S-methyl-5'-thioadenosine phosphorylase

 

S-methyl-5'-thioadenosine phosphorylase (MTAP) catalyses the reversible phosphorylation of S-methyl-5'-thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. It is involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. It is responsible for the first step in the methionine salvage pathway after MTA has been generated from S-adenosylmethionine. It has broad substrate specificity with 6-aminopurine nucleosides as preferred substrates. Despite being also an MTA phosphorylase, the MTAP in thermophilic Sulfolobus solfataricus only has 14% sequence homology to human MTAP.

 

Reference Protein and Structure

Sequence
Q13126 UniProt (2.4.2.28) IPR010044 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1cg6 - STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE AT 1.7 A RESOLUTION (1.7 Å) PDBe PDBsum 1cg6
Catalytic CATH Domains
3.40.50.1580 CATHdb (see all for 1cg6)
Click To Show Structure

Enzyme Reaction (EC:2.4.2.28)

hydrogenphosphate
CHEBI:43474ChEBI
+
5'-S-methyl-5'-thioadenosine
CHEBI:17509ChEBI
→
adenine
CHEBI:16708ChEBI
+
S-methyl-5-thio-alpha-D-ribose 1-phosphate(2-)
CHEBI:58533ChEBI
Alternative enzyme names: 5'-deoxy-5'-methylthioadenosine phosphorylase, 5'-methylthioadenosine phosphorylase, 5'-methylthioadenosine:phosphate methylthio-D-ribosyl-transferase, MTA phosphorylase, MeSAdo phosphorylase, MeSAdo/Ado phosphorylase, Methylthioadenosine nucleoside phosphorylase, Methylthioadenosine phosphorylase, MTAPase, S-methyl-5-thioadenosine:phosphate S-methyl-5-thio-alpha-D-ribosyl-transferase,

Enzyme Mechanism

Introduction

The reaction proceeds via a two step mechanism with the formation of an oxocarbenium-like transition state followed by a nucleophilic attack by the phosphate ion at the anomeric carbon in an SN1-like mechanism.

Catalytic Residues Roles

UniProt PDB* (1cg6)
Asp220 Asp220A Acts as a general acid/base. This residue is buried in the active site and has a significantly modified pKa, allowing it to be protonated in the ground state of the enzyme. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asp222 Asp222A Binds the substrate and helps to stabilise the oxocarbenium ion formed in the reaction. 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

unimolecular elimination by the conjugate base, proton transfer, intermediate formation, overall reactant used, overall product formed, bimolecular nucleophilic addition, intermediate terminated, inferred reaction step, native state of enzyme regenerated

References

  1. Appleby TC et al. (1999), Structure, 7, 629-641. The structure of human 5′-deoxy-5′-methylthioadenosine phosphorylase at 1.7 Å resolution provides insights into substrate binding and catalysis. DOI:10.1016/s0969-2126(99)80084-7. PMID:10404592.
  2. Guan R et al. (2013), Biochemistry, 52, 8313-8322. Thermodynamic analysis of transition-state features in picomolar inhibitors of human 5'-methylthioadenosine phosphorylase. DOI:10.1021/bi401188w. PMID:24148083.
  3. Appleby TC et al. (2001), J Biol Chem, 276, 39232-39242. Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. DOI:10.1074/jbc.M105694200. PMID:11489901.

Step 1. The glycosidic bond is cleaved to give an oxocarbenium ion that is stabilised by the phosphate in the active site. The adenine that is eliminated is protonated by Asp220. The product of this step is a tautomer of adenine, which will readily tautomerise.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp220A hydrogen bond donor
Asp222A electrostatic stabiliser
Asp220A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate formation, overall reactant used, overall product formed

Step 2. Phosphate attacks the oxocarbenium ion intermediate in a nucleophilic addition.

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Catalytic Residues Roles

Residue Roles
Asp222A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, intermediate terminated, overall product formed

Step 3. Asp220 is re-protonated by water

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp220A hydrogen bond acceptor, proton acceptor

Chemical Components

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

Step 1. The glycosidic bond is cleaved to give an oxocarbenium ion that is stabilised by the phosphate in the active site. The adenine that is eliminated is protonated by Asp220. The product of this step is a tautomer of adenine, which will readily tautomerise.

Step 2. Phosphate attacks the oxocarbenium ion intermediate in a nucleophilic addition.

Step 3. Asp220 is re-protonated by water

Products.

Contributors

Gemma L. Holliday, Nozomi Nagano, Craig Porter, Morwenna Hall