1DNP

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1dnpb1	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	C-terminal domain of DNA photolyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dnpb2	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	DNA photolyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dnpa1	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	C-terminal domain of DNA photolyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dnpa2	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	DNA photolyase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cryptochrome/photolyase, N-terminal domain	8044213	3001644	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cryptochrome/photolyase FAD-binding domain	8038338	3000930	SCOP2B (2022-06-29)
A	SCOP2 Family	Cryptochrome/photolyase FAD-binding domain	8025959	4001154	SCOP2 (2022-06-29)
A	SCOP2 Family	Cryptochrome/photolyase, N-terminal domain	8031835	4003847	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cryptochrome/photolyase FAD-binding domain	8038338	3000930	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cryptochrome/photolyase, N-terminal domain	8044213	3001644	SCOP2 (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	FAD_binding_7	e1dnpB1	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
B	DNA_photolyase	e1dnpB2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
A	FAD_binding_7	e1dnpA1	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
A	DNA_photolyase	e1dnpA2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A, B	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA PHOTOLYASE	DNA binding binding organic cyclic compound binding nucleic acid binding DNA photolyase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid deoxyribodipyrimidine photo-lyase activity lyase activity catalytic activity carbon-carbon lyase activity FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA photolyase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid deoxyribodipyrimidine photo-lyase activity lyase activity catalytic activity carbon-carbon lyase activity FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding damaged DNA binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair DNA repair detection of light stimulus response to light stimulus phototransduction detection of external stimulus regulation of biological process regulation of cellular process signaling biological regulation detection of visible light response to external stimulus detection of abiotic stimulus cell communication detection of stimulus response to abiotic stimulus response to radiation signal transduction phototransduction, visible light	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A, B	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A, B	IPR018394	Cryptochrome/DNA photolyase class 1, conserved site, C-terminal	Conserved Site
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR006050	DNA photolyase, N-terminal	Domain
A, B	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	deoxyribodipyrimidine photo-lyase M-CSA #183	DNA is very sensitive to UV-radiation and other damaging agents. One result of UV radiation is the production of cyclobutane-type dimers formed from adjacent pyrimidine bases which block replication and thus have cytotoxic and mutagenic effects. Such damage is, however, effectively repaired by photolyases. Photoreactivation comprises several steps: damage recognition and binding of photolyase to DNA, photon absorption, interchromophoric energy transfer and electron transfer from the chromophore to the DNA. Two cofactors are required by the enzyme, the first, FAD, is essential for the light dependent repair process whilst the second (either 8-hydroxy-5-deazaflavin or 5,10-methenyltetrahydro-folic acid) acts as a light harvesting chromophore. The photolyases are divided into two groups according to their second cofactor.	Defined by 6 residues: GLU:A-274TRP:A-277TRP:A-306ASN:A-341TRP:A-359TRP:A-382 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.99.3 (PDB Primary Data) Search M-CSA Motif + EC 4.1.99.3

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.