ADP-ribose diphosphatase

 

The ADP-ribose-specific Nudix hydrolase from Mycobacterium tuberculosis (MT-ADPRase or ADPR pyrophosphatase) is part of the family of Nudix hydrolases with the characteristic Nudix box that catalyse hydrolysis of nucleoside diphosphate derivatives. Divalent magnesium or manganese ions are required for activity. Differences in binding sites of the M. tuberculosis enzyme and the human homologue suggest a possible target for antituberculosis drug treatment.

 

Reference Protein and Structure

Sequence
O33199 UniProt IPR000086 (Sequence Homologues) (PDB Homologues)
Biological species
Mycobacterium tuberculosis CDC1551 (Bacteria) Uniprot
PDB
1mqw - Structure of the MT-ADPRase in complex with three Mn2+ ions and AMPCPR, a Nudix enzyme (2.3 Å) PDBe PDBsum 1mqw
Catalytic CATH Domains
3.90.79.10 CATHdb (see all for 1mqw)
Cofactors
Manganese(2+) (3)
Click To Show Structure

Enzyme Reaction (EC:3.6.1.13)

ADP-D-ribose(2-)
CHEBI:57967ChEBI
+
water
CHEBI:15377ChEBI
→
aldehydo-D-ribose 5-phosphate(2-)
CHEBI:58273ChEBI
+
hydron
CHEBI:15378ChEBI
+
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
Alternative enzyme names: ADPR-PPase, ADPribose diphosphatase, ADPribose pyrophosphatase, Adenosine diphosphoribose pyrophosphatase, ADP-ribose pyrophosphatase, ADP-ribose phosphohydrolase, ADP-ribose ribophosphohydrolase,

Enzyme Mechanism

Introduction

Glu 142, activated by a metal ion, acts as a general base catalyst in activating a water molecule for nucleophilic attack on the alpha-phosphate of the substrate. the water is also activated by binding to two manganese ions. The charges in the alpha-phosphate are stabilised by the metal ions. Charges in the beta-phosphate are stabilised by a metal ion and the Arg 64 side-chain.

Catalytic Residues Roles

UniProt PDB* (1mqw)
Arg64 Arg64A Activates the substrate and stabilises the leaving group electrostatic stabiliser
Glu142 Glu142A Acts as a general base catalyst to deprotonate the water molecule thus activating it as a nucleophile. metal ligand, proton acceptor
Glu93, Glu97, Ala76 (main-C), Glu142 Glu93A, Glu97A, Ala76A (main-C), Glu142A Form metal 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

proton transfer, bimolecular nucleophilic addition, unimolecular elimination by the conjugate base, coordination to a metal ion, overall reactant used, overall product formed

References

  1. Kang LW et al. (2003), Structure, 11, 1015-1023. Structure and Mechanism of MT-ADPRase, a Nudix Hydrolase from Mycobacterium tuberculosis. DOI:10.1016/s0969-2126(03)00154-0. PMID:12906832.
  2. Furuike Y et al. (2016), Biochemistry, 55, 1801-1812. ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors. DOI:10.1021/acs.biochem.5b00886. PMID:26979298.
  3. Mildvan AS et al. (2005), Arch Biochem Biophys, 433, 129-143. Structures and mechanisms of Nudix hydrolases. DOI:10.1016/j.abb.2004.08.017. PMID:15581572.
  4. Gabelli SB et al. (2002), Biochemistry, 41, 9279-9285. Mechanism of theEscherichia coliADP-Ribose Pyrophosphatase, a Nudix Hydrolase†,‡. DOI:10.1021/bi0259296. PMID:12135348.

Step 1. A water molecule is activated for nucleophilic attack through polarization by Mn2+ and through its deprotonation by Glu 142. The activated water then attacks the Phosphorus of the alpha-phosphate which results in the cleavage of the phosphoanhydride bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg64A electrostatic stabiliser
Ala76A (main-C) metal ligand
Glu93A metal ligand
Glu97A metal ligand
Glu142A metal ligand
Glu142A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, ingold: unimolecular elimination by the conjugate base, coordination to a metal ion, overall reactant used, overall product formed
Download: Image, Marvin File

Step 1. A water molecule is activated for nucleophilic attack through polarization by Mn2+ and through its deprotonation by Glu 142. The activated water then attacks the Phosphorus of the alpha-phosphate which results in the cleavage of the phosphoanhydride bond.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, Charity Hornby