1N08

Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1n08a_	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin kinase-like	ATP-dependent riboflavin kinase-like	Riboflavin kinase	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
B	d1n08b_	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin kinase-like	ATP-dependent riboflavin kinase-like	Riboflavin kinase	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ATP-dependent riboflavin kinase-like	8031550	4002669	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Riboflavin kinase-like	8043928	3000067	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Riboflavin kinase-like	8043928	3000067	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	Flavokinase	e1n08A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Flavokinase	ECOD (1.6)
B	Flavokinase	e1n08B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Flavokinase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.30	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	2.40.30.30	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01687	Riboflavin kinase (Flavokinase)	Riboflavin kinase	This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthet ...	This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism [1]. This domain is thought to have kinase activity [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	putative riboflavin kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding riboflavin kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding metal ion binding	organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process flavin-containing compound metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process riboflavin metabolic process vitamin metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process cellular process phosphorus metabolic process organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process flavin-containing compound metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process riboflavin metabolic process vitamin metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process cellular process phosphorus metabolic process ribose phosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process organic substance biosynthetic process FMN metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process flavin-containing compound biosynthetic process biosynthetic process FMN biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process ribonucleoside monophosphate biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015865	Riboflavin kinase domain, bacterial/eukaryotic	Domain
A, B	IPR023465	Riboflavin kinase domain superfamily	Homologous Superfamily
A, B	IPR023468	Riboflavin kinase	Family

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.