Hydroxymethylpyrimidine kinase
HMPP kinase is a key enzyme in the biosynthetic pathway for the formation of thiamine. The bacterial form of the enzyme described here is a member of the ribokinase/sugar kinase family, meaning that it displays significant sequence and structural homology with a large number of kinases with different substrates such as Adenosine kinase. It is unusual however because it is able to catalyse two consecutive steps in the synthesis of thiamine; phosphorylation of 4-amino-5-hydroxymethyl-5-methyl pyrimidine (HM) to give HMP followed by phosphorylation of HMP to give HMPP. This makes studying the enzyme interesting for understanding the specificity of the active site.
Reference Protein and Structure
- Sequence
-
P55882
(2.7.1.49, 2.7.4.7)
(Sequence Homologues) (PDB Homologues)
- Biological species
-
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (Bacteria)
- PDB
-
1jxh
- 4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium
(2.3 Å)
- Catalytic CATH Domains
-
3.40.1190.20
(see all for 1jxh)
- Cofactors
- Magnesium(2+) (1)
Enzyme Reaction (EC:2.7.1.49)
Enzyme Mechanism
Introduction
HMPP kinase catalyses an SN2 type in line displacement reaction where the substrate acts as the nucleophile to attack the gamma phosphate of ATP, forming a pentavalent phosphate transition state. This is stabilised by Mg2+and Lys 176 at the active site, and collapses to release the end products. Gly210, along with Thr211, Gly212 and Cys213 form the anion hole which also helps stabilise the transition state. A subsequent phosphorylation of the product HMP-P occurs by a similar in line displacement in an overlapping active site.
Catalytic Residues Roles
UniProt | PDB* (1jxh) | ||
Thr208, Thr208 (main-C) | Thr208(230)A, Thr208(230)A (main-C) | Thr208 through its carbonyl and side chain coordinates to Mg2+ ion that in turn stabilises the leaving group ADP. | metal ligand |
Thr211 (main-N), Gly212 (main-N), Cys213 | Thr211(233)A (main-N), Gly212(234)A (main-N), Cys213(235)A | Alongside Gly210, Thr211, Gly212 and Cys213 make up the anion hole in a conserved GTGC motif across the ribokinase family that is able to help stabilise the transition state. | electrostatic stabiliser |
Lys176 | Lys176(198)A | Acts to stabilise the transition state through electrostatic contacts with the gamma phosphate. | electrostatic stabiliser |
Gly210 (main-N) | Gly210(232)A (main-N) | Gly210 is apart of the anion hole and acts to stabilise the transition state through favourable contacts between the gamma phosphate and the amide group of the residue. | electrostatic stabiliser |
Chemical Components
bimolecular nucleophilic substitutionReferences
- Cheng G et al. (2002), Structure, 10, 225-235. Crystal Structure of 4-Amino-5-Hydroxymethyl-2- Methylpyrimidine Phosphate Kinase from Salmonella typhimurium at 2.3 Å Resolution. DOI:10.1016/s0969-2126(02)00708-6. PMID:11839308.
Catalytic Residues Roles
Residue | Roles |
---|---|
Gly210(232)A (main-N) | electrostatic stabiliser |
Lys176(198)A | electrostatic stabiliser |
Thr208(230)A | metal ligand |
Thr208(230)A (main-C) | metal ligand |
Thr211(233)A (main-N) | electrostatic stabiliser |
Gly212(234)A (main-N) | electrostatic stabiliser |
Cys213(235)A | electrostatic stabiliser |