› 3d4j

X-ray diffraction
2.4Å resolution

Crystal structure of Human mevalonate diphosphate decarboxylase

Released:
DOI: 10.2210/pdb3d4j/pdb
PDB entry 3d4j coloured by chain, front view.
PDB entry 3d4j coloured by chain, side view.
PDB entry 3d4j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure.
Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM
Arch Biochem Biophys 480 58-67 (2008)
PMID: 18823933

Function and Biology Details

Reaction catalysed: 
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-547160 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphosphomevalonate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 400 amino acids
Theoretical weight: 43.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P53602 (Residues: 1-400; Coverage: 100%)
Gene names: MPD, MVD
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P21
Unit cell:
a: 86.96Å b: 53.19Å c: 97.79Å
α: 90° β: 107.25° γ: 90°
R-values:
R R work R free
0.218 0.218 0.274
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Enzymes of the mevalonate pathway of isoprenoid biosynthesis.
Miziorko HM. (2011)
2 more

5 mentions without citation

Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure.
Voynova et al. (2008)
4 more