5A8A

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Riboflavin kinase-like	8067083	3000067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Riboflavin kinase-like	8067083	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	e5a8aA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Flavokinase	ECOD (1.6)
B	Flavokinase	e5a8aB1	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	RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF	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 adenylyltransferase activity FMN adenylyltransferase activity nucleotidyltransferase activity	FAD metabolic process flavin-containing compound metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process flavin adenine dinucleotide biosynthetic process flavin adenine dinucleotide metabolic process nucleobase-containing compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process FAD metabolic process flavin-containing compound metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process flavin adenine dinucleotide biosynthetic process flavin adenine dinucleotide metabolic process nucleobase-containing compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process FAD biosynthetic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process organic cyclic compound metabolic process flavin-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process phosphorylation ribose phosphate metabolic process carbohydrate derivative metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process FMN metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process carbohydrate derivative biosynthetic process nucleoside monophosphate biosynthetic process FMN biosynthetic process ribonucleoside monophosphate biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process water-soluble vitamin metabolic process riboflavin metabolic process	-

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	IPR002606	Riboflavin kinase, bacterial	Family
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR023468	Riboflavin kinase	Family
A, B	IPR015864	FAD synthetase	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.