Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.37 kDa 
• Atom Count: 1464 
• Modelled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

2QUZ

Crystal Structure of the activating H-RasK117R mutant in Costello Syndrome, bound to Mg-GDP

• PDB DOI: 10.2210/pdb2QUZ/pdb

• Classification: SIGNALING PROTEIN, HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-08-07 Released: 2007-12-11 
• Deposition Author(s): Parret, A., Scheffzek, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.222 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Literature

Mutation analysis in Costello syndrome: functional and structural characterization of the HRAS p.Lys117Arg mutation.

Denayer, E., Parret, A., Chmara, M., Schubbert, S., Vogels, A., Devriendt, K., Frijns, J.P., Rybin, V., de Ravel, T.J., Shannon, K., Cools, J., Scheffzek, K., Legius, E.

(2008) Hum Mutat 29: 232-239

• PubMed: 17979197 
• DOI: 10.1002/humu.20616
• Primary Citation of Related Structures:  
  2QUZ


• PubMed Abstract: 
  

Costello syndrome is a mental retardation syndrome characterized by high birth weight, postnatal growth retardation, coarse face, loose skin, cardiovascular problems, and tumor predisposition. De novo heterozygous missense mutations in HRAS codon 12 and 13 disturbing the intrinsic GTP hydrolysis cause Costello syndrome. We report a patient with typical Costello syndrome and a novel heterozygous missense mutation in codon 117 (c.350A>G, p.Lys117Arg) of the HRAS gene, resulting in constitutive activation of the RAS/MAPK pathway similar to the typical p.Gly12Ser and p.Gly12Ala mutations. Recombinant HRAS p.Lys117Arg demonstrates normal intrinsic GTP hydrolysis and responsiveness to GTPase-activating proteins, but the nucleotide dissociation rate is increased 80-fold. Consistent with the biochemical data, the crystal structure of the p.Lys117Arg mutant indicates an altered interaction pattern of the side chain that is associated with unfavorable nucleotide binding properties. Together, these data show that a RAS mutation that only perturbs guanine nucleotide binding has similar functional consequences as mutations that impair GTP hydrolysis and causes human disease.

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Organizational Affiliation: 

Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	166	Homo sapiens	Mutation(s): 1  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.222 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.1	α = 90
b = 92.1	β = 90
c = 116.3	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-07 
• Released Date: 2007-12-11 
Deposition Author(s): Parret, A., Scheffzek, K.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations