2PB9 | pdb_00002pb9

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 ThiN	This entry represents thiamine-phosphate synthase ThiN which condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) [1]. Vitamin B1 (th ...	This entry represents thiamine-phosphate synthase ThiN which condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) [1]. Vitamin B1 (thiamine pyrophosphate) is involved in several microbial metabolic functions. Thiamine biosynthesis is accomplished by joining two intermediate molecules that are synthesized separately, HMP-PP and HET-P. In the archaeon Natrialba magadii, ThiE and ThiN, are known to join HMP-PP ( hydroxymethylpyrimidine pyrophosphate) and HET-P (hydroxyethylthiazole phosphate) to generate thiamine phosphate. Whereas ThiE in Natrialba magadii is a mono-functional protein, ThiN exists as a C-terminal domain in a ThiDN fusion protein - examples of all three forms, from various prokaryotes, are found in this entry [1,2]. Another example is the transcriptional repressor ThiR from Haloferax volcanii (SwissProt:D4GSS2) which contains a ThiN domain but it is catalytically inactive as it lacks the conserved Met residue found in the extended alpha-helix near the active site His in ThiN [3]. Moreover, it was shown that thiamine biosynthesis in archaea is regulated by ThiR and not by a riboswitch [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Phosphomethylpyrimidine kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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	pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process vitamin metabolic process sulfur compound biosynthetic process thiamine biosynthetic process biosynthetic process alcohol biosynthetic process sulfur compound metabolic process metabolic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process vitamin metabolic process sulfur compound biosynthetic process thiamine biosynthetic process biosynthetic process alcohol biosynthetic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process primary 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-like	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.