› 2g8i

X-ray diffraction
1.65Å resolution

B. halodurans RNase H catalytic domain D192N mutant in complex with Mn2+ and RNA/DNA hybrid (non-P nick at the active site)

Released:
DOI: 10.2210/pdb2g8i/pdb
PDB entry 2g8i coloured by chain, front view.
PDB entry 2g8i coloured by chain, side view.
PDB entry 2g8i coloured by chain, top view.
Source organism: Halalkalibacterium halodurans
Primary publication:
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.
Nowotny M, Yang W
EMBO J 25 1924-33 (2006)
PMID: 16601679

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115285 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
5'-D(*AP*TP*GP*TP*CP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.82 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided
5'-R(*UP*CP*GP*AP*CP*A)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.88 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 4 x MN
Ligand CL 1 x CL
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 82.118Å b: 37.084Å c: 61.772Å
α: 90° β: 96.53° γ: 90°
R-values:
R R work R free
0.173 0.173 0.202
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

36 review citations

Ribonuclease H: the enzymes in eukaryotes.
Cerritelli et al. (2009)
35 more

2 mentions without citation

Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.
Nowotny et al. (2006)
1 more