› 5v72

X-ray diffraction
2.1Å resolution

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with citrate

Released:
DOI: 10.2210/pdb5v72/pdb
PDB entry 5v72 coloured by chain, front view.
PDB entry 5v72 coloured by chain, side view.
PDB entry 5v72 coloured by chain, top view.
Source organism: Sinorhizobium meliloti 1021
Primary publication:
Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W
Biochemistry 57 963-977 (2018)
PMID: 29309127

Function and Biology Details

Reaction catalysed: 
D-glycerate + NAD(P)(+) = hydroxypyruvate + NAD(P)H
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187880 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-hydroxyacid dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 322 amino acids
Theoretical weight: 34.27 KDa
Source organism: Sinorhizobium meliloti 1021
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92LZ4 (Residues: 1-322; Coverage: 100%)
Gene name: SMc04462
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

4 bound ligands:
Ligand NA 5 x NA
Ligand CL 4 x CL
Ligand GOL 1 x GOL
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 63.188Å b: 157.926Å c: 64.719Å
α: 90° β: 110.74° γ: 90°
R-values:
R R work R free
0.166 0.164 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 citation in other articles

Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.
Shabalin et al. (2018)
8 more

1 mention without citation

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Kutner et al. (2018)