› 6ime

X-ray diffraction
1.55Å resolution

Rv2361c complex with substrate analogues

Released:
DOI: 10.2210/pdb6ime/pdb
PDB entry 6ime coloured by chain, front view.
PDB entry 6ime coloured by chain, side view.
PDB entry 6ime coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.
Ko TP, Xiao X, Guo RT, Huang JW, Liu W, Chen CC
Acta Crystallogr F Struct Biol Commun 75 212-216 (2019)
PMID: 30950820

Function and Biology Details

Reactions catalysed: 
(2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
(2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161410 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Decaprenyl diphosphate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 296 amino acids
Theoretical weight: 33.84 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WFF7 (Residues: 1-296; Coverage: 100%)
Gene names: MTCY27.19, Rv2361c, uppS
Sequence domains: Putative undecaprenyl diphosphate synthase

Ligands and Environments

7 bound ligands:
Ligand GST 2 x GST
Ligand MG 2 x MG
Ligand CL 1 x CL
Ligand CO3 1 x CO3
Ligand DTT 1 x DTT
Ligand GOL 1 x GOL
Ligand ISY 1 x ISY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P212121
Unit cell:
a: 77.711Å b: 89.12Å c: 94.445Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.146 0.145 0.167
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation.
Edani et al. (2020)
1 more

1 mention without citation

Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.
Ko et al. (2019)