› 4weq

X-ray diffraction
2Å resolution

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADP and sulfate

Released:
DOI: 10.2210/pdb4weq/pdb
PDB entry 4weq coloured by chain, front view.
PDB entry 4weq coloured by chain, side view.
PDB entry 4weq 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: 
Glycolate + NADP(+) = glyoxylate + NADPH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187928 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 37.26 KDa
Source organism: Sinorhizobium meliloti 1021
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92T34 (Residues: 1-319; Coverage: 100%)
Gene name: SMc02828
Sequence domains: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
4 bound ligands:
Ligand SO4 3 x SO4
Ligand PEG 1 x PEG
Ligand GOL 1 x GOL
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3221
Unit cell:
a: 108.153Å b: 108.153Å c: 80.657Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.156 0.154 0.196
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

2 mentions without citation

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir et al. (2018)
1 more