› 6e2w

X-ray diffraction
1.95Å resolution

MDDEF in complex with MVAPP, ADP, sulfate and cobalt

Released:
DOI: 10.2210/pdb6e2w/pdb
PDB entry 6e2w coloured by chain, front view.
PDB entry 6e2w coloured by chain, side view.
PDB entry 6e2w coloured by chain, top view.
Source organism: Enterococcus faecalis
Primary publication:
Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.
Chen CL, Paul LN, Mermoud JC, Steussy CN, Stauffacher CV
OpenAccess logo Nat Commun 11 3969 (2020)
PMID: 32769976

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-190288 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
diphosphomevalonate decarboxylase Chain: A
Molecule details ›
Chain: A
Length: 355 amino acids
Theoretical weight: 39.28 KDa
Source organism: Enterococcus faecalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9FD68 (Residues: 1-331; Coverage: 100%)
Gene name: mvaD
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 1 x SO4
Ligand ADP 1 x ADP
Ligand DP6 1 x DP6
Ligand CO 2 x CO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21212
Unit cell:
a: 79.997Å b: 98.071Å c: 45.908Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.219
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Biochemistry of Terpenes and Recent Advances in Plant Protection.
Ninkuu et al. (2021)
7 other articles

1 mention without citation

Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.
Chen et al. (2020)