› 7ody

X-ray diffraction
1.43Å resolution

Cyanophage S-2L MazG-like pyrophosphohydrolase bound to dGDP and three catalytic Mn2+ ions per active site

Released:
DOI: 10.2210/pdb7ody/pdb
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PDB entry 7ody coloured by chain, front view.
PDB entry 7ody coloured by chain, side view.
PDB entry 7ody coloured by chain, top view.
Source organism: Cyanophage S-2L
Primary publication:
Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA.
Czernecki D, Bonhomme F, Kaminski PA, Delarue M
OpenAccess logo Nat Commun 12 4710 (2021)
PMID: 34354070

Function and Biology Details

Reaction catalysed: 
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-105921 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dATP/dGTP diphosphohydrolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 111 amino acids
Theoretical weight: 11.74 KDa
Source organism: Cyanophage S-2L
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A7U3TBV3 (Residues: 1-105; Coverage: 100%)
Gene name: S2L_23
Sequence domains: dATP/dGTP pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand DGI 4 x DGI
Ligand MN 12 x MN
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P212121
Unit cell:
a: 53.59Å b: 91.37Å c: 114.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.164 0.166
Expression system: Escherichia coli

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Citations

2 review citations

Bacteriophage-Encoded DNA Polymerases-Beyond the Traditional View of Polymerase Activities.
Morcinek-Orłowska et al. (2022)
1 more

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