› 4dpy

X-ray diffraction
2.14Å resolution

Crystal structure of Staphylococcus epidermidis S192A mevalonate diphosphate decarboxylase complexed with inhibitor DPGP

Released:
DOI: 10.2210/pdb4dpy/pdb
PDB entry 4dpy coloured by chain, front view.
PDB entry 4dpy coloured by chain, side view.
PDB entry 4dpy coloured by chain, top view.
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 51 5611-21 (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:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190292 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
diphosphomevalonate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 332 amino acids
Theoretical weight: 36.85 KDa
Source organism: Staphylococcus epidermidis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9FD73 (Residues: 1-327; Coverage: 100%)
Gene names: CTJ08_04460, I3V53_03435, MNU40_01505, mvaD
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 2P0 2 x 2P0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2221
Unit cell:
a: 82.678Å b: 101.733Å c: 155.498Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.168 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

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

1 mention without citation

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