2FDC | pdb_00002fdc

Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D [auth B]	d2fdcb2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Nucleotide excision repair enzyme UvrB, C-terminal domain	([Bacillus] caldotenax ) [TaxId: 1395 ],	SCOPe (2.08)
D [auth B]	d2fdcb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Nucleotide excision repair enzyme UvrB, N-terminal domain	([Bacillus] caldotenax ) [TaxId: 1395 ],	SCOPe (2.08)
C [auth A]	d2fdca2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Nucleotide excision repair enzyme UvrB, C-terminal domain	([Bacillus] caldotenax ) [TaxId: 1395 ],	SCOPe (2.08)
C [auth A]	d2fdca1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Nucleotide excision repair enzyme UvrB, N-terminal domain	([Bacillus] caldotenax ) [TaxId: 1395 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8039981	3002019	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8039982	3002019	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8039981	3002019	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8039982	3002019	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)
D [auth B]	UB2H_1	e2fdcB3	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: UvrB interaction domain (From Topology)	T: UvrB interaction domain	F: UB2H_1	ECOD (1.6)
D [auth B]	Helicase_C_8	e2fdcB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_8	ECOD (1.6)
D [auth B]	ResIII	e2fdcB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ResIII	ECOD (1.6)
C [auth A]	Helicase_C_8	e2fdcA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_8	ECOD (1.6)
C [auth A]	ResIII	e2fdcA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ResIII	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
D [auth B]	3.30.2060.10	Alpha Beta	2-Layer Sandwich	Penicillin-binding protein 1b fold	Penicillin-binding protein 1b domain	CATH (4.2.0)
D [auth B]	6.10.140.240	Special	Helix non-globular	Helix Hairpins		CATH (4.2.0)
C [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	5'-D(PCPGPGPCPTPCPCPAPTPCPTPCPTPAPCPCPGPCPAPA)-3'	-	-	-
C [auth A], D [auth B]	UvrABC system protein B	excinuclease ABC activity DNA endonuclease activity endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding excinuclease ABC activity DNA endonuclease activity endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity 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 DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity	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 nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA 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 nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair SOS response	protein-containing complex catalytic complex excinuclease repair complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR024759	UvrB, YAD/RRR-motif-containing domain	Domain
C [auth A], D [auth B]	IPR006935	Helicase/UvrB, N-terminal	Domain
C [auth A], D [auth B]	IPR041471	UvrB, interaction domain	Domain
C [auth A], D [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
C [auth A], D [auth B]	IPR036876	UVR domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C [auth A], D [auth B]	IPR001943	UVR domain	Domain
C [auth A], D [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth A], D [auth B]	IPR004807	UvrABC system, subunit B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.