› 3g3c

X-ray diffraction
3.04Å resolution

Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang

Released:
DOI: 10.2210/pdb3g3c/pdb
PDB entry 3g3c coloured by chain, front view.
PDB entry 3g3c coloured by chain, side view.
PDB entry 3g3c coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Crystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA.
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R
J Mol Biol 399 604-17 (2010)
PMID: 20434457

Function and Biology Details

Reactions catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116266 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA uridine endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 265 amino acids
Theoretical weight: 31.43 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Expression system: Escherichia coli
UniProt:
  • Canonical: O26314 (Residues: 1-257; Coverage: 100%)
Gene name: MTH_212
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-D(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3' Chain: H
Molecule details ›
Chain: H
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Expression system: Not provided
5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3' Chain: I
Molecule details ›
Chain: I
Length: 9 nucleotides
Theoretical weight: 2.73 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand PO4 2 x PO4
Ligand MG 2 x MG
Ligand MRD 1 x MRD
1 modified residue:
Ligand UPS 1 x UPS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21212
Unit cell:
a: 100.354Å b: 79.337Å c: 98.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.236 0.294
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Base excision repair in Archaea: back to the future in DNA repair.
Grasso et al. (2014)
1 more