6D4G | pdb_00006d4g

N-GTPase domain of p190RhoGAP-A

  • Classification: HYDROLASE
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-04-18 Released: 2018-09-12 
  • Deposition Author(s): Stiegler, A.L., Boggon, T.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.290 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The N-Terminal GTPase Domain of p190RhoGAP Proteins Is a PseudoGTPase.

Stiegler, A.L.Boggon, T.J.

(2018) Structure 26: 1451

  • DOI: https://doi.org/10.1016/j.str.2018.07.015
  • Primary Citation Related Structures: 
    6D4G

  • PubMed Abstract: 

    The pseudoGTPases are a rapidly growing and important group of pseudoenzymes. p190RhoGAP proteins are critical regulators of Rho signaling and contain two previously identified pseudoGTPase domains. Here we report that p190RhoGAP proteins contain a third pseudoGTPase domain, termed N-GTPase. We find that GTP constitutively purifies with the N-GTPase domain, and a 2.8-Å crystal structure of p190RhoGAP-A co-purified with GTP reveals an unusual GTP-Mg 2+ binding pocket. Six inserts in N-GTPase indicate perturbed catalytic activity and inability to bind to canonical GTPase activating proteins, guanine nucleotide exchange factors, and effector proteins. Biochemical analysis shows that N-GTPase does not detectably hydrolyze GTP, and exchanges nucleotide only under harsh Mg 2+ chelation. Furthermore, mutational analysis shows that GTP and Mg 2+ binding stabilizes the domain. Therefore, our results support that N-GTPase is a nucleotide binding, non-hydrolyzing, pseudoGTPase domain that may act as a protein-protein interaction domain. Thus, unique among known proteins, p190RhoGAPs contain three pseudoGTPase domains.


  • Organizational Affiliation
    • Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.

Macromolecule Content 

  • Total Structure Weight: 62.35 kDa 
  • Atom Count: 3,379 
  • Modeled Residue Count: 418 
  • Deposited Residue Count: 542 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rho GTPase-activating protein 35
A, B
271Rattus norvegicusMutation(s): 0 
Gene Names: Arhgap35Grlf1P190Ap190ARHOGAP
UniProt
Find proteins for P81128 (Rattus norvegicus)
Explore P81128 
Go to UniProtKB:  P81128
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81128
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.290 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.69α = 90
b = 69.27β = 90
c = 154.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM114621
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102262
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS085078

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description