PDBsum entry 4q21

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Oncogene protein PDB id
Protein chain
169 a.a. *
Waters ×78
* Residue conservation analysis
PDB id:
Name: Oncogene protein
Title: Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins
Structure: C-h-ras p21 protein catalytic domain. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606.
2.00Å     R-factor:   0.195    
Authors: S.-H.Kim
Key ref: M.V.Milburn et al. (1990). Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science, 247, 939-945. PubMed id: 2406906 DOI: 10.1126/science.2406906
25-Sep-91     Release date:   15-Jul-92    
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Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
189 a.a.
169 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     Fc-epsilon receptor signaling pathway   58 terms 
  Biochemical function     nucleotide binding     4 terms  


DOI no: 10.1126/science.2406906 Science 247:939-945 (1990)
PubMed id: 2406906  
Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins.
M.V.Milburn, L.Tong, A.M.deVos, A.Brünger, Z.Yamaizumi, S.Nishimura, S.H.Kim.
Ras proteins participate as a molecular switch in the early steps of the signal transduction pathway that is associated with cell growth and differentiation. When the protein is in its GTP complexed form it is active in signal transduction, whereas it is inactive in its GDP complexed form. A comparison of eight three-dimensional structures of ras proteins in four different crystal lattices, five with a nonhydrolyzable GTP analog and three with GDP, reveals that the "on" and "off" states of the switch are distinguished by conformational differences that span a length of more than 40 A, and are induced by the gamma-phosphate. The most significant differences are localized in two regions: residues 30 to 38 (the switch I region) in the second loop and residues 60 to 76 (the switch II region) consisting of the fourth loop and the short alpha-helix that follows the loop. Both regions are highly exposed and form a continuous strip on the molecular surface most likely to be the recognition sites for the effector and receptor molecule(or molecules). The conformational differences also provide a structural basis for understanding the biological and biochemical changes of the proteins due to oncogenic mutations, autophosphorylation, and GTP hydrolysis, and for understanding the interactions with other proteins.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21125676 E.Vakiani, and D.B.Solit (2011).
KRAS and BRAF: drug targets and predictive biomarkers.
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20949621 L.Gremer, T.Merbitz-Zahradnik, R.Dvorsky, I.C.Cirstea, C.P.Kratz, M.Zenker, A.Wittinghofer, and M.R.Ahmadian (2011).
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20039879 A.Arbeloa, J.Garnett, J.Lillington, R.R.Bulgin, C.N.Berger, S.M.Lea, S.Matthews, and G.Frankel (2010).
EspM2 is a RhoA guanine nucleotide exchange factor.
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20194776 G.Buhrman, G.Holzapfel, S.Fetics, and C.Mattos (2010).
Allosteric modulation of Ras positions Q61 for a direct role in catalysis.
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PDB codes: 3k8y 3k9n 3lbh 3lbi 3lbn
20924370 J.B.Bruning, A.A.Parent, G.Gil, M.Zhao, J.Nowak, M.C.Pace, C.L.Smith, P.V.Afonine, P.D.Adams, J.A.Katzenellenbogen, and K.W.Nettles (2010).
Coupling of receptor conformation and ligand orientation determine graded activity.
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PDB codes: 2qxs 2qzo 3os8 3os9 3osa
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Structure of the dominant negative S17N mutant of Ras.
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PDB code: 3lo5
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Phosphorylation of mouse immunity-related GTPase (IRG) resistance proteins is an evasion strategy for virulent Toxoplasma gondii.
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20830302 Y.Lee, W.Y.Bang, S.Kim, P.Lazar, C.W.Kim, J.D.Bahk, and K.W.Lee (2010).
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Model for eukaryotic tail-anchored protein binding based on the structure of Get3.
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PDB codes: 3ibg 3idq
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Structural insights into formation of an active signaling complex between Rac and phospholipase C gamma 2.
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PDB codes: 2w2t 2w2v 2w2w 2w2x
18568040 A.E.Karnoub, and R.A.Weinberg (2008).
Ras oncogenes: split personalities.
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18258741 A.R.Zurita, and L.Birnbaumer (2008).
The same mutation in Gsalpha and transducin alpha reveals behavioral differences between these highly homologous G protein alpha-subunits.
