5VPZ

Crystal structure of human KRAS G12A mutant in complex with GTP-gamma-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 

wwPDB Validation  3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.

Xu, S.Long, B.N.Boris, G.H.Chen, A.Ni, S.Kennedy, M.A.

(2017) Acta Crystallogr D Struct Biol 73: 970-984

  • DOI: 10.1107/S2059798317015418
  • Primary Citation of Related Structures:  5VP7, 5VPI, 5VPY, 5VQ0, 5VQ1, 5VQ2, 5VQ6, 5VQ8, 5W22

  • PubMed Abstract: 
  • K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated ...

    K-Ras, a molecular switch that regulates cell growth, apoptosis and metabolism, is activated when it undergoes a conformation change upon binding GTP and is deactivated following the hydrolysis of GTP to GDP. Hydrolysis of GTP in water is accelerated by coordination to K-Ras, where GTP adopts a high-energy conformation approaching the transition state. The G12A mutation reduces intrinsic K-Ras GTP hydrolysis by an unexplained mechanism. Here, crystal structures of G12A K-Ras in complex with GDP, GTP, GTPγS and GppNHp, and of Q61A K-Ras in complex with GDP, are reported. In the G12A K-Ras-GTP complex, the switch I region undergoes a significant reorganization such that the Tyr32 side chain points towards the GTP-binding pocket and forms a hydrogen bond to the GTP γ-phosphate, effectively stabilizing GTP in its precatalytic state, increasing the activation energy required to reach the transition state and contributing to the reduced intrinsic GTPase activity of G12A K-Ras mutants.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
GTPase KRas
A, B
170 Homo sapiens Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GSP
Query on GSP

Download SDF File 
Download CCD File 
A, B
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • Space Group: H 3
Unit Cell:
Length (Å) Angle (°)
a = 94.937 α = 90.00
b = 94.937 β = 90.00
c = 121.016 γ = 120.00
Software Package:
Software Name Purpose
PDB_EXTRACT data extraction
SCALA data scaling
REFMAC refinement
PHASER phasing
iMOSFLM data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references