein concentrations.
  J Biol Chem, 271, 12919-12924.  
8663268 J.B.Créchet, A.Bernardi, and A.Parmeggiani (1996).
Distal switch II region of Ras2p is required for interaction with guanine nucleotide exchange factor.
  J Biol Chem, 271, 17234-17240.  
8838585 J.M.Chen, R.Grad, R.Monaco, and M.R.Pincus (1996).
Prediction of the three-dimensional structure of the rap-1A protein from its homology to the ras-gene-encoded p21 protein.
  J Protein Chem, 15, 11-15.  
8895097 J.M.Chen, S.Manolatos, P.W.Brandt-Rauf, R.B.Murphy, R.Monaco, and M.R.Pincus (1996).
Computed three-dimensional structures for the ras-binding domain of the raf-p74 protein complexed with ras-p21 and with its suppressor protein, rap-1A.
  J Protein Chem, 15, 511-518.  
8910526 J.M.Jault, C.Dou, N.B.Grodsky, T.Matsui, M.Yoshida, and W.S.Allison (1996).
The alpha3beta3gamma subcomplex of the F1-ATPase from the thermophilic bacillus PS3 with the betaT165S substitution does not entrap inhibitory MgADP in a catalytic site during turnover.
  J Biol Chem, 271, 28818-28824.  
8702501 J.Marszalek, W.Zhang, T.R.Hupp, C.Margulies, K.M.Carr, S.Cherry, and J.M.Kaguni (1996).
Domains of DnaA protein involved in interaction with DnaB protein, and in unwinding the Escherichia coli chromosomal origin.
  J Biol Chem, 271, 18535-18542.  
8710841 K.A.Maegley, S.J.Admiraal, and D.Herschlag (1996).
Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.
  Proc Natl Acad Sci U S A, 93, 8160-8166.  
8621388 K.Akasaka, M.Tamada, F.Wang, K.Kariya, F.Shima, A.Kikuchi, M.Yamamoto, M.Shirouzu, S.Yokoyama, and T.Kataoka (1996).
Differential structural requirements for interaction of Ras protein with its distinct downstream effectors.
  J Biol Chem, 271, 5353-5360.  
8809781 K.M.Carr, and J.M.Kaguni (1996).
The A184V missense mutation of the dnaA5 and dnaA46 alleles confers a defect in ATP binding and thermolability in initiation of Escherichia coli DNA replication.
  Mol Microbiol, 20, 1307-1318.  
8970737 K.M.Ruppel, and J.A.Spudich (1996).
Structure-function analysis of the motor domain of myosin.
  Annu Rev Cell Dev Biol, 12, 543-573.  
8663354 K.Sato, H.Mori, M.Yoshida, and S.Mizushima (1996).
Characterization of a potential catalytic residue, Asp-133, in the high affinity ATP-binding site of Escherichia coli SecA, translocation ATPase.
  J Biol Chem, 271, 17439-17444.  
  8605880 M.C.Parrini, A.Bernardi, and A.Parmeggiani (1996).
Determinants of Ras proteins specifying the sensitivity to yeast Ira2p and human p120-GAP.
  EMBO J, 15, 1107-1111.  
8756686 M.Geyer, T.Schweins, C.Herrmann, T.Prisner, A.Wittinghofer, and H.R.Kalbitzer (1996).
Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.
  Biochemistry, 35, 10308-10320.  
8626586 M.R.Popoff, E.Chaves-Olarte, E.Lemichez, C.von Eichel-Streiber, M.Thelestam, P.Chardin, D.Cussac, B.Antonny, P.Chavrier, G.Flatau, M.Giry, J.de Gunzburg, and P.Boquet (1996).
Ras, Rap, and Rac small GTP-binding proteins are targets for Clostridium sordellii lethal toxin glucosylation.
  J Biol Chem, 271, 10217-10224.  
8756332 N.Nassar, G.Horn, C.Herrmann, C.Block, R.Janknecht, and A.Wittinghofer (1996).
Ras/Rap effector specificity determined by charge reversal.
  Nat Struct Biol, 3, 723-729.
