1VDD | pdb_00001vdd

Crystal structure of recombinational repair protein RecR

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)
D	d1vddd_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1vddc_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1vddb_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
A	d1vdda_	Multi-domain proteins (alpha and beta)	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	Recombination protein RecR	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	RecR N-terminal domain-like	8055731	3001909	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8041284	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Toprim domain-like	8055733	3000737	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecR N-terminal domain-like	8055731	3001909	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Toprim domain-like	8055733	3000737	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8041284	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8041284	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecR N-terminal domain-like	8055731	3001909	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Toprim domain-like	8055733	3000737	SCOP2B (2022-06-29)
A	SCOP2 Family	RecR zinc finger-like	8028905	4002927	SCOP2 (2022-06-29)
A	SCOP2 Family	RecR N-terminal domain-like	8055730	4007649	SCOP2 (2022-06-29)
A	SCOP2 Family	RecR C-terminal domain-like	8055732	4007650	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8041284	3000068	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecR N-terminal domain-like	8055731	3001909	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Toprim domain-like	8055733	3000737	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)
D	EB1	e1vddD4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: EB1	ECOD (v294.1)
C	Aminotran_5	e1vddC1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: Aminotran_5	ECOD (v294.1)
C	EB1	e1vddC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: EB1	ECOD (v294.1)
B	YozE_SAM_like	e1vddB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: YozE_SAM_like	ECOD (v294.1)
B	C1_1	e1vddB2	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
B	Aminotran_5	e1vddB3	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: Aminotran_5	ECOD (v294.1)
A	RecR_ZnF	e1vddA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: RecR_ZnF	ECOD (v294.1)
A	RecR_HhH	e1vddA1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: RecR_HhH	ECOD (v294.1)
A	Aminotran_5	e1vddA3	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: ARM repeat	T: ARM repeat	F: Aminotran_5	ECOD (v294.1)

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)
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)
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)
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)

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 domain (RecR_ZnF)	RecR, Cys4-zinc finger domain	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 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 zinc finger motif, which consists of four strictly conserved cysteine residues which coordinate a zinc ion. This motif is the most conserved domain in RecR proteins and plays a structural role stabilizing the 3D structure of the protein [3].	Domain
A, B, C, D	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

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 nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process DNA repair double-strand break repair	-

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, zinc finger domain	Domain
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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.