8BPR | pdb_00008bpr

Complex of RecF-RecO-RecR-DNA from Thermus thermophilus (low resolution reconstruction).

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	F_UNCLASSIFIED	e8bprA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8bprB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8bprC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8bprD2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8bprD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e8bprD3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8bprE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8bprE2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8bprE3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8bprF3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8bprF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8bprF2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8bprG1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8bprG2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: F_UNCLASSIFIED	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 (utative)
E	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (utative)
F	1.10.8.420	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
G	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D, E, F	PF21176	RecR, helix-hairpin-helix (RecR_HhH)	RecR, helix-hairpin-helix	-	Motif
C, D, E, F	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
C, D, E, F	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
C, D, E, F	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
G	PF02565	Recombination protein O C terminal (RecO_C)	Recombination protein O C terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA replication and repair protein RecF	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding single-stranded DNA binding nucleic acid binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair SOS response nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm
C, D, E, F	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 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 metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination	-
G	DNA repair protein RecO	-	cellular response to stimulus double-strand break repair response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus double-strand break repair response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination	intracellular organelle bacterial nucleoid cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle nucleoid
H [auth X]	Oligo1	-	-	-
I [auth Y]	Oligo2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR042174	DNA-binding RecF, domain 2	Homologous Superfamily
A, B	IPR001238	DNA-binding, RecF	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D, E, F	IPR023627	Recombination protein RecR	Homologous Superfamily
C, D, E, F	IPR006171	TOPRIM domain	Domain
C, D, E, F	IPR015967	Recombination protein RecR, zinc finger domain	Domain
C, D, E, F	IPR000093	DNA recombination protein RecR	Family
C, D, E, F	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
C, D, E, F	IPR034137	RecR, TOPRIM domain	Domain
G	IPR022572	DNA replication/recombination mediator RecO, N-terminal	Domain
G	IPR042242	Recombination protein O, C-terminal	Homologous Superfamily
G	IPR037278	ARFGAP/RecO-like zinc finger	Homologous Superfamily
G	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G	IPR003717	Recombination protein O, RecO	Family

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.