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18809726 C.L.Brett, R.L.Plemel, B.T.Lobinger, M.Vignali, S.Fields, and A.J.Merz (2008).
Efficient termination of vacuolar Rab GTPase signaling requires coordinated action by a GAP and a protein kinase.
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18230735 J.Deng, P.A.Lewis, E.Greggio, E.Sluch, A.Beilina, and M.R.Cookson (2008).
Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase.
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PDB codes: 2zej 3d6t
19021766 J.Güldenhaupt, Y.Adigüzel, J.Kuhlmann, H.Waldmann, C.Kötting, and K.Gerwert (2008).
Secondary structure of lipidated Ras bound to a lipid bilayer.
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18801747 J.Sudhamsu, G.I.Lee, D.F.Klessig, and B.R.Crane (2008).
The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition.
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PDB code: 3ec1
18713003 L.Gremer, B.Gilsbach, M.R.Ahmadian, and A.Wittinghofer (2008).
Fluoride complexes of oncogenic Ras mutants to study the Ras-RasGap interaction.
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18348980 M.J.Phillips, G.Calero, B.Chan, S.Ramachandran, and R.A.Cerione (2008).
Effector proteins exert an important influence on the signaling-active state of the small GTPase Cdc42.
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PDB code: 2qrz
18393397 M.Soundararajan, A.Turnbull, O.Fedorov, C.Johansson, and D.A.Doyle (2008).
RhoB can adopt a Mg2+ free conformation prior to GEF binding.
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18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
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18536017 d.o. .J.Kim, J.Y.Jang, H.J.Yoon, and S.W.Suh (2008).
Crystal structure of YlqF, a circularly permuted GTPase: implications for its GTPase activation in 50 S ribosomal subunit assembly.
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PDB codes: 3cnl 3cnn 3cno
17186523 J.Gawronski-Salerno, J.S.Coon, P.J.Focia, and D.M.Freymann (2007).
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PDB code: 2iyl
17295319 M.D.Daily, and J.J.Gray (2007).
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PDB code: 2uzi
17575051 W.J.Belden, L.F.Larrondo, A.C.Froehlich, M.Shi, C.H.Chen, J.J.Loros, and J.C.Dunlap (2007).
The band mutation in Neurospora crassa is a dominant allele of ras-1 implicating RAS signaling in circadian output.
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17292915 W.Xie, C.Zhou, and R.H.Huang (2007).
Structure of tRNA dimethylallyltransferase: RNA modification through a channel.
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PDB codes: 3crm 3crq 3crr
16813595 A.B.Trovó-Marqui, and E.H.Tajara (2006).
Neurofibromin: a general outlook.
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16421734 A.S.Madrid, and K.Weis (2006).
Nuclear transport is becoming crystal clear.
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16531227 B.Ford, V.Hornak, H.Kleinman, and N.Nassar (2006).
Structure of a transient intermediate for GTP hydrolysis by ras.
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PDB codes: 1zvq 1zw6
16773572 C.Carta, F.Pantaleoni, G.Bocchinfuso, L.Stella, I.Vasta, A.Sarkozy, C.Digilio, A.Palleschi, A.Pizzuti, P.Grammatico, G.Zampino, B.Dallapiccola, B.D.Gelb, and M.Tartaglia (2006).
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16847854 G.Reuther, K.T.Tan, J.Köhler, C.Nowak, A.Pampel, K.Arnold, J.Kuhlmann, H.Waldmann, and D.Huster (2006).
Structural model of the membrane-bound C terminus of lipid-modified human N-ras protein.
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16395697 J.M.Cheng, M.Ding, A.Aribi, P.Shah, and K.Rao (2006).
Loss of RAB25 expression in breast cancer.
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16307466 K.Kodama, S.Fukuzawa, H.Nakayama, T.Kigawa, K.Sakamoto, T.Yabuki, N.Matsuda, M.Shirouzu, K.Takio, K.Tachibana, and S.Yokoyama (2006).
Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry.
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17031879 L.Brunsveld, J.Kuhlmann, K.Alexandrov, A.Wittinghofer, R.S.Goody, and H.Waldmann (2006).
Lipidated ras and rab peptides and proteins--synthesis, structure, and function.
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16720586 M.Bodén, and T.L.Bailey (2006).
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.
