› 3vmk

X-ray diffraction
1.48Å resolution

3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2

Released:
DOI: 10.2210/pdb3vmk/pdb
PDB entry 3vmk coloured by chain, front view.
PDB entry 3vmk coloured by chain, side view.
PDB entry 3vmk coloured by chain, top view.
Source organism: Shewanella benthica
Primary publication:
Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1.
Nagae T, Kato C, Watanabe N
Acta Crystallogr Sect F Struct Biol Cryst Commun 68 265-8 (2012)
PMID: 22442218

Function and Biology Details

Reaction catalysed: 
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112455 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-isopropylmalate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 375 amino acids
Theoretical weight: 40.68 KDa
Source organism: Shewanella benthica
Expression system: Escherichia coli
UniProt:
  • Canonical: D2YZL2 (Residues: 2-364; Coverage: 100%)
Gene names: SHEWBE_0188, leuB
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand IPM 2 x IPM
Ligand MG 2 x MG
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 51.972Å b: 59.208Å c: 119.779Å
α: 90° β: 95.12° γ: 90°
R-values:
R R work R free
0.195 0.193 0.232
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes.
Jebbar et al. (2015)
6 more

2 mentions without citation

Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1.
Nagae et al. (2012)
1 more