Ribonuclease D
Ribonuclease D is a divalent metal cation dependent exonuclease that acts on tRNA and is involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.
Reference Protein and Structure
- Sequence
-
P09155
(3.1.13.5)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Escherichia coli K-12 (Bacteria)
- PDB
-
1yt3
- Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing
(1.6 Å)
- Catalytic CATH Domains
-
3.30.420.10
(see all for 1yt3)
- Cofactors
- Zinc(2+) (2) Metal MACiE
Enzyme Mechanism
Introduction
This enzyme can convert a tRNA precursor into a mature tRNA. The activated water, coordinated to one of the active site Zn cations attacks at the pentavalent 5' phosphorous centre. The 3' hydroxyl group deprotonates a water molecule, regenerating the Zn hydroxide centre.
Catalytic Residues Roles
| UniProt | PDB* (1yt3) | ||
| Asp28 | Asp28A | Acts as a bidentate ligand between the zinc binding sites. | metal ligand |
| Asp155 | Asp155A | Positioned in exo-site 3, implicated in stabilising and directing the nucleophile. Also forms part of the zinc 1 binding site. | attractive charge-charge interaction, metal ligand, electrostatic stabiliser |
| Tyr151 | Tyr151A | Positioned in exo-site 3, implicated in stabilising and directing the nucleophile | hydrogen bond donor, electrostatic stabiliser |
| Glu30 | Glu30A | Forms part of the zinc 1 binding site. | metal ligand |
| Asp85 | Asp85A | Forms part of the zinc 2 binding site. | metal ligand |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
bimolecular nucleophilic substitution, overall reactant used, overall product formed, decoordination from a metal ion, intermediate formation, proton transfer, coordination, inferred reaction step, native state of enzyme regeneratedReferences
- Zuo Y et al. (2005), Structure, 13, 973-984. Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing. DOI:10.1016/j.str.2005.04.015. PMID:16004870.
- Yang W (2011), Q Rev Biophys, 44, 1-93. Nucleases: diversity of structure, function and mechanism. DOI:10.1017/s0033583510000181. PMID:20854710.
- Phillips S et al. (2003), RNA, 9, 1098-1107. Contribution of domain structure to the RNA 3' end processing and degradation functions of the nuclear exosome subunit Rrp6p. DOI:10.1261/rna.5560903. PMID:12923258.
- Steitz TA et al. (1993), Proc Natl Acad Sci U S A, 90, 6498-6502. A general two-metal-ion mechanism for catalytic RNA. DOI:10.1073/pnas.90.14.6498. PMID:8341661.
Step 1. The hydroxide ion, coordinated to one of the active site Zn cations attacks at the pentavalent 5' phosphorous centre.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp155A | attractive charge-charge interaction, electrostatic stabiliser |
| Tyr151A | hydrogen bond donor, electrostatic stabiliser |
| Asp155A | metal ligand |
| Glu30A | metal ligand |
| Asp28A | metal ligand |
| Asp85A | metal ligand |
Chemical Components
ingold: bimolecular nucleophilic substitution, overall reactant used, overall product formed, decoordination from a metal ion, intermediate formation
Step 2. The 3' hydroxyl group deprotonates a water molecule, regenerating the Zn hydroxide centre.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp155A | electrostatic stabiliser, attractive charge-charge interaction |
| Tyr151A | hydrogen bond donor |
| Asp155A | metal ligand |
| Glu30A | metal ligand |
| Asp28A | metal ligand |
| Asp85A | metal ligand |
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