PDB code: 1gua
8702777 O.Wiborg, C.Andersen, C.R.Knudsen, B.F.Clark, and J.Nyborg (1996).
Mapping Escherichia coli elongation factor Tu residues involved in binding of aminoacyl-tRNA.
  J Biol Chem, 271, 20406-20411.  
  8918462 P.D.Wes, M.Yu, and C.Montell (1996).
RIC, a calmodulin-binding Ras-like GTPase.
  EMBO J, 15, 5839-5848.  
8896589 R.D.Vale (1996).
Switches, latches, and amplifiers: common themes of G proteins and molecular motors.
  J Cell Biol, 135, 291-302.  
  8649376 R.Foster, K.Q.Hu, Y.Lu, K.M.Nolan, J.Thissen, and J.Settleman (1996).
Identification of a novel human Rho protein with unusual properties: GTPase deficiency and in vivo farnesylation.
  Mol Cell Biol, 16, 2689-2699.  
8608143 R.Zhang, V.Villeret, W.N.Lipscomb, and H.J.Fromm (1996).
Kinetics and mechanisms of activation and inhibition of porcine liver fructose-1,6-bisphosphatase by monovalent cations.
  Biochemistry, 35, 3038-3043.  
8605211 T.K.Nomanbhoy, D.A.Leonard, D.Manor, and R.A.Cerione (1996).
Investigation of the GTP-binding/GTPase cycle of Cdc42Hs using extrinsic reporter group fluorescence.
  Biochemistry, 35, 4602-4608.  
8916907 T.Schweins, M.Geyer, H.R.Kalbitzer, A.Wittinghofer, and A.Warshel (1996).
Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras.
  Biochemistry, 35, 14225-14231.  
8919456 T.Shimamoto, and M.Inouye (1996).
Mutational analysis of Era, an essential GTP-binding protein of Escherichia coli.
  FEMS Microbiol Lett, 136, 57-62.  
8663024 W.Miao, L.Eichelberger, L.Baker, and M.S.Marshall (1996).
p120 Ras GTPase-activating protein interacts with Ras-GTP through specific conserved residues.
  J Biol Chem, 271, 15322-15329.  
8706729 W.Zeidler, N.K.Schirmer, C.Egle, S.Ribeiro, R.Kreutzer, and M.Sprinzl (1996).
Limited proteolysis and amino acid replacements in the effector region of Thermus thermophilus elongation factor Tu.
  Eur J Biochem, 239, 265-271.  
  8612578 Y.Paas, A.Devillers-Thiéry, J.P.Changeux, F.Medevielle, and V.I.Teichberg (1996).
Identification of an extracellular motif involved in the binding of guanine nucleotides by a glutamate receptor.
  EMBO J, 15, 1548-1556.  
8938129 Y.Paas, M.Eisenstein, F.Medevielle, V.I.Teichberg, and A.Devillers-Thiéry (1996).
Identification of the amino acid subsets accounting for the ligand binding specificity of a glutamate receptor.
  Neuron, 17, 979-990.  
7499430 A.Schürmann, A.Brauers, S.Massmann, W.Becker, and H.G.Joost (1995).
Cloning of a novel family of mammalian GTP-binding proteins (RagA, RagBs, RagB1) with remote similarity to the Ras-related GTPases.
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7777563 C.Desbiez, C.David, A.Mettouchi, J.Laufs, and B.Gronenborn (1995).
Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication.
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  7609038 C.H.Gross, and S.Shuman (1995).
Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase II, a DExH box RNA helicase.
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7852367 C.Herrmann, G.A.Martin, and A.Wittinghofer (1995).
Quantitative analysis of the complex between p21ras and the Ras-binding domain of the human Raf-1 protein kinase.
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7883001 C.R.Knudsen, I.V.Kjaersgård, O.Wiborg, and B.F.Clark (1995).
Mutation of the conserved Gly94 and Gly126 in elongation factor Tu from Escherichia coli. Elucidation of their structural and functional roles.
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8789192 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
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8789193 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
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7784428 D.W.Deerfield, D.J.Fox, M.Head-Gordon, R.G.Hiskey, and L.G.Pedersen (1995).