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17053066 N.Van Eps, W.M.Oldham, H.E.Hamm, and W.L.Hubbell (2006).
Structural and dynamical changes in an alpha-subunit of a heterotrimeric G protein along the activation pathway.
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16617427 S.Mesentean, S.Fischer, and J.C.Smith (2006).
Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping.
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16220142 A.E.Bednarski, S.C.Elgin, and H.B.Pakrasi (2005).
An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course.
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16196015 F.Peri, C.Airoldi, S.Colombo, E.Martegani, A.S.van Neuren, M.Stein, C.Marinzi, and F.Nicotra (2005).
Design, synthesis and biological evaluation of sugar-derived Ras inhibitors.
  Chembiochem, 6, 1839-1848.  
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.  
15937128 Y.Todaka, Y.Wang, K.Tashiro, N.Nakashima, T.Nishimoto, and T.Sekiguchi (2005).
Association of the GTP-binding protein Gtr1p with Rpc19p, a shared subunit of RNA polymerase I and III in yeast Saccharomyces cerevisiae.
  Genetics, 170, 1515-1524.  
14997535 A.Shurki, and A.Warshel (2004).
Why does the Ras switch "break" by oncogenic mutations?
  Proteins, 55, 1.  
15331784 D.H.Shin, Y.Lou, J.Jancarik, H.Yokota, R.Kim, and S.H.Kim (2004).
Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain.
  Proc Natl Acad Sci U S A, 101, 13198-13203.
PDB code: 1u0l
15653425 E.J.Helmreich (2004).
Structural flexibility of small GTPases. Can it explain their functional versatility?
  Biol Chem, 385, 1121-1136.  
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
15367757 J.Colicelli (2004).
Human RAS superfamily proteins and related GTPases.
  Sci STKE, 2004, RE13.  
14973186 J.Korlach, D.W.Baird, A.A.Heikal, K.R.Gee, G.R.Hoffman, and W.W.Webb (2004).
Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs.
  Proc Natl Acad Sci U S A, 101, 2800-2805.  
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
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.  
12956948 Q.Lin, R.N.Fuji, W.Yang, and R.A.Cerione (2003).
RhoGDI is required for Cdc42-mediated cellular transformation.
  Curr Biol, 13, 1469-1479.  
12557189 S.Datta, N.Ganesh, N.R.Chandra, K.Muniyappa, and M.Vijayan (2003).
Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition.
  Proteins, 50, 474-485.
PDB codes: 1mo3 1mo4 1mo5 1mo6
12628188 S.M.Margarit, H.Sondermann, B.E.Hall, B.Nagar, A.Hoelz, M.Pirruccello, D.Bar-Sagi, and J.Kuriyan (2003).
Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS.
  Cell, 112, 685-695.
PDB codes: 1nvu 1nvv 1nvw 1nvx
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
12297624 D.M.Himmel, S.Gourinath, L.Reshetnikova, Y.Shen, A.G.Szent-Györgyi, and C.Cohen (2002).
Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor.
  Proc Natl Acad Sci U S A, 99, 12645-12650.
PDB codes: 1kk7 1kk8 1kqm 1kwo 1l2o
12093730 G.Buchwald, A.Friebel, J.E.Galán, W.D.Hardt, A.Wittinghofer, and K.Scheffzek (2002).
Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE.
  EMBO J, 21, 3286-3295.
PDB code: 1gzs
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.
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12069788 L.Columbus, and W.L.Hubbell (2002).
A new spin on protein dynamics.
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11988479 M.Shimaoka, J.Takagi, and T.A.Springer (2002).
Conformational regulation of integrin structure and function.
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12296648 S.A.Woods, E.Marmor, M.Feldkamp, N.Lau, A.J.Apicelli, G.Boss, D.H.Gutmann, and A.Guha (2002).
Aberrant G protein signaling in nervous system tumors.
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11294626 A.P.Loh, N.Pawley, L.K.Nicholson, and R.E.Oswald (2001).
An increase in side chain entropy facilitates effector binding: NMR characterization of the side chain methyl group dynamics in Cdc42Hs.
  Biochemistry, 40, 4590-4600.  
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.
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11179219 G.G.Kelley, S.E.Reks, J.M.Ondrako, and A.V.Smrcka (2001).
Phospholipase C(epsilon): a novel Ras effector.
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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.  
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The Rab GTPase family.
