1JXH
4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1jxha_ | Alpha and beta proteins (a/b) | Ribokinase-like | Ribokinase-like | Thiamin biosynthesis kinases | 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) | (Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ], | SCOPe (2.08) |
B | d1jxhb_ | Alpha and beta proteins (a/b) | Ribokinase-like | Ribokinase-like | Thiamin biosynthesis kinases | 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) | (Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Thiamin biosynthesis kinases | 8025056 | 4000762 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Ribokinase-like | 8037435 | 3001268 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | Ribokinase-like | 8037435 | 3001268 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | PfkB | e1jxhA1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Ribokinase-like (From Topology) | T: Ribokinase-like | F: PfkB | ECOD (1.6) |
B | PfkB | e1jxhB1 | A: a/b three-layered sandwiches | X: Rossmann-like | H: Ribokinase-like (From Topology) | T: Ribokinase-like | F: PfkB | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.1190.20 | Alpha Beta | 3-Layer(aba) Sandwich | UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase | Ribokinase | CATH (4.3.0) |
B | 3.40.1190.20 | Alpha Beta | 3-Layer(aba) Sandwich | UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase | Ribokinase | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF08543 | Phosphomethylpyrimidine kinase (Phos_pyr_kin) | Phosphomethylpyrimidine kinase | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR004399 | Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain | Domain | |
IPR029056 | Ribokinase-like | Homologous Superfamily | |
IPR013749 | Pyridoxamine kinase/Phosphomethylpyrimidine kinase | Domain |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
hydroxymethylpyrimidine kinase M-CSA #670 | 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. | Defined by 6 residues: LYS:A-198 [auth A-176]THR:A-230 [auth A-208]GLY:A-232 [auth A-210]THR:A-233 [auth A-211]GLY:A-234 [auth A-212]CYS:A-235 [auth A-213] | EC: 2.7.4.7 (PDB Primary Data) |