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PDBsum entry 1wq1
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protein ligands metals Protein-protein interface(s) links
Complex (gtp-binding/gtpase activation) PDB id
1wq1

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
166 a.a. *
320 a.a. *
Ligands
GDP-AF3
Metals
_MG
Waters ×35
* Residue conservation analysis
PDB id:
1wq1
Name: Complex (gtp-binding/gtpase activation)
Title: Ras-rasgap complex
Structure: H-ras. Chain: r. Fragment: catalytic domain, residues 1 - 166. Synonym: p21ras, ras, harvey-ras. Engineered: yes. P120gap. Chain: g. Fragment: catalytic domain, residues 714 - 1047. Synonym: gap-334, gapette.
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: placenta. Gene: h-ras-1. Expressed in: escherichia coli. Expression_system_taxid: 562. Cellular_location: cytosol. Gene: gene fragment of p120gap posi.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.233     R-free:   0.319
Authors: K.Scheffzek,M.R.Ahmadian,W.Kabsch,L.Wiesmueller,A.Lautwein,F.Schmitz, A.Wittinghofer
Key ref:
K.Scheffzek et al. (1997). The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science, 277, 333-338. PubMed id: 9219684 DOI: 10.1126/science.277.5324.333
Date:
03-Jul-97     Release date:   15-Jul-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas from Homo sapiens
Seq:
Struc: 		189 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
P20936  (RASA1_HUMAN) -  Ras GTPase-activating protein 1 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1047 a.a.
320 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain R: E.C.3.6.5.2  - small monomeric GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 =
GDP
Bound ligand (Het Group name = GDP)
corresponds exactly 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1126/science.277.5324.333 Science 277:333-338 (1997)
PubMed id: 9219684  
 
 
The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.
K.Scheffzek, M.R.Ahmadian, W.Kabsch, L.Wiesmüller, A.Lautwein, F.Schmitz, A.Wittinghofer.
 
  ABSTRACT  
 
The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo view of a segment of the 2F[o] F[c] electron density map (contoured at 1.2 ) covering the active site region in the^ complex, with Ras in blue, GAP-334 in red, and waters in light blue. 		Figure 2.
Fig. 2. The complex between GAP-334 and Ras. (A) Ribbon representation of the complex model drawn with Molscript (52) and^ Raster3D (53) according to the assignment of secondary structure^ elements obtained with the program DSSP (54). The extra and^ catalytic domains of GAP-334 are shown in green and red (respectively), regions of GAP contacting Ras in light brown, Ras in yellow, and^ GDP and AlF[3] as ball-and-stick models. Regions involved in the^ interface are labeled, Sw I and Sw II indicating the switch regions, C the COOH-terminal, and N the NH[2]-terminal. (B) Schematic^ drawing with selected interactions. Polar interactions between individual residues of GAP-334 and Ras are shown as red lines for interactions of side chains, and as red arrows for contacts from side chain to main chain atoms, where the arrowhead marks the residue contributing the main chain group. Yellow lines indicate^ van der Waals or hydrophobic interactions. Some water molecules (marked W) from the interface region are included. Residues belonging to the interacting regions of Ras indicated in (A) are denoted^ with specified boxes, as indicated. Interaction between Lys88 and Thr791 is shown by a dashed arrow, because the electron density in this region is presently not of sufficient quality to unambiguously define the contact. Amino acid abbreviations are in (55).
 
  The above figures are reprinted by permission from the AAAs: Science (1997, 277, 333-338) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Role of Ras/Raf/MEK/ERK signaling in physiological hematopoiesis and leukemia development.
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Structural basis for the molecular evolution of SRP-GTPase activation by protein.
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PDB code: 3syn
21079152 J.E.Niemela, L.Lu, T.A.Fleisher, J.Davis, I.Caminha, M.Natter, L.A.Beer, K.C.Dowdell, S.Pittaluga, M.Raffeld, V.K.Rao, and J.B.Oliveira (2011).
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Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders.
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The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii.
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Structural insight into the membrane insertion of tail-anchored proteins by Get3.
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PDB codes: 3a36 3a37
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Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH.
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Functional study on GTP hydrolysis by the GTP-binding protein from Sulfolobus solfataricus, a member of the HflX family.
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PDB codes: 3kxi 3kxk 3kxl
20186121 B.Sot, C.Kötting, D.Deaconescu, Y.Suveyzdis, K.Gerwert, and A.Wittinghofer (2010).
Unravelling the mechanism of dual-specificity GAPs.
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Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
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21102635 D.Vigil, J.Cherfils, K.L.Rossman, and C.J.Der (2010).
Ras superfamily GEFs and GAPs: validated and tractable targets for cancer therapy?
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20219935 E.A.Niskanen, T.O.Ihalainen, O.Kalliolinna, M.M.Häkkinen, and M.Vihinen-Ranta (2010).
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Allosteric modulation of Ras positions Q61 for a direct role in catalysis.
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PDB codes: 3k8y 3k9n 3lbh 3lbi 3lbn
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Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism.
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PDB codes: 3kqh 3kqk 3kql 3kqn 3kqu
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PDB codes: 3lvq 3lvr
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PDB code: 2l0x
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PDB codes: 3ieu 3iev
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ABC transporters: the power to change.
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  RNA, 15, 67-75.
PDB code: 3ex7
19388050 M.S.Kim, J.Song, and C.Park (2009).
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19201753 M.Sajish, S.Kalayil, S.K.Verma, V.K.Nandicoori, and B.Prakash (2009).
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RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon.
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PDB code: 2zpa
19433443 S.Kupzig, D.Bouyoucef-Cherchalli, S.Yarwood, R.Sessions, and P.J.Cullen (2009).
The ability of GAP1IP4BP to function as a Rap1 GTPase-activating protein (GAP) requires its Ras GAP-related domain and an arginine finger rather than an asparagine thumb.
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19218462 T.McAvoy, M.M.Zhou, P.Greengard, and A.C.Nairn (2009).
Phosphorylation of Rap1GAP, a striatally enriched protein, by protein kinase A controls Rap1 activity and dendritic spine morphology.
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19321438 V.B.Kurella, J.M.Richard, C.L.Parke, L.F.Lecour, H.D.Bellamy, and D.K.Worthylake (2009).
