PDBsum entry 1zvq

Go to PDB code: 
protein ligands metals links
Oncoprotein PDB id
Protein chain
166 a.a. *
_MG ×2
Waters ×79
* Residue conservation analysis
PDB id:
Name: Oncoprotein
Title: Structure of the q61g mutant of ras in the gdp-bound form
Structure: Transforming protein p21/h-ras-1. Chain: a. Synonym: c-h-ras. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hras, hras1. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.188     R-free:   0.229
Authors: B.Ford,N.Nassar
Key ref:
B.Ford et al. (2006). Structure of a transient intermediate for GTP hydrolysis by ras. Structure, 14, 427-436. PubMed id: 16531227 DOI: 10.1016/j.str.2005.12.010
02-Jun-05     Release date:   14-Mar-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
189 a.a.
166 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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


DOI no: 10.1016/j.str.2005.12.010 Structure 14:427-436 (2006)
PubMed id: 16531227  
Structure of a transient intermediate for GTP hydrolysis by ras.
B.Ford, V.Hornak, H.Kleinman, N.Nassar.
The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals a new conformation of switch 2 that bears remarkable structural homology to an intermediate for GTP hydrolysis revealed by targeted molecular dynamics simulations. The mutation increased retention of GTP and inhibited Ras binding to the catalytic site, but not to the distal site of Sos. Most importantly, the thermodynamics of RafRBD binding to Ras are altered even though the structure of switch 1 is not affected by the mutation. Our results suggest that interplay and transmission of structural information between the switch regions are important factors for Ras function. They propose that initiation of GTP hydrolysis sets off the separation of the Ras/effector complex even before the GDP conformation is reached.
  Selected figure(s)  
Figure 2.
Figure 2. Comparison of the Switch Regions of RasQ61G with WT-Ras and RasA59G
(A) Superposition of the switch 1 (Sw 1) and switch 2 (Sw 2) regions of the GppNp bound forms of WT-Ras (yellow) (Pai et al., 1990) and RasQ61G (blue). The GppNp and Mg^2+ ions are in ball-and-stick representation in purple and green, respectively. The water molecule in WT-Ras responsible for the nucleophilic attack on the γ-phosphate (W175) is shown as a yellow sphere; the closest water molecule in the RasQ61G structure is shown as a blue sphere.
(B) Superposition of the switch regions of the GppNp bound forms of RasA59G (gold) (Hall et al., 2002) and RasQ61G (blue). Dotted lines represent hydrogen bonds. For simplicity, only a few residues in each region are shown.
This figure was prepared with Molscript (Kraulis, 1991) and Pymol (
Figure 6.
Figure 6. Evolution of the Switch Regions along the Path for GTP Hydrolysis
(A–D) Backbone atoms of both switch 1 (pink, residues 25–40) and switch 2 (yellow, residues 57–75) are shown along with key side chain residues for simplicity. The guanine nucleotide (GTP/GDP) and the Mg^2+ ion are shown in a ball-and-stick model. (A) The beginning of the path (Ras•GTP) (Pai et al., 1990). (B) Transient intermediate 1 (RasQ61G). (C) Transient intermediate 2 (RasA59G) (Hall et al., 2002). (D) The end of the path (Ras•GDP) (Milburn et al., 1990). Hydrogen bonds between switch regions and other key hydrogen bonds are denoted by dotted lines.
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 427-436) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20949621 L.Gremer, T.Merbitz-Zahradnik, R.Dvorsky, I.C.Cirstea, C.P.Kratz, M.Zenker, A.Wittinghofer, and M.R.Ahmadian (2011).
Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders.
  Hum Mutat, 32, 33-43.  
20018863 M.T.Mazhab-Jafari, C.B.Marshall, M.Smith, G.M.Gasmi-Seabrook, V.Stambolic, R.Rottapel, B.G.Neel, and M.Ikura (2010).
Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics.
  J Biol Chem, 285, 5132-5136.  
20131908 N.Nassar, K.Singh, and M.Garcia-Diaz (2010).
Structure of the dominant negative S17N mutant of Ras.
  Biochemistry, 49, 1970-1974.
PDB code: 3lo5
19300489 B.J.Grant, A.A.Gorfe, and J.A.McCammon (2009).
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.
  PLoS Comput Biol, 5, e1000325.  
19444816 B.R.Brooks, C.L.Brooks, A.D.Mackerell, L.Nilsson, R.J.Petrella, B.Roux, Y.Won, G.Archontis, C.Bartels, S.Boresch, A.Caflisch, L.Caves, Q.Cui, A.R.Dinner, M.Feig, S.Fischer, J.Gao, M.Hodoscek, W.Im, K.Kuczera, T.Lazaridis, J.Ma, V.Ovchinnikov, E.Paci, R.W.Pastor, C.B.Post, J.Z.Pu, M.Schaefer, B.Tidor, R.M.Venable, H.L.Woodcock, X.Wu, W.Yang, D.M.York, and M.Karplus (2009).
CHARMM: the biomolecular simulation program.
  J Comput Chem, 30, 1545-1614.  
18547521 A.A.Gorfe, B.J.Grant, and J.A.McCammon (2008).
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.
  Structure, 16, 885-896.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
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
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.