2D5N | pdb_00002d5n

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2d5na1	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	d2d5na2	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	d2d5nb1	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	d2d5nb2	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	d2d5nc1	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	d2d5nc2	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	d2d5nd1	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	d2d5nd2	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	d2d5nd3	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	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dihydrofolate reductase-like	8037605	3001255	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dihydrofolate reductase-like	8037605	3001255	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	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	Dihydrofolate reductase-like	8037605	3001255	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8037607	3001838	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	e2d5nA2	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	e2d5nA1	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	e2d5nB2	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	e2d5nB1	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	e2d5nC2	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	e2d5nC1	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	e2d5nD2	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	e2d5nD1	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	The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial ...	The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial proteins Swiss:P95872. This family appears to be related to Pfam:PF00186.	Domain

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	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule 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 binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process riboflavin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050765	Riboflavin Biosynthesis HTP Reductase	Family
A, B, C, D	IPR016193	Cytidine deaminase-like	Homologous Superfamily
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

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.