3g38

X-ray diffraction
3.04Å resolution

The catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA

Released:

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
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-116265 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA uridine endonuclease Chain: A
Molecule details ›
Chain: A
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*CP*TP*GP*UP*GP*CP*GP*AP*T)-3' Chain: G
Molecule details ›
Chain: G
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Expression system: Not provided
5'-D(*CP*GP*CP*GP*CP*AP*GP*GP*C)-3' Chain: K
Molecule details ›
Chain: K
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P21212
Unit cell:
a: 79.96Å b: 107.15Å c: 44.27Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.259 0.256 0.328
Expression systems:
  • Escherichia coli
  • Not provided