2P6R | pdb_00002p6r

Crystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA

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)
C [auth A]	d2p6ra1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	RecQ helicase DNA-binding domain-like	Hel308 helicase	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
C [auth A]	d2p6ra2	All alpha proteins	Sec63 N-terminal domain-like	Sec63 N-terminal domain-like	Achaeal helicase C-terminal domain	Hel308 helicase	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
C [auth A]	d2p6ra3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Hel308 helicase	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Tandem AAA-ATPase domain	8003046	4000282	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Family	SF2 helicase DNA-binding domain-like	8003047	4000204	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Family	Hel308 C-terminal domain-like	8003048	4000238	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	RecA-like P-loop NTPases	8017519	3002019	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Winged helix DNA-binding domain	8017517	3000034	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Brl domain-like	8003049	3000115	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Helix-hairpin-helix tandem	8004406	3000163	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	RecA-like P-loop NTPases	8017520	3002019	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)
C [auth A]	PRK02362_1st	e2p6rA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PRK02362_1st	ECOD (1.6)
C [auth A]	HHH_5_1	e2p6rA2	A: alpha arrays	X: HhH/H2TH	H: SAM-like subdomain in Sec63-like proteins (From Topology)	T: SAM-like subdomain in Sec63-like proteins	F: HHH_5_1	ECOD (1.6)
C [auth A]	PRK02362_2nd	e2p6rA3	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: PRK02362_2nd	ECOD (1.6)
C [auth A]	DEAD_1	e2p6rA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
C [auth A]	Helicase_C_5	e2p6rA5	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_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth A]	1.10.3380.30	Mainly Alpha	Orthogonal Bundle	Sec63 N-terminal domain-like fold		CATH (4.3.0)
C [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF20470	Helix-turn-helix domain (HTH_61)	Helix-turn-helix domain	This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.	Domain
C [auth A]	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
C [auth A]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
C [auth A]	PF21280	Archaeal helicase, domain 4 (Helicase_dom4_arc)	Archaeal helicase, domain 4	This entry includes archaeal helicases from the helicase superfamily 2, and represents domain 4 described in [1,3]. This domain folds into a seven alpha-helix bundle structure and seems to be unique within this helicase family. The central helix acts ...	This entry includes archaeal helicases from the helicase superfamily 2, and represents domain 4 described in [1,3]. This domain folds into a seven alpha-helix bundle structure and seems to be unique within this helicase family. The central helix acts as a ratchet and mediates stacking interactions on base moieties of the DNA [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	25-MER	-	-	-
B [auth Y]	5'-D(CPTPAPGPAPGPAPCPTPAPTPCPGPAP*T)-3'	-	-	-
C [auth A]	afUHEL308 HELICASE	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 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 hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity 3'-5' DNA helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA macromolecular conformation isomerase 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 DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR050474	Helicase Hel308/SKI2-like	Family
C [auth A]	IPR022965	ATP-dependent DNA helicase Hel308	Family
C [auth A]	IPR001650	Helicase, C-terminal domain-like	Domain
C [auth A]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
C [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR046931	DNA polymerase theta-like, helix-turn-helix domain	Domain
C [auth A]	IPR048772	ATP-dependent DNA helicase Hel308-like, domain 4	Domain
C [auth A]	IPR011545	DEAD/DEAH-box helicase domain	Domain
C [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.