RNAse II

 

RNAse II catalyses the sequential 3'-5' hydrolysis of single stranded RNA. Catalytic activity of RNAse II is dependent upon the presence of a divalent cation.

 

Reference Protein and Structure

Sequence
P30850 UniProt (3.1.13.1) IPR011804 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
2id0 - Escherichia coli RNase II (2.35 Å) PDBe PDBsum 2id0
Catalytic CATH Domains
(see all for 2id0)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.1.13.1)

messenger RNA
CHEBI:33699ChEBI
+
water
CHEBI:15377ChEBI
→
3'-end ribonucleotide(1-) residue
CHEBI:74896ChEBI
+
5'-end ribonucleotide(1-) residue
CHEBI:137923ChEBI
Alternative enzyme names: 5'-exoribonuclease, Escherichia coli exo-RNase II, BN ribonuclease, RNase II, Exoribonuclease, Ribonuclease II, Ribonuclease Q,

Enzyme Mechanism

Introduction

The hydrolytic water attacks at the phosphorous centre, forming a pentavalent transition state which eliminates the O5' oxygen of the RNA strand and monophosphate nucleoside. The transition sate is stabilised by the presence of the two positively charged groups, the metal cation and Arg500. There are four catalytic aspartate residues howver only Asp209 appears to be essential for catalysis and appears to activate the water for nucleophilic attack along with Arg500. Tyr313 protonates the leaving group.

Catalytic Residues Roles

UniProt PDB* (2id0)
Asp209 Asp209A Increases the reactivity of the water molecule. increase nucleophilicity, activator, electrostatic stabiliser
Asp201, Asp210, Asp207 (main-C) Asp201A, Asp210A, Asp207A (main-C) Coordinate the magnesium ion. metal ligand
Tyr313 Tyr313A Acts as a general acid/base. Donates a proton to the leaving RNA molecule. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator
Arg500 Arg500A The hydrolytic water is thought to be activated by the presence of the positively charged divalent cation and Arg500 [PMID:16957732]. It has been inferred in this annotation that Arg500 acts as general base towards the attacking water molecule. This results in the formation of hydroxide and guanidinium functionalities. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator, electrostatic stabiliser
*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, proton transfer, overall reactant used, overall product formed, native state of enzyme regenerated, inferred reaction step

References

  1. Frazão C et al. (2006), Nature, 443, 110-114. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. DOI:10.1038/nature05080. PMID:16957732.
  2. Barbas A et al. (2008), J Biol Chem, 283, 13070-13076. New insights into the mechanism of RNA degradation by ribonuclease II: identification of the residue responsible for setting the RNase II end product. DOI:10.1074/jbc.M709989200. PMID:18337246.
  3. Zuo Y et al. (2006), Mol Cell, 24, 149-156. Structural Basis for Processivity and Single-Strand Specificity of RNase II. DOI:10.1016/j.molcel.2006.09.004. PMID:16996291.

Step 1. The hydrolytic water attacks at the phosphorous centre, forming a pentavalent transition state which eliminates the O5' oxygen of the RNA strand and monophosphate nucleoside. The transition sate is stabilised by the presence of the magnesium ion and Arg500.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr313A activator, hydrogen bond donor
Arg500A activator, hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Asp209A electrostatic stabiliser, increase nucleophilicity
Asp201A metal ligand
Asp207A (main-C) metal ligand
Asp210A metal ligand
Asp209A activator
Arg500A proton acceptor
Tyr313A proton donor

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall reactant used, overall product formed

Step 2. It is inferred that for active site regeneration, proton transfer must occur between the active site residues. This could, however, occur through solvent molecules rather than directly between the residues themselves.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr313A activator, hydrogen bond acceptor
Arg500A activator, hydrogen bond donor
Asp201A metal ligand
Asp207A (main-C) metal ligand
Asp210A metal ligand
Tyr313A proton acceptor
Arg500A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. The hydrolytic water attacks at the phosphorous centre, forming a pentavalent transition state which eliminates the O5' oxygen of the RNA strand and monophosphate nucleoside. The transition sate is stabilised by the presence of the magnesium ion and Arg500.

Step 2. It is inferred that for active site regeneration, proton transfer must occur between the active site residues. This could, however, occur through solvent molecules rather than directly between the residues themselves.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, James Willey