1RTY | pdb_00001rty

Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128

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	d1rtya_	All alpha proteins	Ferritin-like	Cobalamin adenosyltransferase-like	Cobalamin adenosyltransferase	Putative ATP-binding cobalamin adenosyltransferase YvqK	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1rtyb_	All alpha proteins	Ferritin-like	Cobalamin adenosyltransferase-like	Cobalamin adenosyltransferase	Putative ATP-binding cobalamin adenosyltransferase YvqK	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1rtyc_	All alpha proteins	Ferritin-like	Cobalamin adenosyltransferase-like	Cobalamin adenosyltransferase	Putative ATP-binding cobalamin adenosyltransferase YvqK	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cobalamin adenosyltransferase	8028539	4003724	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cobalamin adenosyltransferase-like	8040918	3001354	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cobalamin adenosyltransferase-like	8040918	3001354	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cobalamin adenosyltransferase-like	8040918	3001354	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	Cob_adeno_trans	e1rtyA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Cobalamin adenosyltransferase (From Topology)	T: Cobalamin adenosyltransferase	F: Cob_adeno_trans	ECOD (1.6)
B	Cob_adeno_trans	e1rtyB1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Cobalamin adenosyltransferase (From Topology)	T: Cobalamin adenosyltransferase	F: Cob_adeno_trans	ECOD (1.6)
C	Cob_adeno_trans	e1rtyC1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Cobalamin adenosyltransferase (From Topology)	T: Cobalamin adenosyltransferase	F: Cob_adeno_trans	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1200.10	Mainly Alpha	Up-down Bundle	Hypothetical Protein Ta1238	Chain: A	CATH (4.3.0)
B	1.20.1200.10	Mainly Alpha	Up-down Bundle	Hypothetical Protein Ta1238	Chain: A	CATH (4.3.0)
C	1.20.1200.10	Mainly Alpha	Up-down Bundle	Hypothetical Protein Ta1238	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01923	Cobalamin adenosyltransferase (Cob_adeno_trans)	Cobalamin adenosyltransferase	Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion ...	Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation [1].The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	yvqk protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding corrinoid adenosyltransferase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process small molecule metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process small molecule metabolic process water-soluble vitamin metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR029499	Corrinoid adenosyltransferase, PduO-type	Family
A, B, C	IPR036451	Cobalamin adenosyltransferase-like superfamily	Homologous Superfamily
A, B, C	IPR016030	Cobalamin adenosyltransferase-like	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.