› 3cmc

X-ray diffraction
1.77Å resolution

Thioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH

Released:
DOI: 10.2210/pdb3cmc/pdb
PDB entry 3cmc coloured by chain, front view.
PDB entry 3cmc coloured by chain, side view.
PDB entry 3cmc coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Trapping of the thioacylglyceraldehyde-3-phosphate dehydrogenase intermediate from Bacillus stearothermophilus. Direct evidence for a flip-flop mechanism.
Moniot S, Bruno S, Vonrhein C, Didierjean C, Boschi-Muller S, Vas M, Bricogne G, Branlant G, Mozzarelli A, Corbier C
J Biol Chem 283 21693-702 (2008)
PMID: 18480053

Function and Biology Details

Reaction catalysed: 
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132434 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyceraldehyde-3-phosphate dehydrogenase Chains: O, P, Q, R
Molecule details ›
Chains: O, P, Q, R
Length: 334 amino acids
Theoretical weight: 35.99 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli HB101
UniProt:
  • Canonical: P00362 (Residues: 2-335; Coverage: 100%)
Gene name: gap
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
4 bound ligands:
Ligand SO4 18 x SO4
Ligand G3H 4 x G3H
Ligand GOL 8 x GOL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P21
Unit cell:
a: 81.67Å b: 122.63Å c: 81.79Å
α: 90° β: 111.12° γ: 90°
R-values:
R R work R free
0.163 0.161 0.198
Expression system: Escherichia coli HB101

Quick links

Citations

1 review citation

From protein structure to function via single crystal optical spectroscopy.
Ronda et al. (2015)
15 other articles

6 mentions without citation

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.
Smart et al. (2012)
5 more