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.
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7596295 E.S.Yaskowiak, and P.E.March (1995).
Small clusters of divergent amino acids surrounding the effector domain mediate the varied phenotypes of EF-G and LepA expression.
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8673720 F.Castellano, A.L.Wilson, and W.A.Maltese (1995).
Intracellular transport and maturation of nascent low density lipoprotein receptor is blocked by mutation in the Ras-related GTP-binding protein, RAB1B.
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  7651383 G.Cullmann, K.Fien, R.Kobayashi, and B.Stillman (1995).
Characterization of the five replication factor C genes of Saccharomyces cerevisiae.
  Mol Cell Biol, 15, 4661-4671.  
8553703 G.L.Kiser, and T.A.Weinert (1995).
GUF1, a gene encoding a novel evolutionarily conserved GTPase in budding yeast.
  Yeast, 11, 1311-1316.  
  7635818 G.Ziegelin, N.A.Linderoth, R.Calendar, and E.Lanka (1995).
Domain structure of phage P4 alpha protein deduced by mutational analysis.
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7775453 I.Just, M.Wilm, J.Selzer, G.Rex, C.von Eichel-Streiber, M.Mann, and K.Aktories (1995).
The enterotoxin from Clostridium difficile (ToxA) monoglucosylates the Rho proteins.
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7883002 I.V.Kjaersgård, C.R.Knudsen, and O.Wiborg (1995).
Mutation of the conserved Gly83 and Gly94 in Escherichia coli elongation factor Tu. Indication of structural pivots.
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7844142 J.D.Miller, S.Tajima, L.Lauffer, and P.Walter (1995).
The beta subunit of the signal recognition particle receptor is a transmembrane GTPase that anchors the alpha subunit, a peripheral membrane GTPase, to the endoplasmic reticulum membrane.
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7738040 J.M.Dugan, C.deWit, L.McConlogue, and W.A.Maltese (1995).
The Ras-related GTP-binding protein, Rab1B, regulates early steps in exocytic transport and processing of beta-amyloid precursor protein.
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8747460 J.O.Lee, L.A.Bankston, M.A.Arnaout, and R.C.Liddington (1995).
Two conformations of the integrin A-domain (I-domain): a pathway for activation?
  Structure, 3, 1333-1340.
PDB code: 1jlm
7642557 J.P.van der Wolk, M.Klose, J.G.de Wit, T.den Blaauwen, R.Freudl, and A.J.Driessen (1995).
Identification of the magnesium-binding domain of the high-affinity ATP-binding site of the Bacillus subtilis and Escherichia coli SecA protein.
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7543023 K.L.Gunderson, and R.R.Kopito (1995).
Conformational states of CFTR associated with channel gating: the role ATP binding and hydrolysis.
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8599650 M.R.Carson, and M.J.Welsh (1995).
Structural and functional similarities between the nucleotide-binding domains of CFTR and GTP-binding proteins.
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7883018 M.Segal, I.Marbach, B.M.Willumsen, and A.Levitzki (1995).
Two distinct regions of Ras participate in functional interaction with GDP-GTP exchangers.
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Codon-dependent conformational change of elongation factor Tu preceding GTP hydrolysis on the ribosome.
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7851434 P.Poullet, J.B.Créchet, A.Bernardi, and A.Parmeggiani (1995).
Properties of the catalytic domain of sdc25p, a yeast GDP/GTP exchange factor of Ras proteins. Complexation with wild-type Ras2p, [S24N]Ras2p and [R80D, N81D]Ras2p.
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7592948 R.H.Mosher, D.J.Camp, K.Yang, M.P.Brown, W.V.Shaw, and L.C.Vining (1995).
Inactivation of chloramphenicol by O-phosphorylation. A novel resistance mechanism in Streptomyces venezuelae ISP5230, a chloramphenicol producer.
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7719851 R.Hilgenfeld (1995).
How do the GTPases really work?
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8749370 R.Hilgenfeld (1995).
Regulatory GTPases.
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7706272 R.J.Zeleznikar, P.P.Dzeja, and N.D.Goldberg (1995).
Adenylate kinase-catalyzed phosphoryl transfer couples ATP utilization with its generation by glycolysis in intact muscle.
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8593186 R.Monaco, J.M.Chen, D.Chung, P.Brandt-Rauf, and M.R.Pincus (1995).
Comparison of the computed three-dimensional structures of oncogenic forms (bound to GDP) of the ras-gene-encoded p21 protein with the structure of the normal (non-transforming) wild-type protein.
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8747433 R.Monaco, J.M.Chen, F.K.Friedman, P.Brandt-Rauf, D.Chung, and M.R.Pincus (1995).
Structural effects of the binding of GTP to the wild-type and oncogenic forms of the ras-gene-encoded p21 proteins.
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7770031 S.Fabry, R.Steigerwald, C.Bernklau, W.Dietmaier, and R.Schmitt (1995).
Structure-function analysis of small G proteins from Volvox and Chlamydomonas by complementation of Saccharomyces cerevisiae YPT/SEC mutations.
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7836458 S.M.Wilbanks, and D.B.McKay (1995).
How potassium affects the activity of the molecular chaperone Hsc70. II. Potassium binds specifically in the ATPase active site.
  J Biol Chem, 270, 2251-2257.
PDB code: 1hpm
8529632 S.Nock, N.Grillenbeck, M.R.Ahmadian, S.Ribeiro, R.Kreutzer, and M.Sprinzl (1995).
Properties of isolated domains of the elongation factor Tu from Thermus thermophilus HB8.
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8591040 S.R.Sprang (1995).
How Ras works: structure of a Rap-Raf complex.
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7612669 T.Samuelsson, M.Olsson, P.M.Wikström, and B.R.Johansson (1995).
The GTPase activity of the Escherichia coli Ffh protein is important for normal growth.
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7719852 T.Schweins, M.Geyer, K.Scheffzek, A.Warshel, H.R.Kalbitzer, and A.Wittinghofer (1995).
Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins.
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  7670369 U.Abele, and G.E.Schulz (1995).
High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.
  Protein Sci, 4, 1262-1271.
PDB codes: 1aky 2aky
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The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the same family.
  Protein Sci, 4, 1577-1586.  
7758452 W.Zeidler, C.Egle, S.Ribeiro, A.Wagner, V.Katunin, R.Kreutzer, M.Rodnina, W.Wintermeyer, and M.Sprinzl (1995).
Site-directed mutagenesis of Thermus thermophilus elongation factor Tu. Replacement of His85, Asp81 and Arg300.
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7858189 A.L.Drayer, and P.J.van Haastert (1994).
Transmembrane signalling in eukaryotes: a comparison between higher and lower eukaryotes.
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8060496 A.Liwo, K.D.Gibson, H.A.Scheraga, P.W.Brandt-Rauf, R.Monaco, and M.R.Pincus (1994).
Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP.
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8293457 A.Wittinghofer (1994).
The structure of transducin G alpha t: more to view than just ras.
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8078910 C.J.Mau, and C.A.West (1994).
Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants.
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8163542 C.Nuoffer, H.W.Davidson, J.Matteson, J.Meinkoth, and W.E.Balch (1994).
A GDP-bound of rab1 inhibits protein export from the endoplasmic reticulum and transport between Golgi compartments.
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7881906 D.Alexeev, R.L.Baxter, and L.Sawyer (1994).
Mechanistic implications and family relationships from the structure of dethiobiotin synthetase.
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PDB code: 1dbs
8048162 D.Bossemeyer (1994).
The glycine-rich sequence of protein kinases: a multifunctional element.
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8026510 D.M.Mueller, V.Indyk, and L.McGill (1994).
ATPase kinetics for wild-type Saccharomyces cerevisiae F1-ATPase and F1-ATPase with the beta-subunit Thr197-->Ser mutation.
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Hydrogen bond interactions of G proteins with the guanine ring moiety of guanine nucleotides.
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7962076 H.Damke, T.Baba, D.E.Warnock, and S.L.Schmid (1994).
Induction of mutant dynamin specifically blocks endocytic coated vesicle formation.