Crystal structure of the GTPase-activating protein-related domain from IQGAP1.
  J Biol Chem, 284, 14857-14865.
PDB code: 3fay
  19454010 V.W.Gautier, L.Gu, N.O'Donoghue, S.Pennington, N.Sheehy, and W.W.Hall (2009).
In vitro nuclear interactome of the HIV-1 Tat protein.
  Retrovirology, 6, 47.  
19074952 Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, and C.D.Hsiao (2009).
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
  Nucleic Acids Res, 37, 804-814.
PDB codes: 2vye 2vyf
19843518 Y.Tong, P.K.Hota, J.Y.Penachioni, M.B.Hamaneh, S.Kim, R.S.Alviani, L.Shen, H.He, W.Tempel, L.Tamagnone, H.W.Park, and M.Buck (2009).
Structure and function of the intracellular region of the plexin-b1 transmembrane receptor.
  J Biol Chem, 284, 35962-35972.
PDB code: 3hm6
18568040 A.E.Karnoub, and R.A.Weinberg (2008).
Ras oncogenes: split personalities.
  Nat Rev Mol Cell Biol, 9, 517-531.  
18309292 A.Scrima, C.Thomas, D.Deaconescu, and A.Wittinghofer (2008).
The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues.
  EMBO J, 27, 1145-1153.
PDB code: 3brw
18434546 C.Kötting, A.Kallenbach, Y.Suveyzdis, A.Wittinghofer, and K.Gerwert (2008).
The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy.
  Proc Natl Acad Sci U S A, 105, 6260-6265.  
  18758236 D.Abankwa, A.A.Gorfe, and J.F.Hancock (2008).
Mechanisms of Ras membrane organization and signalling: Ras on a rocker.
  Cell Cycle, 7, 2667-2673.  
18491388 J.Martin, L.Regad, C.Etchebest, and A.C.Camproux (2008).
Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.
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17599776 J.Milić, R.Seidel, C.F.Becker, R.S.Goody, and M.Engelhard (2008).
Semisynthesis of H-Ras with a glutamic acid methylester at position 61.
  Biopolymers, 90, 399-405.  
18713003 L.Gremer, B.Gilsbach, M.R.Ahmadian, and A.Wittinghofer (2008).
Fluoride complexes of oncogenic Ras mutants to study the Ras-RasGap interaction.
  Biol Chem, 389, 1163-1171.  
18039943 L.Harispe, C.Portela, C.Scazzocchio, M.A.Peñalva, and L.Gorfinkiel (2008).
Ras GTPase-activating protein regulation of actin cytoskeleton and hyphal polarity in Aspergillus nidulans.
  Eukaryot Cell, 7, 141-153.  
18430232 M.Grunt, V.Zárský, and F.Cvrcková (2008).
Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins.
  BMC Evol Biol, 8, 115.  
18502802 M.I.Monine, and J.M.Haugh (2008).
Signal transduction at point-blank range: analysis of a spatial coupling mechanism for pathway crosstalk.
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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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18423189 N.Kannan, and S.S.Taylor (2008).
Rethinking pseudokinases.
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18400179 P.Koenig, M.Oreb, A.Höfle, S.Kaltofen, K.Rippe, I.Sinning, E.Schleiff, and I.Tews (2008).
The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures.
  Structure, 16, 585-596.
PDB codes: 3bb1 3bb3 3bb4
18428421 S.A.Forbes, G.Bhamra, S.Bamford, E.Dawson, C.Kok, J.Clements, A.Menzies, J.W.Teague, P.A.Futreal, and M.R.Stratton (2008).
The Catalogue of Somatic Mutations in Cancer (COSMIC).
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18376416 S.Veltel, R.Gasper, E.Eisenacher, and A.Wittinghofer (2008).
The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3.
  Nat Struct Mol Biol, 15, 373-380.
PDB codes: 3bh6 3bh7
18323856 V.Pena, M.Hothorn, A.Eberth, N.Kaschau, A.Parret, L.Gremer, F.Bonneau, M.R.Ahmadian, and K.Scheffzek (2008).
The C2 domain of SynGAP is essential for stimulation of the Rap GTPase reaction.
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PDB code: 3bxj
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Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
  Nature, 453, 489-484.
PDB codes: 3cmt 3cmu 3cmv 3cmw 3cmx
17368733 B.Fischer, M.Marinov, and A.Arcaro (2007).
Targeting receptor tyrosine kinase signalling in small cell lung cancer (SCLC): what have we learned so far?
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17094109 B.L.Grigorenko, A.V.Nemukhin, M.S.Shadrina, I.A.Topol, and S.K.Burt (2007).
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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The tail of the ParG DNA segregation protein remodels ParF polymers and enhances ATP hydrolysis via an arginine finger-like motif.
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17143896 D.Monleón, M.Martínez-Vicente, V.Esteve, L.Yim, S.Prado, M.E.Armengod, and B.Celda (2007).
Structural insights into the GTPase domain of Escherichia coli MnmE protein.
  Proteins, 66, 726-739.
PDB code: 1rfl
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Protein translocation: checkpoint role for SRP GTPase activation.
  Curr Biol, 17, R980-R982.  
18073111 G.Buhrman, G.Wink, and C.Mattos (2007).
Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf.
  Structure, 15, 1618-1629.
PDB codes: 2rga 2rgb 2rgc 2rgd 2rge 2rgg
17766252 H.Ren, S.X.Dou, P.Rigolet, Y.Yang, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling.
  Nucleic Acids Res, 35, 6029-6041.  
17540168 J.L.Bos, H.Rehmann, and A.Wittinghofer (2007).
GEFs and GAPs: critical elements in the control of small G proteins.
  Cell, 129, 865-877.  
  17392688 K.C.Chen, Y.Zhou, W.Zhang, and M.F.Lou (2007).
Control of PDGF-induced reactive oxygen species (ROS) generation and signal transduction in human lens epithelial cells.
  Mol Vis, 13, 374-387.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
18160044 P.Wendler, J.Shorter, C.Plisson, A.G.Cashikar, S.Lindquist, and H.R.Saibil (2007).
Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
  Cell, 131, 1366-1377.  
