› 3dnf

X-ray diffraction
1.65Å resolution

Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

Released:
DOI: 10.2210/pdb3dnf/pdb
PDB entry 3dnf coloured by chain, front view.
PDB entry 3dnf coloured by chain, side view.
PDB entry 3dnf coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
Structure of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, the terminal enzyme of the non-mevalonate pathway.
Rekittke I, Wiesner J, Röhrich R, Demmer U, Warkentin E, Xu W, Troschke K, Hintz M, No JH, Duin EC, Oldfield E, Jomaa H, Ermler U
J Am Chem Soc 130 17206-7 (2008)
PMID: 19035630

Function and Biology Details

Reaction catalysed: 
Isopentenyl diphosphate + 2 oxidized ferredoxin [iron-sulfur] cluster + H(2)O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130523 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-3-methylbut-2-enyl diphosphate reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 297 amino acids
Theoretical weight: 33.22 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O67625 (Residues: 1-289; Coverage: 100%)
Gene names: aq_1739, ispH, lytB
Sequence domains: LytB protein
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand F3S 2 x F3S
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 60.37Å b: 87.76Å c: 72.4Å
α: 90° β: 95.13° γ: 90°
R-values:
R R work R free
0.194 0.193 0.226
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Radical S-adenosylmethionine enzymes.
Broderick et al. (2014)
9 more

12 mentions without citation

Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis.
Wang et al. (2014)
11 more