1S4M

Crystal structure of flavin binding to FAD synthetase from Thermotoga maritina

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	d1s4ma1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin kinase-like	ATP-dependent riboflavin kinase-like	Riboflavin kinase domain of bifunctional FAD synthetase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1s4ma2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Adenylyltransferase	FMN adenylyltransferase domain of bifunctional FAD synthetase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1s4mb1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin kinase-like	ATP-dependent riboflavin kinase-like	Riboflavin kinase domain of bifunctional FAD synthetase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1s4mb2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Adenylyltransferase	FMN adenylyltransferase domain of bifunctional FAD synthetase	(Thermotoga maritima ) [TaxId: 2336 ],	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	8029926	4002669	SCOP2 (2022-06-29)
A	SCOP2 Family	Adenylyltransferase	8029928	4003834	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Riboflavin kinase-like	8042305	3000067	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidylyl transferase	8042307	3001541	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleotidylyl transferase	8042307	3001541	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Riboflavin kinase-like	8042305	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	e1s4mA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Flavokinase	ECOD (1.6)
A	FAD_syn	e1s4mA2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: FAD_syn	ECOD (1.6)
B	Flavokinase	e1s4mB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Flavokinase	ECOD (1.6)
B	FAD_syn	e1s4mB2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: FAD_syn	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	2.40.30.30	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	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	PF06574	FAD synthetase (FAD_syn)	FAD synthetase	-	Family
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 kinase/FMN adenylyltransferase	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 cation binding metal ion binding	flavin-containing compound metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process riboflavin metabolic process vitamin metabolic process FAD metabolic process nucleotide biosynthetic process flavin adenine dinucleotide biosynthetic process flavin adenine dinucleotide metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process phosphorus metabolic process flavin-containing compound metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process riboflavin metabolic process vitamin metabolic process FAD metabolic process nucleotide biosynthetic process flavin adenine dinucleotide biosynthetic process flavin adenine dinucleotide metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process FAD biosynthetic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process flavin-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process 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	-

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 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.