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PDBsum entry 1lf0

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protein ligands metals links
Signaling protein PDB id
1lf0
Jmol
Contents
Protein chain
166 a.a. *
Ligands
GNP
Metals
_MG
_CA ×2
Waters ×118
* Residue conservation analysis
PDB id:
1lf0
Name: Signaling protein
Title: Crystal structure of rasa59g in the gtp-bound form
Structure: Transforming protein p21/h-ras-1. Chain: a. Fragment: residues 1-166. Synonym: c-h-ras. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.185     R-free:   0.208
Authors: B.E.Hall,D.Bar-Sagi,N.Nassar
Key ref:
B.E.Hall et al. (2002). The structural basis for the transition from Ras-GTP to Ras-GDP. Proc Natl Acad Sci U S A, 99, 12138-12142. PubMed id: 12213964 DOI: 10.1073/pnas.192453199
Date:
10-Apr-02     Release date:   06-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
166 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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: 10.1073/pnas.192453199 Proc Natl Acad Sci U S A 99:12138-12142 (2002)
PubMed id: 12213964  
 
 
The structural basis for the transition from Ras-GTP to Ras-GDP.
B.E.Hall, D.Bar-Sagi, N.Nassar.
 
  ABSTRACT  
 
The conformational changes in Ras that accompany the hydrolysis of GTP are critical to its function as a molecular switch in signaling pathways. Understanding how GTP is hydrolyzed by revealing the sequence of intermediary structures in the reaction is essential for understanding Ras signaling. Until now, no structure of an intermediate in GTP hydrolysis has been experimentally determined for Ras alone. We have solved the crystal structure of the Ala-59 to Gly mutant of Ras, (RasA59G), bound to guanosine 5'-imidotriphosphate or GDP to 1.7-A resolution. In the guanosine 5'-imidotriphosphate-bound form, this mutant adopts a conformation that is intermediate between the GTP- and GDP-bound forms of wild-type Ras and that is similar to what has been predicted by molecular dynamics simulation [Ma, J. P. & Karplus, M. (1997) Proc. Natl. Acad. Sci. USA 94, 11905-11910]. This conformation is stabilized by direct and water-mediated interactions between the switch 1 and switch 2 regions and is characterized by an increase in the binding affinity for GTP. We propose that the structural changes promoted by the Ala-59 to Gly mutation exhibit a discrete conformational state assumed by wild-type Ras during GTP hydrolysis.
 
  Selected figure(s)  
 
Figure 1.
Fig 1. Structural changes induced in Ras switch regions by the glycine for alanine substitution at position 59. Close-up view of Glu-37 (switch 1) and Arg-68 (switch 2) in the crystal structures of wild-type Ras (A) (15) and RasA59G (B) in the GppNp-bound forms. Switch 1 (SwI) and switch 2 (SwII) are in magenta and yellow, respectively. Loop L4 and helix- 2 of switch 2 are labeled. The GppNp and the Mg2+-ion are in light blue, and water molecules (W) are represented by red spheres. Tyr-32 is in pink, Glu-37 in red, and Arg-68 in blue. Hydrogen bonds are represented by dashed lines and the van der Waals interactions between Glu-37 and Tyr-71 (B) are indicated by a dotted line. In wild-type Ras (A), Arg-68 stabilizes the N terminus of the switch 2 region (60-62) through direct or water-mediated hydrogen bonds. In RasA59G (B), Glu-37 makes hydrogen bonds with Arg-68 and van der Waals interactions with Tyr-71, which protects it partially from the solvent. Tyr-64, which is essential for Sos-binding by Ras, adopts a position that inhibits the docking of the two proteins. The catalytic residue Gln-61 is positioned far from W175. Tyr-32 is making a water-mediated hydrogen bond with the -phosphate, and its bulky phenol group is protecting the phosphates from the surrounding solvent. (C) Stereo representation of the superposition of the C of switch 1 and 2 regions between the structures of wild-type Ras (green) and RasA59G (gold) in the GppNp-bound form. The residues of L4 are shown, whereas only the side chains of Tyr-32, Glu-37, Gln-61, Arg-68, and Tyr-71 are shown. The two water molecules (W332 and W349) in wild-type Ras that coordinated Arg-68 and that have been exchanged with the solvent on the reorientation of the switch 2 region, are shown. Prepared with MOLSCRIPT (24) and RASTER3D (25).
Figure 2.
Fig 2. Structural changes that affect the switch 1 and switch 2 regions of Ras along the path for GTP hydrolysis. Structures proceed from the GTP-bound form (Left, PDB coordinates 5P21 [PDB] ), to the intermediate (Center) that is represented by the A59G mutant, and finally to the GDP-bound form (Right, PDB coordinates 4Q21). Water molecules are shown as red spheres; the nucleotide and the Mg2+-ion are in light blue. Switch 1 is in magenta and switch 2 in gold. Close contacts are represented by dotted lines.
 
  Figures were selected by an automated process.  

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.  
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
  20838576 S.Lukman, B.J.Grant, A.A.Gorfe, G.H.Grant, and J.A.McCammon (2010).
The distinct conformational dynamics of K-Ras and H-Ras A59G.
  PLoS Comput Biol, 6, 0.  
20090772 W.A.Andrade, A.M.Silva, V.S.Alves, A.P.Salgado, M.B.Melo, H.M.Andrade, F.V.Dall'Orto, S.A.Garcia, T.N.Silveira, and R.T.Gazzinelli (2010).
Early endosome localization and activity of RasGEF1b, a toll-like receptor-inducible Ras guanine-nucleotide exchange factor.
  Genes Immun, 11, 447-457.  
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.  
17680690 D.A.Kondrashov, W.Zhang, R.Aranda, B.Stec, and G.N.Phillips (2008).
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.
  Proteins, 70, 353-362.
PDB codes: 1jw8 1u7r 1u7s
17189426 B.S.Shin, M.G.Acker, D.Maag, J.R.Kim, J.R.Lorsch, and T.E.Dever (2007).
Intragenic suppressor mutations restore GTPase and translation functions of a eukaryotic initiation factor 5B switch II mutant.
  Mol Cell Biol, 27, 1677-1685.  
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
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
16720586 M.Bodén, and T.L.Bailey (2006).
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.
  Bioinformatics, 22, 1809-1814.  
17084704 S.Boykevisch, C.Zhao, H.Sondermann, P.Philippidou, S.Halegoua, J.Kuriyan, and D.Bar-Sagi (2006).
Regulation of ras signaling dynamics by Sos-mediated positive feedback.
  Curr Biol, 16, 2173-2179.  
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.  
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.