3'(2'),5'-bisphosphate nucleotidase

 

Catalyses the removal of the 3'-phosphate from adenosine 5'-phosphosulfate to reform AMP. This reaction helps drive the sulfur incorporation cycle for pathways such as methionine biosynthesis. Sensitivity of this essential enzyme to sodium and other metal ions results is responsible for characterisation of this enzyme as a salt tolerance protein [PMID:10205895]. Some members of this family are active also as inositol 1-monophosphatase.

 

Reference Protein and Structure

Sequence
P32179 UniProt (3.1.3.7) IPR006239 (Sequence Homologues) (PDB Homologues)
Biological species
Saccharomyces cerevisiae S288c (Baker's yeast) Uniprot
PDB
1qgx - X-RAY STRUCTURE OF YEAST HAL2P (1.6 Å) PDBe PDBsum 1qgx
Catalytic CATH Domains
3.30.540.10 CATHdb 3.40.190.80 CATHdb (see all for 1qgx)
Cofactors
Water (1), Magnesium(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.1.3.7)

adenosine 3',5'-bismonophosphate(4-)
CHEBI:58343ChEBI
+
water
CHEBI:15377ChEBI
→
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
Alternative enzyme names: 3'(2'),5'-bisphosphonucleoside 3'(2')-phosphohydrolase, 3'-phosphoadenylylsulfate 3'-phosphatase, Phosphoadenylate 3'-nucleotidase, DPNPase,

Enzyme Mechanism

Introduction

A water molecule bound to the first site magnesium ion is activated through a proton relay with Asp49 and Thr147. It then attacks the 3'-phosphate group, eliminating the product phosphate and a negatively charged intermediate which subsequently is reprotonated from bulk solvent via a proton relay involving the second ribose hydroxyl group and a water bound to the second magnesium site.

Catalytic Residues Roles

UniProt PDB* (1qgx)
Asp142, Ile144 (main-C) Asp142A, Ile144A (main-C) Forms part of the magnesium 1 binding site. metal ligand
Glu72 Glu72A Acts as a bridging ligand between the two magnesium ions. metal ligand
Asp49, Thr147 Asp49A, Thr147A Asp49 and Thr147 form a proton relay chain with the catalytic water, both act as general acid/bases. Asp49 abstracts a proton from Thr147, which in turn abstracts a proton from the catalytic water, activating it for nucleophilic attack on the substrate 3'-phosphate. proton acceptor, proton donor
Asp145, Asp294 Asp145A, Asp294A Forms part of the magnesium 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

proton transfer, bimolecular nucleophilic addition, overall product formed, overall reactant used, proton relay, inferred reaction step, native state of enzyme regenerated

References

  1. Patel S et al. (2002), J Mol Biol, 320, 1087-1094. Structural Enzymology of Li+-sensitive/Mg2+-dependent Phosphatases. DOI:10.1016/s0022-2836(02)00564-8. PMID:12126627.
  2. Gill R et al. (2005), Acta Crystallogr D Biol Crystallogr, 61, 545-555. High-resolution structure of myo-inositol monophosphatase, the putative target of lithium therapy. DOI:10.1107/S0907444905004038. PMID:15858264.
  3. Albert A et al. (2000), J Mol Biol, 295, 927-938. X-ray structure of yeast Hal2p, a major target of lithium and sodium toxicity, and identification of framework interactions determining cation sensitivity. DOI:10.1006/jmbi.1999.3408. PMID:10656801.
  4. Gil-Mascarell R et al. (1999), Plant J, 17, 373-383. The Arabidopsis HAL2-like gene family includes a novel sodium-sensitive phosphatase. PMID:10205895.

Step 1. Asp49 activates the catalytic water through Thr147. The activated species then initiates a nucleophilic attack on the magnesium bound phosphate, eliminating it from the diphosphate substrate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp294A metal ligand
Asp142A metal ligand
Ile144A (main-C) metal ligand
Glu72A metal ligand
Asp145A metal ligand
Thr147A proton acceptor
Asp49A proton acceptor
Thr147A proton donor, proton relay

Chemical Components

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

Step 2. The intermediate is reprotonated from the bulk solvent via a proton relay through the other ribose sugar, the second magnesium bound water and thence bulk solvent.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp294A metal ligand
Asp142A metal ligand
Ile144A (main-C) metal ligand
Glu72A metal ligand
Asp145A metal ligand

Chemical Components

overall product formed, proton relay, proton transfer

Step 3. Inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp294A metal ligand
Asp142A metal ligand
Ile144A (main-C) metal ligand
Glu72A metal ligand
Asp145A metal ligand
Asp49A proton donor

Chemical Components

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

Step 1. Asp49 activates the catalytic water through Thr147. The activated species then initiates a nucleophilic attack on the magnesium bound phosphate, eliminating it from the diphosphate substrate.

Step 2. The intermediate is reprotonated from the bulk solvent via a proton relay through the other ribose sugar, the second magnesium bound water and thence bulk solvent.

Step 3. Inferred return step.

Products.

Contributors

Alex Gutteridge, Craig Porter, Gemma L. Holliday