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  8313902 H.Stenmark, A.Valencia, O.Martinez, O.Ullrich, B.Goud, and M.Zerial (1994).
Distinct structural elements of rab5 define its functional specificity.
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8203020 I.Rayment, and H.M.Holden (1994).
The three-dimensional structure of a molecular motor.
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The structural and functional basis for the kirromycin resistance of mutant EF-Tu species in Escherichia coli.
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7909812 M.A.Riederer, T.Soldati, A.D.Shapiro, J.Lin, and S.R.Pfeffer (1994).
Lysosome biogenesis requires Rab9 function and receptor recycling from endosomes to the trans-Golgi network.
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7937733 M.B.Berry, B.Meador, T.Bilderback, P.Liang, M.Glaser, and G.N.Phillips (1994).
The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP.
  Proteins, 19, 183-198.
PDB code: 1ank
7957225 M.G.Duyvis, H.Wassink, and H.Haaker (1994).
Pre-steady-state MgATP-dependent proton production and electron transfer by nitrogenase from Azotobacter vinelandii.
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7527136 M.Seki, H.Miyazawa, S.Tada, J.Yanagisawa, T.Yamaoka, S.Hoshino, K.Ozawa, T.Eki, M.Nogami, and K.Okumura (1994).
Molecular cloning of cDNA encoding human DNA helicase Q1 which has homology to Escherichia coli Rec Q helicase and localization of the gene at chromosome 12p12.
  Nucleic Acids Res, 22, 4566-4573.  
8138575 O.Kuge, C.Dascher, L.Orci, T.Rowe, M.Amherdt, H.Plutner, M.Ravazzola, G.Tanigawa, J.E.Rothman, and W.E.Balch (1994).
Sar1 promotes vesicle budding from the endoplasmic reticulum but not Golgi compartments.
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7815090 P.Kern, R.M.Brunne, and G.Folkers (1994).
Nucleotide-binding properties of adenylate kinase from Escherichia coli: a molecular dynamics study in aqueous and vacuum environments.
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8057845 P.Sood, C.G.Lerner, T.Shimamoto, Q.Lu, and M.Inouye (1994).
Characterization of the autophosphorylation of Era, an essential Escherichia coli GTPase.
  Mol Microbiol, 12, 201-208.  
  8289791 R.D.Mosteller, J.Han, and D.Broek (1994).
Identification of residues of the H-ras protein critical for functional interaction with guanine nucleotide exchange factors.
  Mol Cell Biol, 14, 1104-1112.  
  7935432 R.Foster, K.Q.Hu, D.A.Shaywitz, and J.Settleman (1994).
p190 RhoGAP, the major RasGAP-associated protein, binds GTP directly.
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8035212 S.D.Rufino, and T.L.Blundell (1994).
Structure-based identification and clustering of protein families and superfamilies.
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8170391 S.Laalami, A.V.Timofeev, H.Putzer, J.Leautey, and M.Grunberg-Manago (1994).
In vivo study of engineered G-domain mutants of Escherichia coli translation initiation factor IF2.
  Mol Microbiol, 11, 293-302.  
  7969124 S.M.Althoff, S.W.Stevens, and J.A.Wise (1994).
The Srp54 GTPase is essential for protein export in the fission yeast Schizosaccharomyces pombe.
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7986528 S.R.Pfeffer (1994).
Rab GTPases: master regulators of membrane trafficking.
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8051214 S.W.Whiteheart, K.Rossnagel, S.A.Buhrow, M.Brunner, R.Jaenicke, and J.E.Rothman (1994).
N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion.
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7664067 T.Schweins, R.Langen, and A.Warshel (1994).
Why have mutagenesis studies not located the general base in ras p21.
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8200357 T.W.Traut (1994).
The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites.
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  8196614 V.Jung, W.Wei, R.Ballester, J.Camonis, S.Mi, L.Van Aelst, M.Wigler, and D.Broek (1994).
Two types of RAS mutants that dominantly interfere with activators of RAS.
  Mol Cell Biol, 14, 3707-3718.  
7874745 W.Dietmaier, and S.Fabry (1994).
Analysis of the introns in genes encoding small G proteins.
