2OYN | pdb_00002oyn

Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120

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	d2oyna1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin kinase-like	CTP-dependent riboflavin kinase-like	CTP-dependent riboflavin kinase, Rfk	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
A	d2oyna2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Riboflavin kinase-like	8037441	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	CTP-dep_RFKase	e2oynA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: CTP-dep_RFKase	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Hypothetical protein MJ0056	cation binding magnesium ion binding ion binding binding metal ion 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 nucleoside phosphate binding nucleotide binding cation binding magnesium ion binding ion binding binding metal ion 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 nucleoside phosphate binding nucleotide binding heterocyclic compound binding	ribose phosphate metabolic process nucleotide biosynthetic process flavin-containing compound metabolic process carbohydrate derivative metabolic process nucleobase-containing compound 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 ribose phosphate metabolic process nucleotide biosynthetic process flavin-containing compound metabolic process carbohydrate derivative metabolic process nucleobase-containing compound 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 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 nucleoside phosphate biosynthetic process metabolic process cellular 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	IPR023465	Riboflavin kinase domain superfamily	Homologous Superfamily
A	IPR023470	Riboflavin kinase, archaeal	Family
A	IPR053397	Archaeal Riboflavin Kinase	Family
A	IPR023602	Riboflavin kinase domain, CTP-dependent	Domain
A	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.