1R71

Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA

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)
L [auth D]	d1r71d_	All alpha proteins	DNA/RNA-binding 3-helical bundle	KorB DNA-binding domain-like	KorB DNA-binding domain-like	Transcriptional repressor protein KorB DNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth A]	d1r71a_	All alpha proteins	DNA/RNA-binding 3-helical bundle	KorB DNA-binding domain-like	KorB DNA-binding domain-like	Transcriptional repressor protein KorB DNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth B]	d1r71b_	All alpha proteins	DNA/RNA-binding 3-helical bundle	KorB DNA-binding domain-like	KorB DNA-binding domain-like	Transcriptional repressor protein KorB DNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth C]	d1r71c_	All alpha proteins	DNA/RNA-binding 3-helical bundle	KorB DNA-binding domain-like	KorB DNA-binding domain-like	Transcriptional repressor protein KorB DNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth D]	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
I [auth A]	SCOP2 Family	KorB DNA-binding domain-like	8026386	4002305	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2 (2022-06-29)
J [auth B]	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	KorB DNA-binding domain-like	8038765	3001083	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth D]	KorB_N	e1r71D1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KorB_N	ECOD (1.6)
L [auth D]	KorB_DNA_bind	e1r71D2	A: alpha arrays	X: KorB C-terminal domain-like	H: KorB C-terminal domain (From Topology)	T: KorB C-terminal domain	F: KorB_DNA_bind	ECOD (1.6)
I [auth A]	KorB_N	e1r71A2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KorB_N	ECOD (1.6)
I [auth A]	KorB_DNA_bind	e1r71A3	A: alpha arrays	X: KorB C-terminal domain-like	H: KorB C-terminal domain (From Topology)	T: KorB C-terminal domain	F: KorB_DNA_bind	ECOD (1.6)
J [auth B]	KorB_N	e1r71B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KorB_N	ECOD (1.6)
J [auth B]	KorB_DNA_bind	e1r71B2	A: alpha arrays	X: KorB C-terminal domain-like	H: KorB C-terminal domain (From Topology)	T: KorB C-terminal domain	F: KorB_DNA_bind	ECOD (1.6)
K [auth C]	KorB_N	e1r71C1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KorB_N	ECOD (1.6)
K [auth C]	KorB_DNA_bind	e1r71C2	A: alpha arrays	X: KorB C-terminal domain-like	H: KorB C-terminal domain (From Topology)	T: KorB C-terminal domain	F: KorB_DNA_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth D]	1.10.10.730	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	KorB DNA-binding domain	CATH (4.3.0)
L [auth D]	6.10.250.140	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
I [auth A]	1.10.10.730	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	KorB DNA-binding domain	CATH (4.3.0)
I [auth A]	6.10.250.140	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
J [auth B]	1.10.10.730	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	KorB DNA-binding domain	CATH (4.3.0)
J [auth B]	6.10.250.140	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
K [auth C]	1.10.10.730	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	KorB DNA-binding domain	CATH (4.3.0)
K [auth C]	6.10.250.140	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
I [auth A], J [auth B], K [auth C], L [auth D]	PF08535	KorB domain (KorB)	KorB domain	This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal ...	This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon [1]. This domain includes the DNA-binding HTH motif [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], D [auth J], E [auth G], H [auth K]	5'-D(AP(BRU)PTPTPTPAPGPCPGPGPCPTPAPAPAPAP*G)-3'	-	-	-
B [auth I], C [auth F], F [auth L], G [auth H]	5'-D(CP(BRU)PTPTPTPAPGPCPCPGPCPTPAPAPAPAP*(BRU))-3'	-	-	-
I [auth A], J [auth B], K [auth C], L [auth D]	Transcriptional repressor protein korB	DNA binding binding nucleic acid binding identical protein binding protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cell cycle chromosome segregation cell cycle process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth C], L [auth D]	IPR037048	KorB, C-terminal domain superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR042075	KorB DNA-binding domain	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR036086	ParB/Sulfiredoxin superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR050336	Chromosome-partitioning and nucleoid occlusion protein	Family
I [auth A], J [auth B], K [auth C], L [auth D]	IPR008988	Transcriptional repressor, C-terminal	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D]	IPR010575	KorB, C-terminal	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR013741	Repressor KorB domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR004437	ParB/RepB/Spo0J partition protein	Domain
I [auth A], J [auth B], K [auth C], L [auth D]	IPR003115	ParB/Sulfiredoxin	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.