› 2pkp

X-ray diffraction
2.1Å resolution

Crystal structure of 3-isopropylmalate dehydratase (leuD)from Methhanocaldococcus Jannaschii DSM2661 (MJ1271)

Released:
DOI: 10.2210/pdb2pkp/pdb
PDB entry 2pkp coloured by chain, front view.
PDB entry 2pkp coloured by chain, side view.
PDB entry 2pkp coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii DSM 2661
Primary publication:
Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit.
Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE
Biochemistry 49 2687-96 (2010)
PMID: 20170198

Function and Biology Details

Reaction catalysed: 
(1a) (R)-2-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176674 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methanogen homoaconitase small subunit Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 18.69 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58667 (Residues: 1-170; Coverage: 100%)
Gene names: MJ1271, hacB
Sequence domains: Aconitase C-terminal domain
Structure domains: Aconitase, domain 4

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2221
Unit cell:
a: 90.992Å b: 108.283Å c: 45.449Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.201 0.248
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Convergent strategies in biosynthesis.
Dairi et al. (2011)
1 more

1 mention without citation

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis.
Karuppasamy et al. (2009)