1WP9

Crystal structure of Pyrococcus furiosus Hef helicase domain

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	d1wp9a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d1wp9a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
B	d1wp9b2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
B	d1wp9b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
C	d1wp9c2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
C	d1wp9c1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
D	d1wp9d2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
D	d1wp9d1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
E	d1wp9e2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
E	d1wp9e1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
F	d1wp9f2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, C-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
F	d1wp9f1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	putative ATP-dependent RNA helicase PF2015, N-terminal domain	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Tandem AAA-ATPase domain	8020819	4000282	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8033199	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8033199	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8033199	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8033199	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8033199	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8033200	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8033199	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)
A	PRK13766	e1wp9A3	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
A	DEAD	e1wp9A1	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	ECOD (1.6)
A	Helicase_C_1	e1wp9A4	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_1	ECOD (1.6)
B	PRK13766	e1wp9B3	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
B	DEAD	e1wp9B2	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	ECOD (1.6)
B	Helicase_C_1	e1wp9B1	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_1	ECOD (1.6)
C	PRK13766	e1wp9C2	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
C	DEAD	e1wp9C3	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	ECOD (1.6)
C	Helicase_C_1	e1wp9C1	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_1	ECOD (1.6)
D	PRK13766	e1wp9D2	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
D	DEAD	e1wp9D1	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	ECOD (1.6)
D	Helicase_C_1	e1wp9D3	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_1	ECOD (1.6)
E	PRK13766	e1wp9E3	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
E	DEAD	e1wp9E2	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	ECOD (1.6)
E	Helicase_C_1	e1wp9E1	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_1	ECOD (1.6)
F	PRK13766	e1wp9F2	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: PRK13766	ECOD (1.6)
F	DEAD	e1wp9F1	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	ECOD (1.6)
F	Helicase_C_1	e1wp9F3	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_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.20.1320.20	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3	hef helicase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF21210	Putative ATP-dependent RNA helicase, helical bundle (RNA_helicase_helical)	Putative ATP-dependent RNA helicase, helical bundle	This domain is found in the putative ATP-dependent RNA helicase from Pyrococcus furiosus (PF2015) and similar archaeal proteins. PF2015 is a Hef helicase that processes flap- or fork-DNA structures. This protein shows an SF2 helicase domain in the N- ...	This domain is found in the putative ATP-dependent RNA helicase from Pyrococcus furiosus (PF2015) and similar archaeal proteins. PF2015 is a Hef helicase that processes flap- or fork-DNA structures. This protein shows an SF2 helicase domain in the N-terminal two-thirds and an XPF/Mus81-type nuclease domain in the C-terminal one-third. The SF2 helicase domain is organised into three structural subdomains. This entry represents the second of them, which is composed of six alpha-helices that are tightly assembled into a hydrophobic core. Its surface is positively charged, suggesting that it is a potential DNA binding region [1].	Domain
A, B, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	ATP-dependent RNA helicase, putative	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity cation binding metal ion binding identical protein binding protein binding	cellular response to stimulus response to stimulus cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress cellular response to stimulus response to stimulus cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process cellular response to stress DNA damage response response to stress nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR041663	DisA/LigA, helix-hairpin-helix motif	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR041755	Archaeal Hef helicase/nuclease, insert domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006166	ERCC4 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.