17468740 S.Gras, V.Chaumont, B.Fernandez, P.Carpentier, F.Charrier-Savournin, S.Schmitt, C.Pineau, D.Flament, A.Hecker, P.Forterre, J.Armengaud, and D.Housset (2007).
Structural insights into a new homodimeric self-activated GTPase family.
  EMBO Rep, 8, 569-575.
PDB codes: 1yr6 1yr7 1yr8 1yr9 1yra 1yrb 2oxr
17384584 S.Schubbert, K.Shannon, and G.Bollag (2007).
Hyperactive Ras in developmental disorders and cancer.
  Nat Rev Cancer, 7, 295-308.  
  18007958 W.B.Bowne, J.Michl, M.H.Bluth, M.E.Zenilman, and M.R.Pincus (2007).
Novel peptides from the RAS-p21 and p53 proteins for the treatment of cancer.
  Cancer Ther, 5, 331-344.  
16813595 A.B.Trovó-Marqui, and E.H.Tajara (2006).
Neurofibromin: a general outlook.
  Clin Genet, 70, 1.  
16511497 A.Ghosh, G.J.Praefcke, L.Renault, A.Wittinghofer, and C.Herrmann (2006).
How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP.
  Nature, 440, 101-104.
PDB codes: 2b8w 2b92 2bc9 2d4h
16763562 A.Scrima, and A.Wittinghofer (2006).
Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element.
  EMBO J, 25, 2940-2951.
PDB codes: 2gj8 2gj9 2gja
16628222 A.Seybert, M.R.Singleton, N.Cook, D.R.Hall, and D.B.Wigley (2006).
Communication between subunits within an archaeal clamp-loader complex.
  EMBO J, 25, 2209-2218.
PDB codes: 2chg 2chq 2chv
16356724 A.Wittinghofer (2006).
Phosphoryl transfer in Ras proteins, conclusive or elusive?
  Trends Biochem Sci, 31, 20-23.  
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
16968776 C.Kötting, M.Blessenohl, Y.Suveyzdis, R.S.Goody, A.Wittinghofer, and K.Gerwert (2006).
A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein.
  Proc Natl Acad Sci U S A, 103, 13911-13916.  
16607279 F.Chiaradonna, E.Sacco, R.Manzoni, M.Giorgio, M.Vanoni, and L.Alberghina (2006).
Ras-dependent carbon metabolism and transformation in mouse fibroblasts.
  Oncogene, 25, 5391-5404.  
16537406 G.Rumbaugh, J.P.Adams, J.H.Kim, and R.L.Huganir (2006).
SynGAP regulates synaptic strength and mitogen-activated protein kinases in cultured neurons.
  Proc Natl Acad Sci U S A, 103, 4344-4351.  
17114577 J.A.Walker, A.V.Tchoudakova, P.T.McKenney, S.Brill, D.Wu, G.S.Cowley, I.K.Hariharan, and A.Bernards (2006).
Reduced growth of Drosophila neurofibromatosis 1 mutants reflects a non-cell-autonomous requirement for GTPase-Activating Protein activity in larval neurons.
  Genes Dev, 20, 3311-3323.  
16374872 J.Bonet, G.Caltabiano, A.K.Khan, M.A.Johnston, C.Corbí, A.Gómez, X.Rovira, J.Teyra, and J.Villà-Freixa (2006).
The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study.
  Proteins, 63, 65-77.  
16515591 M.E.Beiner, H.Niv, R.Haklai, G.Elad-Sfadia, Y.Kloog, and G.Ben-Baruch (2006).
Ras antagonist inhibits growth and chemosensitizes human epithelial ovarian cancer cells.
  Int J Gynecol Cancer, 16, 200-206.  
17088537 S.Chen, J.T.Do, Q.Zhang, S.Yao, F.Yan, E.C.Peters, H.R.Schöler, P.G.Schultz, and S.Ding (2006).
Self-renewal of embryonic stem cells by a small molecule.
  Proc Natl Acad Sci U S A, 103, 17266-17271.  
16431904 S.Kupzig, D.Deaconescu, D.Bouyoucef, S.A.Walker, Q.Liu, C.L.Polte, O.Daumke, T.Ishizaki, P.J.Lockyer, A.Wittinghofer, and P.J.Cullen (2006).
GAP1 family members constitute bifunctional Ras and Rap GTPase-activating proteins.
  J Biol Chem, 281, 9891-9900.  
16630817 T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, and S.Yokoyama (2006).
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
  Cell, 125, 287-300.
PDB code: 2db3
16691442 U.Ashery, O.Yizhar, B.Rotblat, G.Elad-Sfadia, B.Barkan, R.Haklai, and Y.Kloog (2006).
Spatiotemporal organization of Ras signaling: rasosomes and the galectin switch.
  Cell Mol Neurobiol, 26, 471-495.  
16855591 X.Pan, S.Eathiraj, M.Munson, and D.G.Lambright (2006).
TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism.
  Nature, 442, 303-306.
PDB code: 2g77
16307476 A.Eberth, R.Dvorsky, C.F.Becker, A.Beste, R.S.Goody, and M.R.Ahmadian (2005).
Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins.
  Biol Chem, 386, 1105-1114.  
15738386 A.Y.Goldstein, Y.N.Jan, and L.Luo (2005).
Function and regulation of Tumbleweed (RacGAP50C) in neuroblast proliferation and neuronal morphogenesis.
  Proc Natl Acad Sci U S A, 102, 3834-3839.  
15906320 B.L.Grigorenko, A.V.Nemukhin, I.A.Topol, R.E.Cachau, and S.K.Burt (2005).
QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.
  Proteins, 60, 495-503.  
16052311 B.L.Grigorenko, A.V.Nemukhin, R.E.Cachau, I.A.Topol, and S.K.Burt (2005).
Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.
  J Mol Model, 11, 503-508.  
15884070 C.Kötting, and K.Gerwert (2005).
Proteins in action monitored by time-resolved FTIR spectroscopy.
  Chemphyschem, 6, 881-888.  
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.  
16118622 E.Gyan, M.Frew, D.Bowen, C.Beldjord, C.Preudhomme, C.Lacombe, P.Mayeux, F.Dreyfus, F.Porteu, and M.Fontenay (2005).
Mutation in RAP1 is a rare event in myelodysplastic syndromes.
  Leukemia, 19, 1678-1680.  
