1UB0

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ub0a_	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)	(Thermus thermophilus ) [TaxId: 274 ],	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	8022509	4000762	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8034889	3001268	SCOP2 (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	e1ub0A1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08543	Phosphomethylpyrimidine kinase (Phos_pyr_kin)	Phosphomethylpyrimidine kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phosphomethylpyrimidine Kinase	phosphomethylpyrimidine kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process organic substance metabolic process thiamine biosynthetic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process organic substance metabolic process thiamine biosynthetic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic process water-soluble vitamin metabolic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular metabolic process vitamin metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process metabolic process cellular process thiamine-containing compound biosynthetic process primary alcohol metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004399	Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain	Domain
A	IPR001763	Rhodanese-like domain	Domain
A	IPR029056	Ribokinase-like	Homologous Superfamily
A	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.