2B3Z

Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2b3za1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	RibD C-terminal domain-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2b3za2	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2b3zb1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	RibD C-terminal domain-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2b3zb2	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2b3zc1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	RibD C-terminal domain-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2b3zc2	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2b3zd1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	RibD C-terminal domain-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2b3zd2	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	Riboflavin biosynthesis protein RibD	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2b3zd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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	RibD C-terminal domain-like	8025226	4003207	SCOP2 (2022-06-29)
A	SCOP2 Family	Deoxycytidylate deaminase-like	8025228	4000564	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dihydrofolate reductase-like	8037605	3001255	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytidine deaminase-like	8037607	3001838	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dihydrofolate reductase-like	8037605	3001255	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dihydrofolate reductase-like	8037605	3001255	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Dihydrofolate reductase-like	8037605	3001255	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	dCMP_cyt_deam_1	e2b3zA2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
A	RibD_C	e2b3zA1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
B	dCMP_cyt_deam_1	e2b3zB2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
B	RibD_C	e2b3zB1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
C	dCMP_cyt_deam_1	e2b3zC2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
C	RibD_C	e2b3zC1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
D	dCMP_cyt_deam_1	e2b3zD2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
D	RibD_C	e2b3zD1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
C	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
C	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
D	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00383	Cytidine and deoxycytidylate deaminase zinc-binding region (dCMP_cyt_deam_1)	Cytidine and deoxycytidylate deaminase zinc-binding region	-	Domain
A, B, C, D	PF01872	RibD C-terminal domain (RibD_C)	RibD C-terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Riboflavin biosynthesis protein ribD	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines hydrolase activity catalytic activity deaminase activity diaminohydroxyphosphoribosylaminopyrimidine deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 5-amino-6-(5-phosphoribosylamino)uracil reductase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines hydrolase activity catalytic activity deaminase activity diaminohydroxyphosphoribosylaminopyrimidine deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 5-amino-6-(5-phosphoribosylamino)uracil reductase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process organic cyclic compound metabolic process flavin-containing compound biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process organic cyclic compound metabolic process flavin-containing compound biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process small molecule metabolic process cellular process water-soluble vitamin metabolic process riboflavin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR024072	Dihydrofolate reductase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR011549	Riboflavin-specific deaminase, C-terminal	Domain
A, B, C, D	IPR004794	Riboflavin biosynthesis protein RibD	Family
A, B, C, D	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D	IPR002734	Bacterial bifunctional deaminase-reductase, C-terminal	Domain
A, B, C, D	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A, B, C, D	IPR016193	Cytidine deaminase-like	Homologous Superfamily

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.