16117800 G.A.Khan, G.Bhattacharya, P.C.Mailander, J.L.Meza, L.A.Hansen, and D.Chakravarti (2005).
Harvey-ras gene expression and epidermal cell proliferation in dibenzo[a,l]pyrene-treated early preneoplastic SENCAR mouse skin.
  J Invest Dermatol, 125, 567-574.  
16288287 K.Du, and P.N.Tsichlis (2005).
Regulation of the Akt kinase by interacting proteins.
  Oncogene, 24, 7401-7409.  
15843165 K.Giehl (2005).
Oncogenic Ras in tumour progression and metastasis.
  Biol Chem, 386, 193-205.  
16852982 M.Klähn, S.Braun-Sand, E.Rosta, and A.Warshel (2005).
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.
  J Phys Chem B, 109, 15645-15650.  
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.  
16051167 N.Mitin, K.L.Rossman, and C.J.Der (2005).
Signaling interplay in Ras superfamily function.
  Curr Biol, 15, R563-R574.  
16072036 P.I.Hanson, and S.W.Whiteheart (2005).
AAA+ proteins: have engine, will work.
  Nat Rev Mol Cell Biol, 6, 519-529.  
16356760 R.Blum, and Y.Kloog (2005).
Tailoring Ras-pathway--inhibitor combinations for cancer therapy.
  Drug Resist Updat, 8, 369-380.  
15726588 R.Mishra, S.K.Gara, S.Mishra, and B.Prakash (2005).
Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis.
  Proteins, 59, 332-338.  
15837192 S.Pasqualato, and J.Cherfils (2005).
Crystallographic evidence for substrate-assisted GTP hydrolysis by a small GTP binding protein.
  Structure, 13, 533-540.
PDB code: 1oix
16141317 T.F.Reubold, S.Eschenburg, A.Becker, M.Leonard, S.L.Schmid, R.B.Vallee, F.J.Kull, and D.J.Manstein (2005).
Crystal structure of the GTPase domain of rat dynamin 1.
  Proc Natl Acad Sci U S A, 102, 13093-13098.
PDB code: 2aka
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
15458651 A.Lammens, A.Schele, and K.P.Hopfner (2004).
Structural biochemistry of ATP-driven dimerization and DNA-stimulated activation of SMC ATPases.
  Curr Biol, 14, 1778-1782.
PDB codes: 1xew 1xex
14997535 A.Shurki, and A.Warshel (2004).
Why does the Ras switch "break" by oncogenic mutations?
  Proteins, 55, 1.  
15454080 D.Gai, R.Zhao, D.Li, C.V.Finkielstein, and X.S.Chen (2004).
Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen.
  Cell, 119, 47-60.
PDB codes: 1svl 1svm 1svo
15070725 D.J.Crampton, S.Guo, D.E.Johnson, and C.C.Richardson (2004).
The arginine finger of bacteriophage T7 gene 4 helicase: role in energy coupling.
  Proc Natl Acad Sci U S A, 101, 4373-4378.  
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.  
15583390 F.Bonneau, I.D'Angelo, S.Welti, G.Stier, J.Ylänne, and K.Scheffzek (2004).
Expression, purification and preliminary crystallographic characterization of a novel segment from the neurofibromatosis type 1 protein.
  Acta Crystallogr D Biol Crystallogr, 60, 2364-2367.  
15189163 F.S.Willard, R.J.Kimple, and D.P.Siderovski (2004).
Return of the GDI: the GoLoco motif in cell division.
  Annu Rev Biochem, 73, 925-951.  
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.  
14732924 H.Fensterer, K.Giehl, M.Buchholz, V.Ellenrieder, A.Buck, H.A.Kestler, G.Adler, P.Gierschik, and T.M.Gress (2004).
Expression profiling of the influence of RAS mutants on the TGFB1-induced phenotype of the pancreatic cancer cell line PANC-1.
  Genes Chromosomes Cancer, 39, 224-235.  
15263068 K.L.Norman, K.Hirasawa, A.D.Yang, M.A.Shields, and P.W.Lee (2004).
Reovirus oncolysis: the Ras/RalGEF/p38 pathway dictates host cell permissiveness to reovirus infection.
  Proc Natl Acad Sci U S A, 101, 11099-11104.  
15558053 M.A.Oliva, S.C.Cordell, and J.Löwe (2004).
Structural insights into FtsZ protofilament formation.
  Nat Struct Mol Biol, 11, 1243-1250.
PDB codes: 1w58 1w59 1w5a 1w5b 1w5e 1w5f
14648615 N.Gresh, and G.B.Shi (2004).
Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation.
  J Comput Chem, 25, 160-168.  
15141215 O.Daumke, M.Weyand, P.P.Chakrabarti, I.R.Vetter, and A.Wittinghofer (2004).
The GTPase-activating protein Rap1GAP uses a catalytic asparagine.
  Nature, 429, 197-201.
PDB code: 1srq
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
15210950 T.Hishida, Y.W.Han, S.Fujimoto, H.Iwasaki, and H.Shinagawa (2004).
Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer.
  Proc Natl Acad Sci U S A, 101, 9573-9577.  
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.  
15340059 Y.Li, K.Inoki, and K.L.Guan (2004).
Biochemical and functional characterizations of small GTPase Rheb and TSC2 GAP activity.
  Mol Cell Biol, 24, 7965-7975.  
12618308 A.Bernards (2003).
GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila.
  Biochim Biophys Acta, 1603, 47-82.  
14517228 C.Chaudhry, G.W.Farr, M.J.Todd, H.S.Rye, A.T.Brunger, P.D.Adams, A.L.Horwich, and P.B.Sigler (2003).
Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics.
  EMBO J, 22, 4877-4887.
PDB codes: 1pcq 1pf9
12640130 C.Xia, W.Ma, L.J.Stafford, C.Liu, L.Gong, J.F.Martin, and M.Liu (2003).
GGAPs, a new family of bifunctional GTP-binding and GTPase-activating proteins.
  Mol Cell Biol, 23, 2476-2488.  
12774115 D.Li, R.Zhao, W.Lilyestrom, D.Gai, R.Zhang, J.A.DeCaprio, E.Fanning, A.Jochimiak, G.Szakonyi, and X.S.Chen (2003).
Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.
  Nature, 423, 512-518.