  Curr Genet, 26, 497-505.  
8081756 W.Huang, Y.Lindqvist, G.Schneider, K.J.Gibson, D.Flint, and G.Lorimer (1994).
Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution.
  Structure, 2, 407-414.
PDB code: 1dts
  7849601 W.R.Taylor, T.P.Flores, and C.A.Orengo (1994).
Multiple protein structure alignment.
  Protein Sci, 3, 1858-1870.  
8393791 A.Löw, M.Sprinzl, and H.G.Faulhammer (1993).
Affinity labeling of c-H-ras p21 consensus elements with periodate-oxidized GDP and GTP.
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8386636 A.Löw, M.Sprinzl, and S.Limmer (1993).
Nucleotide binding and GTP hydrolysis by the 21-kDa product of the c-H-ras gene as monitored by proton-NMR spectroscopy.
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8101525 A.M.van der Bliek, T.E.Redelmeier, H.Damke, E.J.Tisdale, E.M.Meyerowitz, and S.L.Schmid (1993).
Mutations in human dynamin block an intermediate stage in coated vesicle formation.
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8388779 B.R.Conklin, and H.R.Bourne (1993).
Structural elements of G alpha subunits that interact with G beta gamma, receptors, and effectors.
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8451239 C.W.Müller, and G.E.Schulz (1993).
Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop.
  Proteins, 15, 42-49.
PDB codes: 1e4v 1e4y
  8384554 D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, and R.Huber (1993).
Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24).
  EMBO J, 12, 849-859.
PDB code: 1cdk
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Tryptophan W207 in transducin T alpha is the fluorescence sensor of the G protein activation switch and is involved in the effector binding.
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8234268 H.H.Chung, D.R.Benson, V.W.Cornish, and P.G.Schultz (1993).
Probing the role of loop 2 in Ras function with unnatural amino acids.
  Proc Natl Acad Sci U S A, 90, 10145-10149.  
8378348 H.Koide, T.Satoh, M.Nakafuku, and Y.Kaziro (1993).
GTP-dependent association of Raf-1 with Ha-Ras: identification of Raf as a target downstream of Ras in mammalian cells.
  Proc Natl Acad Sci U S A, 90, 8683-8686.  
8335685 J.S.Herskovits, C.C.Burgess, R.A.Obar, and R.B.Vallee (1993).
Effects of mutant rat dynamin on endocytosis.
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  8443593 L.C.Seefeldt, and L.E.Mortenson (1993).
Increasing nitrogenase catalytic efficiency for MgATP by changing serine 16 of its Fe protein to threonine: use of Mn2+ to show interaction of serine 16 with Mg2+.
  Protein Sci, 2, 93.  
8293576 L.Chen, L.J.Zhang, P.Greer, P.S.Tung, and M.F.Moran (1993).
A murine CDC25/ras-GRF-related protein implicated in Ras regulation.
  Dev Genet, 14, 339-346.  
8436180 M.E.Peter, T.Wileman, and C.Terhorst (1993).
Covalent binding of guanine nucleotides to the CD3-gamma chain of the T cell receptor/CD3 complex.
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8069622 M.Kjeldgaard, P.Nissen, S.Thirup, and J.Nyborg (1993).
The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.
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PDB code: 1eft
8234290 T.C.Thomas, C.J.Schmidt, and E.J.Neer (1993).
G-protein alpha o subunit: mutation of conserved cysteines identifies a subunit contact surface and alters GDP affinity.
  Proc Natl Acad Sci U S A, 90, 10295-10298.  
8227141 T.Connolly, and R.Gilmore (1993).
GTP hydrolysis by complexes of the signal recognition particle and the signal recognition particle receptor.
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1738245 A.M.Spiegel (1992).
Heterotrimeric GTP-binding proteins: an expanding family of signal transducers.
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  1378397 A.Pause, and N.Sonenberg (1992).
Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor eIF-4A.
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1547491 C.H.Berlot, and H.R.Bourne (1992).
Identification of effector-activating residues of Gs alpha.
  Cell, 68, 911-922.  
