3VDP

Structure and biochemical studies of the recombination mediator protein RecR in RecFOR pathway

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d3vdpd_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
A	d3vdpa_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
B	d3vdpb_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)
C	d3vdpc_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Caldanaerobacter subterraneus subsp. tengcongensis MB4 ) [TaxId: 273068 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	HHH_1	e3vdpD2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_1	ECOD (1.6)
D	Toprim_4	e3vdpD3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_4	ECOD (1.6)
D	UNK_F_TYPE	e3vdpD1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: UNK_F_TYPE	ECOD (1.6)
A	HHH_1	e3vdpA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_1	ECOD (1.6)
A	Toprim_4	e3vdpA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_4	ECOD (1.6)
A	UNK_F_TYPE	e3vdpA3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: UNK_F_TYPE	ECOD (1.6)
B	HHH_1	e3vdpB3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_1	ECOD (1.6)
B	Toprim_4	e3vdpB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_4	ECOD (1.6)
B	UNK_F_TYPE	e3vdpB2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: UNK_F_TYPE	ECOD (1.6)
C	HHH_1	e3vdpC2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_1	ECOD (1.6)
C	Toprim_4	e3vdpC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: Toprim_4	ECOD (1.6)
C	UNK_F_TYPE	e3vdpC3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.8.420	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	3.30.60.80	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
D	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
D	6.10.250.240	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.8.420	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.30.60.80	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
A	6.10.250.240	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.10.8.420	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.60.80	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
B	6.10.250.240	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.10.8.420	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.30.60.80	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
C	6.10.250.240	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF21176	RecR, helix-hairpin-helix (RecR_HhH)	RecR, helix-hairpin-helix	-	Motif
A, B, C, D	PF21175	RecR, C-terminal (RecR_C)	RecR, C-terminal	The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair. It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA. RecR is a zinc metalloprotein consist ...	The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair. It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA. RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif (Pfam:PF02132) and a Toprim domain (Pfam:PF13662) and a C-terminal domain comprising a Walker B motif and a C-terminal helix [1,2]. This is the C-terminal domain of RecR, which has a divergent Walker B motif, suggesting a nucleotide binding site [1,2].	Domain
A, B, C, D	PF02132	RecR, Cys4-zinc finger motif (RecR_ZnF)	RecR, Cys4-zinc finger motif	-	Motif
A, B, C, D	PF13662	Toprim domain (Toprim_4)	Toprim domain	The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Recombination protein recR	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	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 DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023627	Recombination protein RecR	Homologous Superfamily
A, B, C, D	IPR006171	TOPRIM domain	Domain
A, B, C, D	IPR015967	Recombination protein RecR, conserved site	Conserved Site
A, B, C, D	IPR000093	DNA recombination protein RecR	Family
A, B, C, D	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, B, C, D	IPR034137	RecR, TOPRIM domain	Domain

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.