PDB code: 1n25
12796721 E.Shohami, I.Yatsiv, A.Alexandrovich, R.Haklai, G.Elad-Sfadia, R.Grossman, A.Biegon, and Y.Kloog (2003).
The Ras inhibitor S-trans, trans-farnesylthiosalicylic acid exerts long-lasting neuroprotection in a mouse closed head injury model.
  J Cereb Blood Flow Metab, 23, 728-738.  
12842038 G.Buhrman, V.de Serrano, and C.Mattos (2003).
Organic solvents order the dynamic switch II in Ras crystals.
  Structure, 11, 747-751.
PDB codes: 1p2s 1p2t 1p2u 1p2v
12932732 G.R.Andersen, P.Nissen, and J.Nyborg (2003).
Elongation factors in protein biosynthesis.
  Trends Biochem Sci, 28, 434-441.  
12914699 H.Kettenberger, K.J.Armache, and P.Cramer (2003).
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
  Cell, 114, 347-357.
PDB code: 1pqv
12601689 H.Wu, and S.M.King (2003).
Backbone dynamics of dynein light chains.
  Cell Motil Cytoskeleton, 54, 267-273.  
12778136 M.Malumbres, and M.Barbacid (2003).
RAS oncogenes: the first 30 years.
  Nat Rev Cancer, 3, 459-465.  
12486265 R.A.Sperling, J.F.Bates, E.F.Chua, A.J.Cocchiarella, D.M.Rentz, B.R.Rosen, D.L.Schacter, and M.S.Albert (2003).
fMRI studies of associative encoding in young and elderly controls and mild Alzheimer's disease.
  J Neurol Neurosurg Psychiatry, 74, 44-50.  
14567920 S.Lee, M.E.Sowa, Y.H.Watanabe, P.B.Sigler, W.Chiu, M.Yoshida, and F.T.Tsai (2003).
The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state.
  Cell, 115, 229-240.
PDB code: 1qvr
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
12654246 T.Schwartz, and G.Blobel (2003).
Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor.
  Cell, 112, 793-803.
PDB code: 1nrj
12842041 W.K.Wang, V.Tereshko, P.Boccuni, D.MacGrogan, S.D.Nimer, and D.J.Patel (2003).
Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets.
  Structure, 11, 775-789.
PDB codes: 1oyx 1oz2 1oz3
12738886 Y.Feng, S.Yu, T.K.Lasell, A.P.Jadhav, E.Macia, P.Chardin, P.Melancon, M.Roth, T.Mitchison, and T.Kirchhausen (2003).
Exo1: a new chemical inhibitor of the exocytic pathway.
  Proc Natl Acad Sci U S A, 100, 6469-6474.  
12574122 Y.Ohba, K.Kurokawa, and M.Matsuda (2003).
Mechanism of the spatio-temporal regulation of Ras and Rap1.
  EMBO J, 22, 859-869.  
12044161 A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, and L.N.Johnson (2002).
Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.
  Biochemistry, 41, 7301-7311.
PDB code: 1gy3
11790850 A.G.Evdokimov, J.E.Tropea, K.M.Routzahn, and D.S.Waugh (2002).
Crystal structure of the Yersinia pestis GTPase activator YopE.
  Protein Sci, 11, 401-408.
PDB code: 1hy5
11844750 A.L.Davidson (2002).
Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters.
  J Bacteriol, 184, 1225-1233.  
11959500 D.Jeruzalmi, M.O'Donnell, and J.Kuriyan (2002).
Clamp loaders and sliding clamps.
  Curr Opin Struct Biol, 12, 217-224.  
12082117 D.L.Ippolito, P.A.Temkin, S.L.Rogalski, and C.Chavkin (2002).
N-terminal tyrosine residues within the potassium channel Kir3 modulate GTPase activity of Galphai.
  J Biol Chem, 277, 32692-32696.  
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.  
12202034 J.J.Zhu, Y.Qin, M.Zhao, L.Van Aelst, and R.Malinow (2002).
Ras and Rap control AMPA receptor trafficking during synaptic plasticity.
  Cell, 110, 443-455.  
12203529 J.Kuhlmann, A.Tebbe, M.Völkert, M.Wagner, K.Uwai, and H.Waldmann (2002).
Photoactivatable synthetic Ras proteins: "baits" for the identification of plasma-membrane-bound binding partners of Ras.
  Angew Chem Int Ed Engl, 41, 2546-2550.  
12389613 M.Schaich, and T.Illmer (2002).
Mdr1 gene expression and mutations in Ras proto-oncogenes in acute myeloid leukemia.
  Leuk Lymphoma, 43, 1345-1354.  
11863460 P.J.O'Brien, and D.Herschlag (2002).
Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.
  Biochemistry, 41, 3207-3225.  
11748202 R.Krall, J.Sun, K.J.Pederson, and J.T.Barbieri (2002).
In vivo rho GTPase-activating protein activity of Pseudomonas aeruginosa cytotoxin ExoS.
  Infect Immun, 70, 360-367.  
12080332 R.Zhao, E.J.Collins, R.B.Bourret, and R.E.Silversmith (2002).
Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ.
  Nat Struct Biol, 9, 570-575.
PDB code: 1kmi
11867708 S.Liu, R.A.Cerione, and J.Clardy (2002).
Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity.
  Proc Natl Acad Sci U S A, 99, 2743-2747.
PDB code: 1kv3
11295286 A.Walentinsson, and G.Levan (2001).
Ras gene mutations in 7,12-dimethylbenz[a]anthracene (DMBA)-induced rat sarcomas.
  Cancer Lett, 166, 47-53.  
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.  
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.  
11166556 I.Callebaut, J.de Gunzburg, B.Goud, and J.P.Mornon (2001).
RUN domains: a new family of domains involved in Ras-like GTPase signaling.
  Trends Biochem Sci, 26, 79-83.  
11171984 J.Chen, S.Sharma, F.A.Quiocho, and A.L.Davidson (2001).
Trapping the transition state of an ATP-binding cassette transporter: evidence for a concerted mechanism of maltose transport.
  Proc Natl Acad Sci U S A, 98, 1525-1530.  
11748613 K.C.Chang, and N.N.Chuang (2001).
GTPase stimulation in shrimp Ras(Q(61)K) with geranylgeranyl pyrophosphate but not mammalian GAP.
