› 1yt3

X-ray diffraction
1.6Å resolution

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Released:
DOI: 10.2210/pdb1yt3/pdb
PDB entry 1yt3 coloured by chain, front view.
PDB entry 1yt3 coloured by chain, side view.
PDB entry 1yt3 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.
Zuo Y, Wang Y, Malhotra A
Structure 13 973-84 (2005)
PMID: 16004870

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140575 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonuclease D Chain: A
Molecule details ›
Chain: A
Length: 375 amino acids
Theoretical weight: 42.78 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P09155 (Residues: 1-375; Coverage: 100%)
Gene names: JW1793, b1804, rnd
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 7 x SO4
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 51Å b: 80.1Å c: 103.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.216
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The critical role of RNA processing and degradation in the control of gene expression.
Arraiano et al. (2010)
6 more

13 mentions without citation

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