5TRD | pdb_00005trd

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

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)
B	SCOP2B Superfamily	Riboflavin kinase-like	8003227	3000067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8017611	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8017611	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Riboflavin kinase-like	8003227	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)
B	CTP-dep_RFKase	e5trdB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: CTP-dep_RFKase	ECOD (1.6)
B	Fe_dep_repress_1	e5trdB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress_1	ECOD (1.6)
A	CTP-dep_RFKase	e5trdA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: CTP-dep_RFKase	ECOD (1.6)
A	Fe_dep_repress_1	e5trdA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	2.40.30.30	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	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	PF01982	Domain of unknown function DUF120 (CTP-dep_RFKase)	Domain of unknown function DUF120	This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally simil ...	This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels. Swiss:O28174 has this domain attached to Pfam:PF00325.	Domain
A, B	PF13545	Crp-like helix-turn-helix domain (HTH_Crp_2)	Crp-like helix-turn-helix domain	This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth H]	DNA (5'-D(PTPTPTPAPCPTPCPGPTPGPAPAPTPTPAPGPTPAP*A)-3')	-	-	-
C [auth G]	DNA (5'-D(APTPTPAPCPTPAPAPTPTPCPAPCPGPAPGPTPAP*A)-3')	-	-	-
A, B	Riboflavin kinase	DNA binding binding nucleic acid binding riboflavin kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding DNA binding binding nucleic acid binding riboflavin kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process ribose phosphate metabolic process nucleotide biosynthetic process flavin-containing compound metabolic process carbohydrate derivative metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process FMN metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process flavin-containing compound biosynthetic process FMN biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process ribonucleoside monophosphate biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process riboflavin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023465	Riboflavin kinase domain superfamily	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR012318	Crp-type HTH domain	Domain
A, B	IPR023602	Riboflavin kinase domain, CTP-dependent	Domain
A, B	IPR039063	Riboflavin kinase, CTP-dependent	Family

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.