  J Exp Zool, 290, 642-651.  
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
11246021 M.Kosloff, and Z.Selinger (2001).
Substrate assisted catalysis -- application to G proteins.
  Trends Biochem Sci, 26, 161-166.  
11577743 M.Sakurai, H.Adachi, and K.Sutoh (2001).
Mutational analyses of Dictyostelium IQGAP-related protein GApa: possible interaction with small GTPases in cytokinesis.
  Biosci Biotechnol Biochem, 65, 1912-1916.  
11592394 M.Völkert, M.Wagner, C.Peters, and H.Waldmann (2001).
The chemical biology of Ras lipidation.
  Biol Chem, 382, 1133-1145.  
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.  
11828490 R.Gail, B.Costisella, M.R.Ahmadian, and A.Wittinghofer (2001).
Ras-mediated cleavage of a GTP analogue by a novel mechanism.
  Chembiochem, 2, 570-575.  
11301005 R.Puertollano, P.A.Randazzo, J.F.Presley, L.M.Hartnell, and J.S.Bonifacino (2001).
The GGAs promote ARF-dependent recruitment of clathrin to the TGN.
  Cell, 105, 93.  
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.  
11294623 X.Zhu, E.Kim, A.L.Boman, A.Hodel, W.Cieplak, and R.A.Kahn (2001).
ARF binds the C-terminal region of the Escherichia coli heat-labile toxin (LTA1) and competes for the binding of LTA2.
  Biochemistry, 40, 4560-4568.  
11013213 A.Rak, R.Fedorov, K.Alexandrov, S.Albert, R.S.Goody, D.Gallwitz, and A.J.Scheidig (2000).
Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins.
  EMBO J, 19, 5105-5113.
PDB code: 1fkm
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
11163217 C.E.Stebbins, and J.E.Galán (2000).
Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.
  Mol Cell, 6, 1449-1460.
PDB codes: 1g4u 1g4w
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
10880458 D.Mohr, W.Wintermeyer, and M.V.Rodnina (2000).
Arginines 29 and 59 of elongation factor G are important for GTP hydrolysis or translocation on the ribosome.
  EMBO J, 19, 3458-3464.  
10931345 D.S.Black, and J.B.Bliska (2000).
The RhoGAP activity of the Yersinia pseudotuberculosis cytotoxin YopE is required for antiphagocytic function and virulence.
  Mol Microbiol, 37, 515-527.  
10966476 E.M.Ross, and T.M.Wilkie (2000).
GTPase-activating proteins for heterotrimeric G proteins: regulators of G protein signaling (RGS) and RGS-like proteins.
  Annu Rev Biochem, 69, 795-827.  
10801496 G.Montoya, K.Kaat, R.Moll, G.Schäfer, and I.Sinning (2000).
The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex.
  Structure, 8, 515-525.
PDB codes: 1j8m 1j8y
10676813 H.Song, P.Mugnier, A.K.Das, H.M.Webb, D.R.Evans, M.F.Tuite, B.A.Hemmings, and D.Barford (2000).
The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis.
  Cell, 100, 311-321.
PDB code: 1dt9
11173079 J.S.Bertram (2000).
The molecular biology of cancer.
  Mol Aspects Med, 21, 167-223.  
10873854 K.Braig, R.I.Menz, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2000).
Structure of bovine mitochondrial F(1)-ATPase inhibited by Mg(2+) ADP and aluminium fluoride.
  Structure, 8, 567-573.
PDB codes: 1e1q 1e1r
10672031 M.Lener, I.R.Horn, A.Cardinale, S.Messina, U.B.Nielsen, S.M.Rybak, H.R.Hoogenboom, A.Cattaneo, and S.Biocca (2000).
Diverting a protein from its cellular location by intracellular antibodies. The case of p21Ras.
  Eur J Biochem, 267, 1196-1205.  
  10701366 M.R.Pincus, P.W.Brandt-Rauf, J.Michl, R.P.Carty, and F.K.Friedman (2000).
ras-p21-induced cell transformation: unique signal transduction pathways and implications for the design of new chemotherapeutic agents.
  Cancer Invest, 18, 39-50.  
10937867 M.Sprinzl, S.Brock, Y.Huang, P.Milovnik, M.Nanninga, M.Nesper-Brock, H.Rütthard, and K.Szkaradkiewicz (2000).
Regulation of GTPases in the bacterial translation machinery.
  Biol Chem, 381, 367-375.  
10937868 M.V.Rodnina, H.Stark, A.Savelsbergh, H.J.Wieden, D.Mohr, N.B.Matassova, F.Peske, T.Daviter, C.O.Gualerzi, and W.Wintermeyer (2000).
GTPases mechanisms and functions of translation factors on the ribosome.
  Biol Chem, 381, 377-387.  
10924155 S.Nadanaciva, J.Weber, and A.E.Senior (2000).
New probes of the F1-ATPase catalytic transition state reveal that two of the three catalytic sites can assume a transition state conformation simultaneously.
  Biochemistry, 39, 9583-9590.  
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.  
11006529 Y.Kloog, and A.D.Cox (2000).
RAS inhibitors: potential for cancer therapeutics.
  Mol Med Today, 6, 398-402.  
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
10370239 A.M.van der Bliek (1999).
Is dynamin a regular motor or a master regulator?
  Trends Cell Biol, 9, 253-254.  
10387017 B.A.Posner, S.Mukhopadhyay, J.J.Tesmer, A.G.Gilman, and E.M.Ross (1999).
Modulation of the affinity and selectivity of RGS protein interaction with G alpha subunits by a conserved asparagine/serine residue.
  Biochemistry, 38, 7773-7779.  
  10469432 B.Weiss, G.Bollag, and K.Shannon (1999).
Hyperactive Ras as a therapeutic target in neurofibromatosis type 1.
  Am J Med Genet, 89, 14-22.  
10555980 D.L.Graham, J.F.Eccleston, C.W.Chung, and P.N.Lowe (1999).
Magnesium fluoride-dependent binding of small G proteins to their GTPase-activating proteins.
  Biochemistry, 38, 14981-14987.  
