4D2I

Crystal structure of the HerA hexameric DNA translocase from Sulfolobus solfataricus bound to AMP-PNP

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8047641	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ATP synthase alpha/beta N-terminal domain-like	8052654	3001034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TrwB/VirB4 insert domain-like	8056659	3002354	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8047641	3002019	SCOP2B (2022-06-29)
A	SCOP2 Family	VirB4-like	8049764	4004010	SCOP2 (2022-06-29)
A	SCOP2 Family	VirB4 insert domain-like	8091680	4007755	SCOP2 (2022-06-29)
A	SCOP2 Family	HAS barrel domain-like	8044779	4004128	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8047641	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TrwB/VirB4 insert domain-like	8056659	3002354	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ATP synthase alpha/beta N-terminal domain-like	8052654	3001034	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	HAS-barrel	e4d2iB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HAS-barrel	ECOD (1.6)
B	DUF853	e4d2iB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DUF853	ECOD (1.6)
A	HAS-barrel	e4d2iA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HAS-barrel	ECOD (1.6)
A	DUF853	e4d2iA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DUF853	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09378	HAS barrel domain (HAS-barrel)	HAS barrel domain	The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the f ...	The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family [1].	Domain
A, B	PF01935	Helicase HerA, central domain (DUF87)	Helicase HerA, central domain	This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequ ...	This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus [2]. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle [3]. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.	Domain
A, B	PF05872	Helicase HerA-like C-terminal (HerA_C)	Helicase HerA-like C-terminal	HerA is a DNA helicase able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential f ...	HerA is a DNA helicase able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus [2]. This entry represents the C-terminal domain of HerA which seems to be involved in the conversion of ATP hydrolysis into DNA translocation [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HERA	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 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 catalytic activity, acting on a nucleic acid helicase activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance 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
A, B	IPR018538	Helicase HerA, barrel domain	Domain
A, B	IPR002789	Helicase HerA, central domain	Domain
A, B	IPR033186	Helicase HerA-like C-terminal	Domain
A, B	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.