› 3g10

X-ray diffraction
2.6Å resolution

Structure of S. pombe Pop2p - Mg2+ and Mn2+ bound form

Released:
DOI: 10.2210/pdb3g10/pdb
PDB entry 3g10 coloured by chain, front view.
PDB entry 3g10 coloured by chain, side view.
PDB entry 3g10 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site.
Andersen KR, Jonstrup AT, Van LB, Brodersen DE
RNA 15 850-61 (2009)
PMID: 19307292

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage of poly(A) to 5'-AMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130797 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Poly(A) ribonuclease pop2 Chain: A
Molecule details ›
Chain: A
Length: 333 amino acids
Theoretical weight: 37.32 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli
UniProt:
  • Canonical: O74856 (Residues: 4-335; Coverage: 99%)
Gene names: SPCC18.06c, caf1, pop2
Sequence domains: CAF1 family ribonuclease
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P212121
Unit cell:
a: 53.124Å b: 53.991Å c: 95.646Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.187 0.23
Expression system: Escherichia coli

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Citations

8 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
7 more

18 mentions without citation

Viruses Like Sugars: How to Assess Glycan Involvement in Viral Attachment.
Mathez et al. (2021)
17 more