  Genome Biol, 2, REVIEWS3007.  
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
11329253 M.Rohrer, T.F.Prisner, O.Brügmann, H.Käss, M.Spoerner, A.Wittinghofer, and H.R.Kalbitzer (2001).
Structure of the metal-water complex in Ras x GDP studied by high-field EPR spectroscopy and 31P NMR spectroscopy.
  Biochemistry, 40, 1884-1889.  
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
11746832 M.Suzui, S.Sugie, H.Mori, M.Okuno, T.Tanaka, and H.Moriwaki (2001).
Different mutation status of the beta-catenin gene in carcinogen-induced colon, brain, and oral tumors in rats.
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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.  
11327834 T.Soderberg, and C.D.Poulter (2001).
Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues.
  Biochemistry, 40, 1734-1740.  
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.  
11031231 K.H.Downing (2000).
Structural basis for the interaction of tubulin with proteins and drugs that affect microtubule dynamics.
  Annu Rev Cell Dev Biol, 16, 89.  
10933780 T.M.Glennon, J.Villà, and A.Warshel (2000).
How does GAP catalyze the GTPase reaction of Ras? A computer simulation study.
  Biochemistry, 39, 9641-9651.  
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
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
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The molecular perspective: the ras oncogene.
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10647185 H.J.Müller-Dieckmann, A.A.Grantz, and S.H.Kim (1999).
The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1.
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PDB code: 1dcf
10512836 H.Yagi, K.Tozawa, N.Sekino, T.Iwabuchi, M.Yoshida, and H.Akutsu (1999).
Functional conformation changes in the TF(1)-ATPase beta subunit probed by 12 tyrosine residues.
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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.
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10431174 J.Cherfils, and P.Chardin (1999).
GEFs: structural basis for their activation of small GTP-binding proteins.
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10427091 J.Drgonová, T.Drgon, D.H.Roh, and E.Cabib (1999).
The GTP-binding protein Rho1p is required for cell cycle progression and polarization of the yeast cell.
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10090289 J.Zeng, H.R.Treutlein, and T.Simonson (1999).
Molecular dynamics simulations of the Ras:Raf and Rap:Raf complexes.
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Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding.
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  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.
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PDB code: 1a4r
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.
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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.
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10469145 P.Meyer, J.Janin, and S.Baudet-Nessler (1999).
p55-hGRF, a short natural form of the Ras-GDP exchange factor high yield production and characterization.
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10619026 R.Maesaki, K.Ihara, T.Shimizu, S.Kuroda, K.Kaibuchi, and T.Hakoshima (1999).
The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1.
  Mol Cell, 4, 793-803.
PDB code: 1cxz
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.
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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.
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PDB code: 1ega
9868372 A.E.Stellwagen, and N.L.Craig (1998).
Mobile DNA elements: controlling transposition with ATP-dependent molecular switches.
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Interaction of a novel GDP exchange inhibitor with the Ras protein.
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GTP hydrolysis is not important for Ypt1 GTPase function in vesicular transport.
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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.
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PDB code: 1bof
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RhoA effector mutants reveal distinct effector pathways for cytoskeletal reorganization, SRF activation and transformation.
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Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching.
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GEF-mediated GDP/GTP exchange by monomeric GTPases: a regulatory role for Mg2+?
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The role of ligand binding in the kinetic folding mechanism of human p21(H-ras) protein.
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Structural analysis of the GAP-related domain from neurofibromin and its implications.
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PDB code: 1nf1
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Structural basis for the interaction of Ras with RalGDS.
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Characterizing semilocal motions in proteins by NMR relaxation studies.
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Identification of regulators for Ypt1 GTPase nucleotide cycling.
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Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing.
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X-ray structures of the MgADP, MgATPgammaS, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain.
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PDB codes: 1mma 1mmg 1mmn
9230689 A.M.Gulick, and I.Rayment (1997).
Structural studies on myosin II: communication between distant protein domains.
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9309221 C.T.Farrar, C.J.Halkides, and D.J.Singel (1997).
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Microtubule interaction site of the kinesin motor.
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Structural and functional analysis of a mutant Ras protein that is insensitive to nitric oxide activation.
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Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.
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PDB codes: 1kao 2rap
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Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.
