› 1ydn

X-ray diffraction
2.3Å resolution

Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural Genomics Target LR35.

Released:
DOI: 10.2210/pdb1ydn/pdb
PDB entry 1ydn coloured by chain, front view.
PDB entry 1ydn coloured by chain, side view.
PDB entry 1ydn coloured by chain, top view.
Source organism: Brucella melitensis bv. 1 str. 16M
Primary publication:
Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds.
Forouhar F, Hussain M, Farid R, Benach J, Abashidze M, Edstrom WC, Vorobiev SM, Xiao R, Acton TB, Fu Z, Kim JJ, Miziorko HM, Montelione GT, Hunt JF
J Biol Chem 281 7533-45 (2006)
PMID: 16330546

Function and Biology Details

Reaction catalysed: 
(S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187044 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hydroxymethylglutaryl-CoA lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 295 amino acids
Theoretical weight: 31.64 KDa
Source organism: Brucella melitensis bv. 1 str. 16M
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8YEF2 (Residues: 1-287; Coverage: 100%)
Gene name: BMEI1926
Sequence domains: HMGL-like
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand CA 4 x CA
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P21
Unit cell:
a: 82.272Å b: 86.399Å c: 87.683Å
α: 90° β: 118.7° γ: 90°
R-values:
R R work R free
0.275 0.271 0.304
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity.
Lietzan et al. (2014)
1 more

1 mention without citation

An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism.
Wang et al. (2019)