› 4ejy

X-ray diffraction
2Å resolution

Structure of MBOgg1 in complex with high affinity DNA ligand

Released:
DOI: 10.2210/pdb4ejy/pdb
PDB entry 4ejy coloured by chain, front view.
PDB entry 4ejy coloured by chain, side view.
PDB entry 4ejy coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Primary publication:
Crystal structures of MBOgg1 in complex with two abasic DNA ligands.
Yu H, Yang M, Zhang XE, Bi L, Jiang T
J Struct Biol 181 252-63 (2013)
PMID: 23246782

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117421 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-(apurinic or apyrimidinic site) lyase Chains: A, B
Molecule details ›
Chains: A, B
Length: 311 amino acids
Theoretical weight: 36.19 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8R5T9 (Residues: 1-297; Coverage: 100%)
Gene names: AlkA, TTE0574
Sequence domains:
Structure domains:
DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 16 nucleotides
Theoretical weight: 4.71 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Not provided
DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 16 nucleotides
Theoretical weight: 4.94 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 56.613Å b: 102.884Å c: 67.284Å
α: 90° β: 90.18° γ: 90°
R-values:
R R work R free
0.224 0.222 0.258
Expression systems:
  • Escherichia coli
  • Not provided

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