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Identification of an essential Caulobacter crescentus gene encoding a member of the Obg family of GTP-binding proteins.
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9219684 K.Scheffzek, M.R.Ahmadian, W.Kabsch, L.Wiesmüller, A.Lautwein, F.Schmitz, and A.Wittinghofer (1997).
The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.
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PDB code: 1wq1
9253406 L.Huang, X.Weng, F.Hofer, G.S.Martin, and S.H.Kim (1997).
Three-dimensional structure of the Ras-interacting domain of RalGDS.
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PDB code: 1lxd
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.
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Rab7: NMR and kinetics analysis of intact and C-terminal truncated constructs.
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Genetic interactions with Rap1 and Ras1 reveal a second function for the fat facets deubiquitinating enzyme in Drosophila eye development.
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Cellular functions regulated by Src family kinases.
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Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
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PDB code: 1aa9
8939752 A.M.Berghuis, E.Lee, A.S.Raw, A.G.Gilman, and S.R.Sprang (1996).
Structure of the GDP-Pi complex of Gly203-->Ala gialpha1: a mimic of the ternary product complex of galpha-catalyzed GTP hydrolysis.
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High frequency (139.5 GHz) electron paramagnetic resonance characterization of Mn(II)-H2(17)O interactions in GDP and GTP forms of p21 ras.
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8785318 C.A.Smith, and I.Rayment (1996).
Active site comparisons highlight structural similarities between myosin and other P-loop proteins.
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A recombinant peptide model of the first nucleotide-binding fold of the cystic fibrosis transmembrane conductance regulator: comparison of wild-type and delta F508 mutant forms.
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Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.
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Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.
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Elucidation of a MgATP signal transduction pathway in the nitrogenase iron protein: formation of a conformation resembling the MgATP-bound state by protein engineering.
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Switches, latches, and amplifiers: common themes of G proteins and molecular motors.
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TC21 causes transformation by Raf-independent signaling pathways.
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8736554, A.Aevarsson, M.Garber, J.Zheltonosova, and A.Liljas (1996).
The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange.
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PDB code: 1dar
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Loss of Raf-1-binding activity of v-Ha-Ras by the deletion of amino acid residues 64-72 and 143-151.
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Mutational analysis of Era, an essential GTP-binding protein of Escherichia coli.
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Limited proteolysis and amino acid replacements in the effector region of Thermus thermophilus elongation factor Tu.
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Neurofibromatosis type 1 and Ras-mediated signaling: filling in the GAPs.
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8548282 B.Bax, and H.Jhoti (1995).
Protein-protein interactions. Putting the pieces together.
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Molecular characterization of the in vivo alkylating agent resistant murine EMT-6 mammary carcinoma tumors.
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Rac GTPase interacts with GAPs and target proteins through multiple effector sites.
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A method to predict functional residues in proteins.
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The NADPH oxidase complex of phagocytic leukocytes: a biochemical and cytochemical view.
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Two distinct regions of Ras participate in functional interaction with GDP-GTP exchangers.
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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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Regulatory GTPases.
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DNA-strand exchange promoted by RecA protein in the absence of ATP: implications for the mechanism of energy transduction in protein-promoted nucleic acid transactions.
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The GTPase activity of the Escherichia coli Ffh protein is important for normal growth.
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Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins.
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The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the same family.
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Site-directed mutagenesis of Thermus thermophilus elongation factor Tu. Replacement of His85, Asp81 and Arg300.
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Rab 7: an important regulator of late endocytic membrane traffic.
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Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus.
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PDB code: 1elo
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The structure of transducin G alpha t: more to view than just ras.
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Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants.
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G proteins: critical control points for transmembrane signals.
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The ABC of EF-G.
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Ultrastructural localization of the small GTP-binding protein Rap1 in human platelets and megakaryocytes.
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Distinct structural elements of rab5 define its functional specificity.
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Biochemical characterization of the essential GTP-binding protein Obg of Bacillus subtilis.
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Pre-steady-state MgATP-dependent proton production and electron transfer by nitrogenase from Azotobacter vinelandii.
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Elongation factor Tu: a regulatory GTPase with an integrated effector.
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Identification of residues of the H-ras protein critical for functional interaction with guanine nucleotide exchange factors.
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p190 RhoGAP, the major RasGAP-associated protein, binds GTP directly.
