1GIT | pdb_00001git

STRUCTURE OF GTP-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.279 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1GIT

This is version 1.4 of the entry. See complete history

Literature

Structure of the GDP-Pi complex of Gly203-->Ala gialpha1: a mimic of the ternary product complex of galpha-catalyzed GTP hydrolysis.

Berghuis, A.M.Lee, E.Raw, A.S.Gilman, A.G.Sprang, S.R.

(1996) Structure 4: 1277-1290

  • DOI: https://doi.org/10.1016/s0969-2126(96)00136-0
  • Primary Citation Related Structures: 
    1GIT

  • PubMed Abstract: 

    G proteins play a vital role in transmembrane signalling events. In their inactive form G proteins exist as heterotrimers consisting of an alpha subunit, complexed with GDP and a dimer of betagamma subunits. Upon stimulation by receptors, G protein alpha subunits exchange GDP for GTP and dissociate from betagamma . Thus activated, alphasubunits stimulate or inhibit downstream effectors. The duration of the activated state corresponds to the single turnover rate of GTP hydrolysis, which is typically in the range of seconds. In Gialpha1, the Gly203-->Ala mutation reduces the affinity of the substrate for Mg2+, inhibits a key conformational step that occurs upon GTP binding and consequently inhibits the release of betagamma subunits from the GTP complex. The structure of the Gly203-->Ala mutant of Gialpha1 (G203AGialpha1) bound to the slowly hydrolyzing analog of GTP (GTPgammaS) has been determined in order to elucidate the structural changes that take place during hydrolysis. We have determined the three dimensional structure of a Gly203-->Ala mutant of Gialpha1 at 2.6 A resolution. Although crystals were grown in the presence of GTPgammaS and Mg2+, the catalytic site contains a molecule of GDP and a phosphate ion, but no Mg2+. The phosphate ion is bound to a site near that occupied by the gamma-phosphate of GTPgammaS in the activated wild-type alpha subunit. A region of the protein, termed the Switch II helix, twists and bends to adopt a conformation that is radically different from that observed in other Gialpha1 subunit complexes. Under the conditions of crystallization, the Gly203-->Ala mutation appears to stabilize a conformation that may be similar, although perhaps not identical, to the transient ternary product complex of Gialpha1-catalyzed GTP hydrolysis. The rearrangement of the Switch II helix avoids a potential steric conflict caused by the mutation. However, it appears that dissociation of the gamma-phosphate from the pentacoordinate intermediate also requires a conformational change in Switch II. Thus, a conformational rearrangement of the Switch II helix may be required in Galpha-catalyzed GTP hydrolysis.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75235-9050, USA. sprang@howie.swmed.edu

Macromolecule Content 

  • Total Structure Weight: 40.82 kDa 
  • Atom Count: 2,594 
  • Modeled Residue Count: 317 
  • Deposited Residue Count: 353 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G PROTEIN GI ALPHA 1353Rattus norvegicusMutation(s): 1 
EC: 3.6.5
UniProt
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10824
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.279 (Depositor) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.1α = 90
b = 77.1β = 90
c = 144.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-02-07
    Changes: Data collection