› 3ver

X-ray diffraction
2.34Å resolution

Crystal structure of the O-carbamoyltransferase TobZ in complex with carbamoyl adenylate intermediate

Released:
DOI: 10.2210/pdb3ver/pdb
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PDB entry 3ver coloured by chain, front view.
PDB entry 3ver coloured by chain, side view.
PDB entry 3ver 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: 63.45 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

3 bound ligands:
Ligand FE2 1 x FE2
Ligand NA 1 x NA
Ligand CA0 2 x CA0
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6122
Unit cell:
a: 99.262Å b: 99.262Å c: 281.323Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.172 0.169 0.224
Expression system: Streptomyces lividans TK24

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Citations

8 review citations

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

1 mention without citation

Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases.
Jin et al. (2023)

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