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

Source organism: Staphylococcus epidermidis
Biochemical function: carboxy-lyase activity
Biological process: isopentenyl diphosphate biosynthetic process, mevalonate pathway
Cellular component: cytosol

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EC 4.1.1.33: Diphosphomevalonate decarboxylase

Reaction catalysed:
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
Systematic name:
ATP:(R)-5-diphosphomevalonate carboxy-lyase (adding ATP; isopentenyl-diphosphate-forming)
Alternative Name(s):
  • 5-pyrophosphomevalonate decarboxylase
  • ATP:(R)-5-diphosphomevalonate carboxy-lyase (dehydrating)
  • Mevalonate 5-diphosphate decarboxylase
  • Mevalonate diphosphate decarboxylase
  • Mevalonate pyrophosphate decarboxylase
  • Mevalonate-5-pyrophosphate decarboxylase
  • Pyrophosphomevalonate decarboxylase
  • Pyrophosphomevalonic acid decarboxylase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF18376
Domain description: Mevalonate 5-diphosphate decarboxylase C-terminal domain
Occurring in:
  1. diphosphomevalonate decarboxylase
The deposited structure of PDB entry 4dpy contains 2 copies of Pfam domain PF18376 (Mevalonate 5-diphosphate decarboxylase C-terminal domain) in diphosphomevalonate decarboxylase. Showing 1 copy in chain A.

PF22700
Domain description: Diphosphomevalonate decarboxylase-like N-terminal domain
Occurring in:
  1. diphosphomevalonate decarboxylase

InterPro InterPro annotations
IPR036554
Domain description: GHMP kinase, C-terminal domain superfamily
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR041431
Domain description: Mvd1, C-terminal
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR006204
Domain description: GHMP kinase N-terminal domain
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR029765
Domain description: Diphosphomevalonate decarboxylase
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR020568
Domain description: Ribosomal protein uS5 domain 2-type superfamily
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR005935
Domain description: Diphosphomevalonate/phosphomevalonate decarboxylase
Occurring in:
  1. diphosphomevalonate decarboxylase
IPR014721
Domain description: Small ribosomal subunit protein uS5 domain 2-type fold, subgroup
Occurring in:
  1. diphosphomevalonate decarboxylase

Structure domains

CATH CATH domains
3.30.70.890
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: GHMP kinase, C-terminal domain
Occurring in:
  1. diphosphomevalonate decarboxylase
The deposited structure of PDB entry 4dpy contains 2 copies of CATH domain 3.30.70.890 (Alpha-Beta Plaits) in diphosphomevalonate decarboxylase. Showing 1 copy in chain A.
3.30.230.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Ribosomal Protein S5; domain 2
Homology: Ribosomal Protein S5; domain 2
Occurring in:
  1. diphosphomevalonate decarboxylase
The deposited structure of PDB entry 4dpy contains 2 copies of CATH domain 3.30.230.10 (Ribosomal Protein S5; domain 2) in diphosphomevalonate decarboxylase. Showing 1 copy in chain A.

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