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Molecular evolution of SRP cycle components: functional implications.
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The Srp54 GTPase is essential for protein export in the fission yeast Schizosaccharomyces pombe.
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GTP-binding proteins. Structures, interactions and relationships.
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Why have mutagenesis studies not located the general base in ras p21.
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Two types of RAS mutants that dominantly interfere with activators of RAS.
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Carboxyl-terminal amino acid residues in elongation factor G essential for ribosome association and translocation.
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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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Rab17, a novel small GTPase, is specific for epithelial cells and is induced during cell polarization.
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From EF-Tu to p21ras and back again.
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Structural elements of G alpha subunits that interact with G beta gamma, receptors, and effectors.
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Posttranslational processing of the ras superfamily of small GTP-binding proteins.
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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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Probing the role of loop 2 in Ras function with unnatural amino acids.
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GTP-dependent association of Raf-1 with Ha-Ras: identification of Raf as a target downstream of Ras in mammalian cells.
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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.  
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.
  Structure, 1, 35-50.
PDB code: 1eft
8504133 M.Noda (1993).
Structures and functions of the K rev-1 transformation suppressor gene and its relatives.
  Biochim Biophys Acta, 1155, 97.  
8212134 M.S.Marshall (1993).
The effector interactions of p21ras.
  Trends Biochem Sci, 18, 250-254.  
8466475 P.A.Hargrave, H.E.Hamm, and K.P.Hofmann (1993).
Interaction of rhodopsin with the G-protein, transducin.
  Bioessays, 15, 43-50.  
  8514750 R.B.Bourret, S.K.Drake, S.A.Chervitz, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. II. Analysis of activated mutants by 19F NMR and protein engineering.
  J Biol Chem, 268, 13089-13096.  
  8514749 S.K.Drake, R.B.Bourret, L.A.Luck, M.I.Simon, and J.J.Falke (1993).
Activation of the phosphosignaling protein CheY. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering.
  J Biol Chem, 268, 13081-13088.  
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.
  J Cell Biol, 123, 799-807.  
1547491 C.H.Berlot, and H.R.Bourne (1992).
Identification of effector-activating residues of Gs alpha.
  Cell, 68, 911-922.  
1565661 G.G.Privé, M.V.Milburn, L.Tong, 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.  
1586371 J.Downward (1992).
Regulatory mechanisms for ras proteins.
  Bioessays, 14, 177-184.  
1633420 J.Downward (1992).
Regulation of p21ras by GTPase activating proteins and guanine nucleotide exchange proteins.
  Curr Opin Genet Dev, 2, 13-18.  
1466766 J.Fujita-Yoshigaki, Y.Ito, K.Yamasaki, Y.Muto, T.Miyazawa, S.Nishimura, and S.Yokoyama (1992).
Guanine-nucleotide binding activity, interaction with GTPase-activating protein and solution conformation of the human c-Ha-Ras protein catalytic domain are retained upon deletion of C-terminal 18 amino acid residues.
  J Protein Chem, 11, 731-739.  
1324849 J.Senyshyn, W.E.Balch, and R.W.Holz (1992).
Synthetic peptides of the effector-binding domain of rab enhance secretion from digitonin-permeabilized chromaffin cells.
  FEBS Lett, 309, 41-46.  
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.
  Mol Cell Biol, 12, 631-637.  
1422147 K.Yamasaki, Y.Muto, Y.Ito, M.Wälchli, T.Miyazawa, S.Nishimura, and S.Yokoyama (1992).
A 1H-15N NMR study of human c-Ha-ras protein: biosynthetic incorporation of 15N-labeled amino acids.
  J Biomol NMR, 2, 71-82.  
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.
  Eur J Biochem, 206, 537-546.  
  1620108 M.Bun-Ya, S.Harashima, and Y.Oshima (1992).
Putative GTP-binding protein, Gtr1, associated with the function of the Pho84 inorganic phosphate transporter in Saccharomyces cerevisiae.
  Mol Cell Biol, 12, 2958-2966.  
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.  
  1628612 M.Y.Mistou, E.Jacquet, P.Poullet, H.Rensland, P.Gideon, I.Schlichting, A.Wittinghofer, and A.Parmeggiani (1992).
Mutations of Ha-ras p21 that define important regions for the molecular mechanism of the SDC25 C-domain, a guanine nucleotide dissociation stimulator.
