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PDBsum entry 3lo5

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protein ligands metals Protein-protein interface(s) links
Oncoprotein PDB id
3lo5
Jmol
Contents
Protein chains
144 a.a. *
155 a.a. *
151 a.a. *
Ligands
GDP ×3
SO4
Metals
_CA ×4
Waters ×66
* Residue conservation analysis
PDB id:
3lo5
Name: Oncoprotein
Title: Crystal structure of the dominant negative s17n mutant of ras
Structure: Gtpase hras. Chain: a, c, e. Fragment: h-ras (unp residues 1-166). Synonym: transforming protein p21, p21ras, h-ras-1, c-h- ras, ha-ras, gtpase hras, n-terminally processed. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: h-ras, hras, hras1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.57Å     R-factor:   0.241     R-free:   0.296
Authors: N.Nassar,K.Singh,M.Garcia-Diaz
Key ref: N.Nassar et al. (2010). Structure of the dominant negative S17N mutant of Ras. Biochemistry, 49, 1970-1974. PubMed id: 20131908
Date:
03-Feb-10     Release date:   02-Mar-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
144 a.a.*
Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
155 a.a.*
Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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

 

 
Biochemistry 49:1970-1974 (2010)
PubMed id: 20131908  
 
 
Structure of the dominant negative S17N mutant of Ras.
N.Nassar, K.Singh, M.Garcia-Diaz.
 
  ABSTRACT  
 
The use of the dominant negative mutant of Ras has been crucial in elucidating the cellular signaling of Ras in response to the activation of various membrane-bound receptors. Although several point mutants of Ras exhibit a dominant negative effect, the asparagine to serine mutation at position 17 (S17N) remains the most popular and the most effective at inhibiting the activation of endogenous Ras. It is now widely accepted that the dominant negative effect is due to the ability of the mutant to sequester upstream activators and its inability to activate downstream effectors. Here, we present the crystal structure of RasS17N in the GDP-bound form. In the three molecules that populate the asymmetric unit, the Mg(2+) ion that normally coordinates the beta-phosphate is absent because of steric hindrance from the Asn17 side chain. Instead, a Ca(2+) ion is coordinating the alpha-phosphate. Also absent from one molecule is electron density for Phe28, a conserved residue that normally stabilizes the nucleotide's guanine base. Except for Phe28, the nucleotide makes conserved interactions with Ras. Combined, the inability of Phe28 to stabilize the guanine base and the absence of a Mg(2+) ion to neutralize the negative charges on the phosphates explain the weaker affinity of GDP for Ras. Our data suggest that the absence of the Mg(2+) should also dramatically affect GTP binding to Ras and the proper positioning of Thr35 necessary for the activation of switch 1 and the binding to downstream effectors, a prerequisite for the triggering of signaling pathways.