2PB9

Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase

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)
B	d2pb9b_	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	Phosphomethylpyrimidine kinase C-terminal domain-like	Phosphomethylpyrimidine kinase	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
A	d2pb9a1	Alpha and beta proteins (a/b)	AraD/HMP-PK domain-like	AraD/HMP-PK domain-like	Phosphomethylpyrimidine kinase C-terminal domain-like	Phosphomethylpyrimidine kinase	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	AraD/HMP-PK domain-like	8035504	3001331	SCOP2B (2022-06-29)
A	SCOP2 Family	Phosphomethylpyrimidine kinase C-terminal domain-like	8023124	4002436	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	AraD/HMP-PK domain-like	8035504	3001331	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)
B	ThiP_synth	e2pb9B1	A: a+b three layers	X: AraD-like aldolase/epimerase (From Topology)	H: AraD-like aldolase/epimerase (From Topology)	T: AraD-like aldolase/epimerase	F: ThiP_synth	ECOD (1.6)
A	ThiP_synth	e2pb9A1	A: a+b three layers	X: AraD-like aldolase/epimerase (From Topology)	H: AraD-like aldolase/epimerase (From Topology)	T: AraD-like aldolase/epimerase	F: ThiP_synth	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)
A	3.40.225.10	Alpha Beta	3-Layer(aba) Sandwich	L-fuculose-1-phosphate Aldolase	Class II aldolase/adducin N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF10120	Thiamine-phosphate synthase ThiN (ThiN)	Thiamine-phosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphomethylpyrimidine kinase	phosphomethylpyrimidine kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups hydroxymethylpyrimidine kinase activity phosphotransferase activity, alcohol group as acceptor	phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic hydroxy compound metabolic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic hydroxy compound metabolic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process thiamine 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 water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process thiamine-containing compound biosynthetic process primary alcohol metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004399	Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain	Domain
A, B	IPR036409	Class II aldolase/adducin N-terminal domain superfamily	Homologous Superfamily
A, B	IPR019293	Thiamine-phosphate synthase ThiN	Domain
A, B	IPR029056	Ribokinase-like	Homologous Superfamily
A, B	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.