3'-5' exoribonuclease 1

 

3'-5' exoribonuclease (3'hExo) from Homo sapiens is a DEDDh family member. It contains the invariant DEDD working with H sequence of residues. 3'hExo targets human histone mRNAs and degrades them in a 3' to 5' direction in a sequence specific manner.

 

Reference Protein and Structure

Sequence
Q8IV48 UniProt (3.1.-.-) IPR013520 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1w0h - Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP (1.59 Å) PDBe PDBsum 1w0h
Catalytic CATH Domains
3.30.420.10 CATHdb (see all for 1w0h)
Cofactors
Magnesium(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.1.-.-)

RNA (poly(A))
CHEBI:8756ChEBI
+
water
CHEBI:15377ChEBI
→
RNA (poly(A))
CHEBI:8756ChEBI

Enzyme Mechanism

Introduction

His 293 acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack. The activated water molecule nucleophilically attacks the last phosphorus atom, breaking the phosphodiester bond of the terminal residue of the oligonucleotide chain. A negatively charged, pentacoordinate intermediate is formed, which is stabilised by the MgA ion. Glu 136 deprotonates the O atom of the intermediate, collapsing it to form the products.

Catalytic Residues Roles

UniProt PDB* (1w0h)
Asp298, Asp234, Asp134 Asp298(180)A, Asp234(116)A, Asp134(16)A Form the magnesium binding site metal ligand
His293 His293(175)A Acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack. proton acceptor, electrostatic stabiliser
Glu136 Glu136(18)A Deprotonates the pentacoordinate intermediate, causing it to collapse to form the products. proton acceptor, metal ligand, 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

proton transfer, bimolecular nucleophilic addition, intermediate formation, overall reactant used, unimolecular elimination by the conjugate base, intermediate collapse, inferred reaction step, overall product formed

References

  1. Cheng Y et al. (2004), J Mol Biol, 343, 305-312. Crystallographic Structure of the Nuclease Domain of 3′hExo, a DEDDh Family Member, Bound to rAMP. DOI:10.1016/j.jmb.2004.08.055. PMID:15451662.

Step 1. His293 abstracts a proton from a water which can then acts as a nucleophile and attacks the last phosphorus atom.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu136(18)A electrostatic stabiliser
His293(175)A electrostatic stabiliser
Asp134(16)A metal ligand
Asp234(116)A metal ligand
Asp298(180)A metal ligand
Glu136(18)A metal ligand
His293(175)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used

Step 2. The deprotonation of the five-coordinate phosphorane intermediate by Glu126 initiates an elimination which results in the cleavage of the phosphodiester bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu136(18)A electrostatic stabiliser
His293(175)A electrostatic stabiliser
Asp134(16)A metal ligand
Asp234(116)A metal ligand
Asp298(180)A metal ligand
Glu136(18)A metal ligand, proton acceptor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base, intermediate collapse, inferred reaction step, overall product formed
Download: Image, Marvin File

Step 1. His293 abstracts a proton from a water which can then acts as a nucleophile and attacks the last phosphorus atom.

Step 2. The deprotonation of the five-coordinate phosphorane intermediate by Glu126 initiates an elimination which results in the cleavage of the phosphodiester bond.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, Charity Hornby