1OBF

The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes xylosoxidans at 1.7A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of Glyceraldehyde 3-Phosphate Dehydrogenase from Alcaligenes Xylosoxidans at 1.7 A Resolution

Antonyuk, S.V.Eady, R.R.Strange, R.W.Hasnain, S.S.

(2003) Acta Crystallogr.,Sect.D 59: 835


  • PubMed Abstract: 
  • The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Gram-negative denitrifying bacterial species Alcaligenes xylosoxidans was purified and crystallized as a contaminant protein during purification of nitrous oxide reductase. This is ...

    The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Gram-negative denitrifying bacterial species Alcaligenes xylosoxidans was purified and crystallized as a contaminant protein during purification of nitrous oxide reductase. This is the first structure of a GAPDH from a denitrifying species. The crystal structure was solved at 1.7 A resolution by molecular replacement using the structure of GAPDH from Bacillus stearothermophilus as a starting model. The quality of the structure enabled the amino-acid sequence of the A. xylosoxidans GAPDH to be assigned. The structure is that of the apo-enzyme, lacking the NAD+ cofactor and with the active-site residue Cys154 oxidized. The global structure of the enzyme has a homotetrameric quaternary structure similar to that observed for its bacterial and eukaryotic counterparts. The essential role of Cys154 in the enzyme activity has been confirmed. In monomer O two half-occupancy sulfate ions were found at the active site, which are analogous to the substrate and the "attacking" phosphate seen in B. stearothermophilus. One half-occupancy sulfate ion is also located in the substrate-binding site of monomer P.


    Organizational Affiliation

    Molecular Biophysics Group, CCLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
O, P
335Alcaligenes xylosoxydans xylosoxydansMutation(s): 0 
EC: 1.2.1.-
Find proteins for P83696 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P83696
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
O, P
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
O, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
P
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
O, P
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 88.984α = 90.00
b = 146.622β = 90.00
c = 146.622γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-12
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance