3GPL

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	recD_rel	e3gplA4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: recD_rel	ECOD (1.6)
A	HHH_4	e3gplA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HHH_4	ECOD (1.6)
A	AAA_19	e3gplA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_19	ECOD (1.6)
A	UvrD_C_2	e3gplA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C_2	ECOD (1.6)
B	recD_rel	e3gplB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: recD_rel	ECOD (1.6)
B	HHH_4	e3gplB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HHH_4	ECOD (1.6)
B	AAA_19	e3gplB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_19	ECOD (1.6)
B	UvrD_C_2	e3gplB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C_2	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	2.30.30.940	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	1.10.10.2220	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		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	2.30.30.940	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13604	AAA domain (AAA_30)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.	Domain
A, B	PF13538	UvrD-like helicase C-terminal domain (UvrD_C_2)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
A, B	PF18335	ATP-dependent RecD-like DNA helicase SH3 domain (SH3_13)	ATP-dependent RecD-like DNA helicase SH3 domain	This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities ...	This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life [2]. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Exodeoxyribonuclease V, subunit RecD, putative	ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity 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 isomerase activity 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 single-stranded DNA helicase activity	nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
C [auth X], D [auth Y]	5'-D(TTPTPTPTPTPTPT)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050534	Coronaviruses polyprotein 1ab	Family
A, B	IPR041451	ATP-dependent RecD2 DNA helicase, SH3 domain	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR027785	UvrD-like helicase C-terminal domain	Domain
A, B	IPR006345	ATP-dependent RecD2 DNA helicase	Family
A, B	IPR029493	ATP-dependent RecD2 DNA helicase-like, helix-hairpin-helix domain	Domain
A, B	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.