  EMBO J, 11, 2391-2397.  
  1569938 N.C.Walworth, P.Brennwald, A.K.Kabcenell, M.Garrett, and P.Novick (1992).
Hydrolysis of GTP by Sec4 protein plays an important role in vesicular transport and is stimulated by a GTPase-activating protein in Saccharomyces cerevisiae.
  Mol Cell Biol, 12, 2017-2028.  
  1563351 O.Nielsen, J.Davey, and R.Egel (1992).
The ras1 function of Schizosaccharomyces pombe mediates pheromone-induced transcription.
  EMBO J, 11, 1391-1395.  
  1569940 P.Gideon, J.John, M.Frech, A.Lautwein, R.Clark, J.E.Scheffler, and A.Wittinghofer (1992).
Mutational and kinetic analyses of the GTPase-activating protein (GAP)-p21 interaction: the C-terminal domain of GAP is not sufficient for full activity.
  Mol Cell Biol, 12, 2050-2056.  
1371881 P.J.Padfield, W.E.Balch, and J.D.Jamieson (1992).
A synthetic peptide of the rab3a effector domain stimulates amylase release from permeabilized pancreatic acini.
  Proc Natl Acad Sci U S A, 89, 1656-1660.  
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.
  J Biomol NMR, 2, 639-646.  
  1569942 T.Munder, and P.Fürst (1992).
The Saccharomyces cerevisiae CDC25 gene product binds specifically to catalytically inactive ras proteins in vivo.
  Mol Cell Biol, 12, 2091-2099.  
2056968 A.Iolascon, A.Lania, M.Badiali, A.Pession, G.Saglio, F.Giangaspero, E.Miraglia del Giudice, S.Perrotta, and S.Cutillo (1991).
Analysis of N-ras gene mutations in medulloblastomas by polymerase chain reaction and oligonucleotide probes in formalin-fixed, paraffin-embedded tissues.
  Med Pediatr Oncol, 19, 240-245.  
2052624 A.Valencia, M.Kjeldgaard, E.F.Pai, and C.Sander (1991).
GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.
  Proc Natl Acad Sci U S A, 88, 5443-5447.  
1785141 A.Wittinghofer, and E.F.Pai (1991).
The structure of Ras protein: a model for a universal molecular switch.
  Trends Biochem Sci, 16, 382-387.  
  1645767 B.B.Fredholm (1991).
Diversity in receptor signalling: cellular individuality and the search for selective drugs.
  J Intern Med, 229, 391-406.  
2009134 B.L.Stegelmeier, N.A.Gillett, A.H.Rebar, and G.Kelly (1991).
The molecular progression of plutonium-239-induced rat lung carcinogenesis: Ki-ras expression and activation.
  Mol Carcinog, 4, 43-51.  
  1990290 C.Dascher, R.Ossig, D.Gallwitz, and H.D.Schmitt (1991).
Identification and structure of four yeast genes (SLY) that are able to suppress the functional loss of YPT1, a member of the RAS superfamily.
  Mol Cell Biol, 11, 872-885.  
  1922022 C.L.Farnsworth, and L.A.Feig (1991).
Dominant inhibitory mutations in the Mg(2+)-binding site of RasH prevent its activation by GTP.
  Mol Cell Biol, 11, 4822-4829.  
1986384 C.S.Mimura, S.R.Holbrook, and G.F.Ames (1991).
Structural model of the nucleotide-binding conserved component of periplasmic permeases.
  Proc Natl Acad Sci U S A, 88, 84-88.  
1751548 H.Haubruck, and F.McCormick (1991).
Ras p21: effects and regulation.
  Biochim Biophys Acta, 1072, 215-229.  
1918138 H.Plutner, A.D.Cox, S.Pind, R.Khosravi-Far, J.R.Bourne, R.Schwaninger, C.J.Der, and W.E.Balch (1991).
Rab1b regulates vesicular transport between the endoplasmic reticulum and successive Golgi compartments.
  J Cell Biol, 115, 31-43.  
  2009858 J.Becker, T.J.Tan, H.H.Trepte, and D.Gallwitz (1991).
Mutational analysis of the putative effector domain of the GTP-binding Ypt1 protein in yeast suggests specific regulation by a novel GAP activity.