12106362 C.Hahnel, K.Gottmann, A.Wittinghofer, and H.D.Lux (1992).
p21ras Oncogene Protein Selectively Increases Low-voltage-activated Ca2+ Current Density in Embryonic Chick Dorsal Root Ganglion Neurons.
  Eur J Neurosci, 4, 361-368.  
1565661 G.G.Privé, M.V.Milburn, L.Tong, A.M.de Vos, Z.Yamaizumi, S.Nishimura, and S.H.Kim (1992).
X-ray crystal structures of transforming p21 ras mutants suggest a transition-state stabilization mechanism for GTP hydrolysis.
  Proc Natl Acad Sci U S A, 89, 3649-3653.  
1554412 K.G.Higinbotham, J.M.Rice, and A.O.Perantoni (1992).
Activating point mutation in Ki-ras codon 63 in a chemically induced rat renal tumor.
  Mol Carcinog, 5, 136-139.  
  1732735 K.Tanaka, D.R.Wood, B.K.Lin, M.Khalil, F.Tamanoi, and J.F.Cannon (1992).
A dominant activating mutation in the effector region of RAS abolishes IRA2 sensitivity.
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1597193 L.Ménard, E.Tomhave, P.J.Casey, R.J.Uhing, R.Snyderman, and J.R.Didsbury (1992).
Rac1, a low-molecular-mass GTP-binding-protein with high intrinsic GTPase activity and distinct biochemical properties.
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1528078 M.D.Walkinshaw (1992).
Protein targets for structure-based drug design.
  Med Res Rev, 12, 317-372.  
  1486840 M.W.Anderson, S.H.Reynolds, M.You, and R.M.Maronpot (1992).
Role of proto-oncogene activation in carcinogenesis.
  Environ Health Perspect, 98, 13-24.  
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Mutations of Ha-ras p21 that define important regions for the molecular mechanism of the SDC25 C-domain, a guanine nucleotide dissociation stimulator.
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1740128 M.Y.Mistou, R.H.Cool, and A.Parmeggiani (1992).
Effects of ions on the intrinsic activities of c-H-ras protein p21. A comparison with elongation factor Tu.
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Mutational and kinetic analyses of the GTPase-activating protein (GAP)-p21 interaction: the C-terminal domain of GAP is not sufficient for full activity.
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1315314 P.J.Rapiejko, and R.Gilmore (1992).
Protein translocation across the ER requires a functional GTP binding site in the alpha subunit of the signal recognition particle receptor.
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Purification and characterization of a mutant DnaB protein specifically defective in ATP hydrolysis.
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1337001 S.L.Campbell-Burk, P.J.Domaille, M.A.Starovasnik, W.Boucher, and E.D.Laue (1992).
Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166).GDP using a novel 4D NMR strategy.
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  1569942 T.Munder, and P.Fürst (1992).
The Saccharomyces cerevisiae CDC25 gene product binds specifically to catalytically inactive ras proteins in vivo.
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1284540 T.V.Strong, L.S.Smit, S.Nasr, D.L.Wood, J.L.Cole, M.C.Iannuzzi, R.C.Stern, and F.S.Collins (1992).
Characterization of an intron 12 splice donor mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene.
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Mechanism and regulation of eukaryotic protein synthesis.
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GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.
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1785141 A.Wittinghofer, and E.F.Pai (1991).
The structure of Ras protein: a model for a universal molecular switch.
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1648482 F.Boege, E.Neumann, and E.J.Helmreich (1991).
Structural heterogeneity of membrane receptors and GTP-binding proteins and its functional consequences for signal transduction.
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1751548 H.Haubruck, and F.McCormick (1991).
Ras p21: effects and regulation.
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1918138 H.Plutner, A.D.Cox, S.Pind, R.Khosravi-Far, J.R.Bourne, R.Schwaninger, C.J.Der, and W.E.Balch (1991).
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Protein-tyrosine kinases regulate the phosphorylation, protein interactions, subcellular distribution, and activity of p21ras GTPase-activating protein.
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1907974 T.Oka, S.Nishikawa, and A.Nakano (1991).
Reconstitution of GTP-binding Sar1 protein function in ER to Golgi transport.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.