9893994 D.L.Graham, J.F.Eccleston, and P.N.Lowe (1999).
The conserved arginine in rho-GTPase-activating protein is essential for efficient catalysis but not for complex formation with Rho.GDP and aluminum fluoride.
  Biochemistry, 38, 985-991.  
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.  
10449336 F.Wieland, and C.Harter (1999).
Mechanisms of vesicle formation: insights from the COP system.
  Curr Opin Cell Biol, 11, 440-446.  
10590312 G.Elad, A.Paz, R.Haklai, D.Marciano, A.Cox, and Y.Kloog (1999).
Targeting of K-Ras 4B by S-trans,trans-farnesyl thiosalicylic acid.
  Biochim Biophys Acta, 1452, 228-242.  
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
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.  
10102276 J.Goldberg (1999).
Structural and functional analysis of the ARF1-ARFGAP complex reveals a role for coatomer in GTP hydrolysis.
  Cell, 96, 893-902.  
10591105 J.Ménétrey, and J.Cherfils (1999).
Structure of the small G protein Rap2 in a non-catalytic complex with GTP.
  Proteins, 37, 465-473.
PDB code: 3rap
10320361 J.Wei, and T.S.Leyh (1999).
Isomerization couples chemistry in the ATP sulfurylase-GTPase system.
  Biochemistry, 38, 6311-6316.  
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
10535735 M.R.Sawaya, S.Guo, S.Tabor, C.C.Richardson, and T.Ellenberger (1999).
Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7.
  Cell, 99, 167-177.
PDB codes: 1cr0 1cr1 1cr2 1cr4
10523302 M.Versele, J.H.de Winde, and J.M.Thevelein (1999).
A novel regulator of G protein signalling in yeast, Rgs2, downregulates glucose-activation of the cAMP pathway through direct inhibition of Gpa2.
  EMBO J, 18, 5577-5591.  
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.  
10545982 P.J.Goulder, and B.D.Walker (1999).
The great escape - AIDS viruses and immune control.
  Nat Med, 5, 1233-1235.  
10232922 P.J.Sheffield, U.Derewenda, J.Taylor, T.J.Parsons, and Z.S.Derewenda (1999).
Expression, purification and crystallization of a BH domain from the GTPase regulatory protein associated with focal adhesion kinase.
  Acta Crystallogr D Biol Crystallogr, 55, 356-359.  
10394366 R.C.Hillig, L.Renault, I.R.Vetter, T.Drell, A.Wittinghofer, and J.Becker (1999).
The crystal structure of rna1p: a new fold for a GTPase-activating protein.
  Mol Cell, 3, 781-791.
PDB code: 1yrg
10194333 R.Russell, A.Wali Karzai, A.F.Mehl, and R.McMacken (1999).
DnaJ dramatically stimulates ATP hydrolysis by DnaK: insight into targeting of Hsp70 proteins to polypeptide substrates.
  Biochemistry, 38, 4165-4176.  
10508155 S.Albert, E.Will, and D.Gallwitz (1999).
Identification of the catalytic domains and their functionally critical arginine residues of two yeast GTPase-activating proteins specific for Ypt/Rab transport GTPases.
  EMBO J, 18, 5216-5225.  
10200157 S.J.Admiraal, B.Schneider, P.Meyer, J.Janin, M.Véron, D.Deville-Bonne, and D.Herschlag (1999).
Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
  Biochemistry, 38, 4701-4711.
PDB code: 1b4s
10583404 S.Müller, C.von Eichel-Streiber, and M.Moos (1999).
Impact of amino acids 22-27 of Rho-subfamily GTPases on glucosylation by the large clostridial cytotoxins TcsL-1522, TcdB-1470 and TcdB-8864.
  Eur J Biochem, 266, 1073-1080.  
10387006 S.Nadanaciva, J.Weber, and A.E.Senior (1999).
The role of beta-Arg-182, an essential catalytic site residue in Escherichia coli F1-ATPase.
  Biochemistry, 38, 7670-7677.  
10569931 S.Nadanaciva, J.Weber, S.Wilke-Mounts, and A.E.Senior (1999).
Importance of F1-ATPase residue alpha-Arg-376 for catalytic transition state stabilization.
  Biochemistry, 38, 15493-15499.  
10361307 T.S.Vincent, J.E.Fraylick, E.M.McGuffie, and J.C.Olson (1999).
ADP-ribosylation of oncogenic Ras proteins by pseudomonas aeruginosa exoenzyme S in vivo.
  Mol Microbiol, 32, 1054-1064.  
10462759 V.Benard, G.M.Bokoch, and B.A.Diebold (1999).
Potential drug targets: small GTPases that regulate leukocyte function.
  Trends Pharmacol Sci, 20, 365-370.  
10601011 V.Mandiyan, J.Andreev, J.Schlessinger, and S.R.Hubbard (1999).
Crystal structure of the ARF-GAP domain and ankyrin repeats of PYK2-associated protein beta.
  EMBO J, 18, 6890-6898.
PDB code: 1dcq
10074926 Y.Egozi, B.Weisz, M.Gana-Weisz, G.Ben-Baruch, and Y.Kloog (1999).
Growth inhibition of ras-dependent tumors in nude mice by a potent ras-dislodging antagonist.
  Int J Cancer, 80, 911-918.  
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.  
9826650 A.Lavie, N.Ostermann, R.Brundiers, R.S.Goody, J.Reinstein, M.Konrad, and I.Schlichting (1998).
Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
  Proc Natl Acad Sci U S A, 95, 14045-14050.
PDB codes: 4tmk 5tmp
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9521762 B.E.Bernstein, and W.G.Hol (1998).
Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism.
  Biochemistry, 37, 4429-4436.  
9548756 B.Zhang, and Y.Zheng (1998).
Regulation of RhoA GTP hydrolysis by the GTPase-activating proteins p190, p50RhoGAP, Bcr, and 3BP-1.
  Biochemistry, 37, 5249-5257.  
  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.  
9605973 C.Lu, J.Stricker, and H.P.Erickson (1998).
FtsZ from Escherichia coli, Azotobacter vinelandii, and Thermotoga maritima--quantitation, GTP hydrolysis, and assembly.
  Cell Motil Cytoskeleton, 40, 71-86.  
9646865 D.Barford, A.K.Das, and M.P.Egloff (1998).
The structure and mechanism of protein phosphatases: insights into catalysis and regulation.
