› 5gmd

X-ray diffraction
1.5Å resolution

Crystal structure of Sulfolobus solfataricus diphosphomevalonate decarboxylase in complex with ATP-gamma-S

Released:
DOI: 10.2210/pdb5gmd/pdb
PDB entry 5gmd coloured by chain, front view.
PDB entry 5gmd coloured by chain, side view.
PDB entry 5gmd coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase.
Motoyama K, Unno H, Hattori A, Takaoka T, Ishikita H, Kawaide H, Yoshimura T, Hemmi H
J Biol Chem 292 2457-2469 (2017)
PMID: 28003359

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-188978 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphosphomevalonate decarboxylase Chain: A
Molecule details ›
Chain: A
Length: 325 amino acids
Theoretical weight: 37.08 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97UL5 (Residues: 1-325; Coverage: 100%)
Gene name: SSO2989
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand DP6 1 x DP6
Ligand AGS 1 x AGS
Ligand AMP 1 x AMP
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: R32
Unit cell:
a: 151.238Å b: 151.238Å c: 104.416Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.165 0.192
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate.
Hayakawa et al. (2018)
3 more

3 mentions without citation

A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase.
Motoyama et al. (2017)
2 more