› 4du8

X-ray diffraction
2.1Å resolution

Crystal structure of Staphylococcus epidermidis D283A mevalonate diphosphate decarboxylase complexed with inhibitor DPGP

Released:
DOI: 10.2210/pdb4du8/pdb
PDB 4du8 coloured by chain and viewed from the front.
PDB 4du8 coloured by chain and viewed from the side.
PDB 4du8 coloured by chain and viewed from the top.
Source organism: Staphylococcus epidermidis
Primary publication:
STRUCTURAL BASIS FOR NUCLEOTIDE BINDING AND REACTION CATALYSIS IN MEVALONATE DIPHOSPHATE DECARBOXYLASE.
Barta ML, McWhorter WJ, Miziorko HM, Geisbrecht BV
Biochemistry (2012)
PMID: 22734632

Function and Biology Details

Reaction catalysed: 
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
diphosphomevalonate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 332 amino acids
Theoretical weight: 36.83 KDa
Source organism: Staphylococcus epidermidis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9FD73 (Residues: 1-327; Coverage: 100%)
Gene names: FHG76_00400, FHQ17_11140, I3V53_03435, mvaD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 2P0 2 x 2P0
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-BM-B
Spacegroup: C2221
Unit cell:
a: 82.966Å b: 102.05Å c: 155.143Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.239
Expression system: Escherichia coli BL21(DE3)

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Citations

13 citation in other articles

The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov.
Scholz et al. (2016)
12 more

2 mentions without citation

Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Barta et al. (2012)
1 more