› 3vet

X-ray diffraction
2.2Å resolution

Crystal structure of the O-carbamoyltransferase TobZ in complex with Tobramycin, carbamoyl phosphate and ADP

Released:
DOI: 10.2210/pdb3vet/pdb
PDB entry 3vet coloured by chain, front view.
PDB entry 3vet coloured by chain, side view.
PDB entry 3vet coloured by chain, top view.
Source organism: Streptoalloteichus tenebrarius
Primary publication:
The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction.
Parthier C, Görlich S, Jaenecke F, Breithaupt C, Bräuer U, Fandrich U, Clausnitzer D, Wehmeier UF, Böttcher C, Scheel D, Stubbs MT
Angew Chem Int Ed Engl 51 4046-52 (2012)
PMID: 22383337

Function and Biology Details

Reaction catalysed: 
(1a) carbamoyl phosphate + ATP + H(2)O = diphosphate + O-carbamoyladenylate + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180687 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
nebramycin 5' synthase Chain: A
Molecule details ›
Chain: A
Length: 576 amino acids
Theoretical weight: 63.42 KDa
Source organism: Streptoalloteichus tenebrarius
Expression system: Streptomyces lividans TK24
UniProt:
  • Canonical: Q70IY1 (Residues: 1-570; Coverage: 100%)
Gene names: tacA, tobZ
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand ADP 2 x ADP
Ligand CP 1 x CP
Ligand TOY 1 x TOY
Ligand MN 1 x MN
Ligand K 1 x K
Ligand FE2 1 x FE2
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6122
Unit cell:
a: 98.818Å b: 98.818Å c: 280.908Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.167 0.165 0.204
Expression system: Streptomyces lividans TK24

Quick links

Citations

6 review citations

Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA.
Thiaville et al. (2014)
5 more

7 mentions without citation

Sources and Fates of Carbamyl Phosphate: A Labile Energy-Rich Molecule with Multiple Facets.
Shi et al. (2018)
6 more