  Annu Rev Biophys Biomol Struct, 27, 133-164.  
  9683493 D.Trusca, S.Scott, C.Thompson, and D.Bramhill (1998).
Bacterial SOS checkpoint protein SulA inhibits polymerization of purified FtsZ cell division protein.
  J Bacteriol, 180, 3946-3953.  
9546212 E.F.Pai (1998).
The alpha and beta of turning on a molecular switch.
  Nat Struct Biol, 5, 259-263.  
9476900 E.Mossessova, J.M.Gulbis, and J.Goldberg (1998).
Structure of the guanine nucleotide exchange factor Sec7 domain of human arno and analysis of the interaction with ARF GTPase.
  Cell, 92, 415-423.  
9628483 E.Nogales, K.H.Downing, L.A.Amos, and J.Löwe (1998).
Tubulin and FtsZ form a distinct family of GTPases.
  Nat Struct Biol, 5, 451-458.  
  9865950 H.Käck, J.Sandmark, K.J.Gibson, G.Schneider, and Y.Lindqvist (1998).
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
  Protein Sci, 7, 2560-2566.
PDB codes: 1bs1 1dam
9790530 J.Goldberg (1998).
Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching.
  Cell, 95, 237-248.  
  9710582 J.H.Chang, J.C.Pratt, S.Sawasdikosol, R.Kapeller, and S.J.Burakoff (1998).
The small GTP-binding protein Rho potentiates AP-1 transcription in T cells.
  Mol Cell Biol, 18, 4986-4993.  
9581761 J.H.Kim, D.Liao, L.F.Lau, and R.L.Huganir (1998).
SynGAP: a synaptic RasGAP that associates with the PSD-95/SAP90 protein family.
  Neuron, 20, 683-691.  
9562564 J.J.Dumas, and D.G.Lambright (1998).
Gs alpha meets its target--shedding light on a key signal transduction event.
  Structure, 6, 407-411.  
9843482 J.L.Bos (1998).
All in the family? New insights and questions regarding interconnectivity of Ras, Rap1 and Ral.
  EMBO J, 17, 6776-6782.  
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.  
9648208 K.Ajtai, F.Dai, S.Park, C.R.Zayas, Y.M.Peyser, A.Muhlrad, and T.P.Burghardt (1998).
Near UV circular dichroism from biomimetic model compounds define the coordination geometry of vanadate centers in MeVi- and MeADPVi-rabbit myosin subfragment 1 complexes in solution.
  Biophys Chem, 71, 205-220.  
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
9817843 M.D.Feese, H.R.Faber, C.E.Bystrom, D.W.Pettigrew, and S.J.Remington (1998).
Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation.
  Structure, 6, 1407-1418.
PDB codes: 1bu6 1glf
9846874 N.Nassar, G.R.Hoffman, D.Manor, J.C.Clardy, and R.A.Cerione (1998).
Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP.
  Nat Struct Biol, 5, 1047-1052.
PDB codes: 1grn 2ngr
9653114 S.F.Betz, A.Schnuchel, H.Wang, E.T.Olejniczak, R.P.Meadows, B.P.Lipsky, E.A.Harris, D.E.Staunton, and S.W.Fesik (1998).
Solution structure of the cytohesin-1 (B2-1) Sec7 domain and its interaction with the GTPase ADP ribosylation factor 1.
  Proc Natl Acad Sci U S A, 95, 7909-7914.
PDB code: 1bc9
9631293 S.J.Gamblin, and S.J.Smerdon (1998).
GTPase-activating proteins and their complexes.
  Curr Opin Struct Biol, 8, 195-201.  
  9763446 S.Jones, C.J.Richardson, R.J.Litt, and N.Segev (1998).
Identification of regulators for Ypt1 GTPase nucleotide cycling.
  Mol Biol Cell, 9, 2819-2837.  
9482864 S.Vincent, M.Brouns, M.J.Hart, and J.Settleman (1998).
Evidence for distinct mechanisms of transition state stabilization of GTPases by fluoride.
  Proc Natl Acad Sci U S A, 95, 2210-2215.  
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.  
9790533 X.Liu, H.Wang, M.Eberstadt, A.Schnuchel, E.T.Olejniczak, R.P.Meadows, J.M.Schkeryantz, D.A.Janowick, J.E.Harlan, E.A.Harris, D.E.Staunton, and S.W.Fesik (1998).
NMR structure and mutagenesis of the N-terminal Dbl homology domain of the nucleotide exchange factor Trio.
  Cell, 95, 269-277.  
  9614177 Y.Zhu, L.M.Traub, and S.Kornfeld (1998).
ADP-ribosylation factor 1 transiently activates high-affinity adaptor protein complex AP-1 binding sites on Golgi membranes.
  Mol Biol Cell, 9, 1323-1337.  
9382787 A.Wittinghofer (1997).
Signaling mechanistics: aluminum fluoride for molecule of the year.
  Curr Biol, 7, R682-R685.  
  9348333 E.M.Hogan, B.A.Davis, and W.F.Boron (1997).
Intracellular Cl- dependence of Na-H exchange in barnacle muscle fibers under normotonic and hypertonic conditions.
  J Gen Physiol, 110, 629-639.  
9302988 J.P.Noel (1997).
Turning off the Ras switch with the flick of a finger.
  Nat Struct Biol, 4, 677-680.  
9371764 K.M.Druey, and J.H.Kehrl (1997).
Inhibition of regulator of G protein signaling function by two mutant RGS4 proteins.
  Proc Natl Acad Sci U S A, 94, 12851-12856.  
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.  
9302992 M.R.Ahmadian, P.Stege, K.Scheffzek, and A.Wittinghofer (1997).
Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras.
  Nat Struct Biol, 4, 686-689.  
9434906 S.R.Sprang (1997).
G proteins, effectors and GAPs: structure and mechanism.
  Curr Opin Struct Biol, 7, 849-856.  
9391039 Y.Liu, A.E.Ruoho, V.D.Rao, and J.H.Hurley (1997).
Catalytic mechanism of the adenylyl and guanylyl cyclases: modeling and mutational analysis.
  Proc Natl Acad Sci U S A, 94, 13414-13419.
PDB codes: 1awk 1awl 1awm 1awn
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.

 

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