5'-nucleotidase (mitochondrial)

 

Mitochondrial 5'-(3') deoxyribonucleotidase (dNT-2) dephosphorylates thymidine and deoxyuridine monophosphates, thus regulates the precursors for mitochondrial DNA synthesis and protects mitochondrial DNA replication from excess dTTP.

 

Reference Protein and Structure

Sequence
Q9NPB1 UniProt (3.1.3.-) IPR010708 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1q91 - Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T (1.6 Å) PDBe PDBsum 1q91
Catalytic CATH Domains
3.40.50.1000 CATHdb (see all for 1q91)
Cofactors
Water (2), Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.1.3.5)

nucleoside 5'-monophosphate(2-)
CHEBI:58043ChEBI
+
water
CHEBI:15377ChEBI
→
hydrogenphosphate
CHEBI:43474ChEBI
+
ribonucleoside
CHEBI:18254ChEBI
Alternative enzyme names: 5'-AMP nucleotidase, 5'-AMPase, 5'-adenylic phosphatase, 5'-mononucleotidase, AMP phosphatase, AMP phosphohydrolase, AMPase, IMP 5'-nucleotidase, UMPase, Adenosine 5'-phosphatase, Adenosine monophosphatase, Snake venom 5'-nucleotidase, Thimidine monophosphate nucleotidase, Uridine 5'-nucleotidase,

Enzyme Mechanism

Introduction

A mechanism is proposed based on crystal structure. Asp41 nucleophilically attacks the phosphate to form a phosphoenzyme intermediate. Asp43 is positioned to firstly serve as an acid, promoting the protonation of the leaving deoxyribose moiety and then serves as a base to activate the water nucleophile which hydrolyse the covalent enzyme-substrate intermediate.

Catalytic Residues Roles

UniProt PDB* (1q91)
Asp41 Asp41(10)A It acts as a nucleophile to attack the phosphate to form a phosphoenzyme intermediate. covalently attached, nucleophile, nucleofuge, metal ligand
Asp176, Asp43 (main-N), Asp41 Asp176(145)A, Asp43(12)A (main-N), Asp41(10)A Coordinate the magnesium ion. metal ligand
Asp43 Asp43(12)A It acts as an acid, promoting the protonation of the leaving deoxyribose moiety and it serves as a base to activate the water nucleophile which hydrolyse the covalent enzyme-substrate intermediate. increase nucleophilicity, proton acceptor, proton donor
*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, overall reactant used, intermediate formation, bimolecular nucleophilic substitution, overall product formed, intermediate terminated

References

  1. Rinaldo-Matthis A et al. (2002), Nat Struct Biol, 9, 779-787. Crystal structure of a human mitochondrial deoxyribonucleotidase. DOI:10.1038/nsb846. PMID:12352955.
  2. Seifried A et al. (2013), FEBS J, 280, 549-571. Human HAD phosphatases: structure, mechanism, and roles in health and disease. DOI:10.1111/j.1742-4658.2012.08633.x. PMID:22607316.

Step 1. Asp41 attacks the phosphate group leading to a phospho-enzyme intermediate being formed. Asp43 donates a proton to the nucleoside leaving group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp41(10)A covalently attached, metal ligand
Asp43(12)A (main-N) metal ligand
Asp176(145)A metal ligand
Asp43(12)A proton donor
Asp41(10)A nucleophile

Chemical Components

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

Step 2. Asp43 then activates a water molecule which attacks the phosphate, leading to the collapse of the intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp41(10)A metal ligand
Asp43(12)A (main-N) metal ligand
Asp176(145)A metal ligand
Asp43(12)A increase nucleophilicity
Asp43(12)A proton acceptor
Asp41(10)A nucleofuge

Chemical Components

proton transfer, overall product formed, ingold: bimolecular nucleophilic substitution, intermediate terminated
Download: Image, Marvin File

Step 1. Asp41 attacks the phosphate group leading to a phospho-enzyme intermediate being formed. Asp43 donates a proton to the nucleoside leaving group.

Step 2. Asp43 then activates a water molecule which attacks the phosphate, leading to the collapse of the intermediate.

Products.

Contributors

Mei Leung, Gemma L. Holliday, James Willey