  EMBO J, 10, 785-792.  
  1656212 J.D.Hildebrandt, R.Day, C.L.Farnsworth, and L.A.Feig (1991).
A mutation in the putative Mg(2+)-binding site of Gs alpha prevents its activation by receptors.
  Mol Cell Biol, 11, 4830-4838.  
  1907494 M.A.Lochrie, J.E.Mendel, P.W.Sternberg, and M.I.Simon (1991).
Homologous and unique G protein alpha subunits in the nematode Caenorhabditis elegans.
  Cell Regul, 2, 135-154.  
1665976 M.Murakami (1991).
Occurrence of beta-turn potentials around nuclear and nucleolar localization sequences.
  J Protein Chem, 10, 469-473.  
1906178 P.Van Der Sluijs, M.Hull, A.Zahraoui, A.Tavitian, B.Goud, and I.Mellman (1991).
The small GTP-binding protein rab4 is associated with early endosomes.
  Proc Natl Acad Sci U S A, 88, 6313-6317.  
1905764 R.T.Miller (1991).
Transmembrane signalling through G proteins.
  Kidney Int, 39, 421-429.  
1713431 S.Damjanovich, and C.Pieri (1991).
Electroimmunology: membrane potential, ion-channel activities, and stimulatory signal transduction in human T lymphocytes from young and elderly.
  Ann N Y Acad Sci, 621, 29-39.  
2191303 A.T.Brünger, M.V.Milburn, L.Tong, A.M.deVos, J.Jancarik, Z.Yamaizumi, S.Nishimura, E.Ohtsuka, and S.H.Kim (1990).
Crystal structure of an active form of RAS protein, a complex of a GTP analog and the HRAS p21 catalytic domain.
  Proc Natl Acad Sci U S A, 87, 4849-4853.  
  2196171 E.F.Pai, U.Krengel, G.A.Petsko, R.S.Goody, W.Kabsch, and A.Wittinghofer (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.
PDB code: 5p21
  2114975 H.Plutner, R.Schwaninger, S.Pind, and W.E.Balch (1990).
Synthetic peptides of the Rab effector domain inhibit vesicular transport through the secretory pathway.
  EMBO J, 9, 2375-2383.  
2127644 J.Downward (1990).
The ras superfamily of small GTP-binding proteins.
  Trends Biochem Sci, 15, 469-472.  
2085379 J.M.Chen, G.Lee, P.W.Brandt-Rauf, R.B.Murphy, S.Rackovsky, and M.R.Pincus (1990).
Comparison of the predicted structure for the activated form of the P21 protein with the X-ray crystal structure.
  J Protein Chem, 9, 543-547.  
2164718 J.T.Parsons (1990).
Closing the GAP in a signal transduction pathway.
  Trends Genet, 6, 169-171.  
1980105 K.Harmark, R.H.Cool, B.F.Clark, and A.Parmeggiani (1990).
The functional and structural roles of residues Gln114 and Glu117 in elongation factor Tu.
  Eur J Biochem, 194, 731-737.  
2124704 K.Shinjo, J.G.Koland, M.J.Hart, V.Narasimhan, D.I.Johnson, T.Evans, and R.A.Cerione (1990).
Molecular cloning of the gene for the human placental GTP-binding protein Gp (G25K): identification of this GTP-binding protein as the human homolog of the yeast cell-division-cycle protein CDC42.
  Proc Natl Acad Sci U S A, 87, 9853-9857.  
  2122236 S.Munemitsu, M.A.Innis, R.Clark, F.McCormick, A.Ullrich, and P.Polakis (1990).
Molecular cloning and expression of a G25K cDNA, the human homolog of the yeast cell cycle gene CDC42.
  Mol Cell Biol, 10, 5977-5982.  
2199064 U.Krengel, I.Schlichting, A.Scherer, R.Schumann, M.Frech, J.John, W.Kabsch, E.F.Pai, and A.Wittinghofer (1990).
Three-dimensional structures of H-ras p21 mutants: molecular basis for their inability to function as signal switch molecules.
  Cell, 62, 539-548.
PDB codes: 221p 421p 521p 621p 721p
2077687 W.E.Balch (1990).
Small GTP-binding proteins in vesicular transport.
  Trends Biochem Sci, 15, 473-477.  
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