1C0W

CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN

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)
C [auth A]	d1c0wa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
C [auth A]	d1c0wa2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
C [auth A]	d1c0wa3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
D [auth B]	d1c0wb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
D [auth B]	d1c0wb2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
D [auth B]	d1c0wb3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
E [auth C]	d1c0wc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
E [auth C]	d1c0wc2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
E [auth C]	d1c0wc3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
F [auth D]	d1c0wd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
F [auth D]	d1c0wd2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
F [auth D]	d1c0wd3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Diphtheria toxin repressor (DtxR)	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003184	3000034	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	DtxR dimerization domain-like	8003186	3000063	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	DtxR dimerization domain-like	8003186	3000063	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Transcriptional regulator domain	8003191	3000121	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003184	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003184	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	DtxR dimerization domain-like	8003186	3000063	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	DtxR dimerization domain-like	8003186	3000063	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003184	3000034	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)
C [auth A]	FeoA_1	e1c0wA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: FeoA_1	ECOD (1.6)
C [auth A]	Fe_dep_repress	e1c0wA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
C [auth A]	Fe_dep_repr_C	e1c0wA3	A: alpha duplicates or obligate multimers	X: Iron-dependent repressor protein, dimerization domain (From Topology)	H: Iron-dependent repressor protein, dimerization domain (From Topology)	T: Iron-dependent repressor protein, dimerization domain	F: Fe_dep_repr_C	ECOD (1.6)
D [auth B]	FeoA_1	e1c0wB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: FeoA_1	ECOD (1.6)
D [auth B]	Fe_dep_repress	e1c0wB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
D [auth B]	Fe_dep_repr_C	e1c0wB3	A: alpha duplicates or obligate multimers	X: Iron-dependent repressor protein, dimerization domain (From Topology)	H: Iron-dependent repressor protein, dimerization domain (From Topology)	T: Iron-dependent repressor protein, dimerization domain	F: Fe_dep_repr_C	ECOD (1.6)
E [auth C]	FeoA_1	e1c0wC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: FeoA_1	ECOD (1.6)
E [auth C]	Fe_dep_repress	e1c0wC3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
E [auth C]	Fe_dep_repr_C	e1c0wC1	A: alpha duplicates or obligate multimers	X: Iron-dependent repressor protein, dimerization domain (From Topology)	H: Iron-dependent repressor protein, dimerization domain (From Topology)	T: Iron-dependent repressor protein, dimerization domain	F: Fe_dep_repr_C	ECOD (1.6)
F [auth D]	FeoA_1	e1c0wD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: FeoA_1	ECOD (1.6)
F [auth D]	Fe_dep_repress	e1c0wD2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
F [auth D]	Fe_dep_repr_C	e1c0wD3	A: alpha duplicates or obligate multimers	X: Iron-dependent repressor protein, dimerization domain (From Topology)	H: Iron-dependent repressor protein, dimerization domain (From Topology)	T: Iron-dependent repressor protein, dimerization domain	F: Fe_dep_repr_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth A]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
C [auth A]	6.10.140.1920	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth B]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
D [auth B]	2.30.30.90	Mainly Beta	Roll	SH3 type barrels.	Ferrous iron transport protein A (FeoA)	CATH (4.3.0)
E [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E [auth C]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
E [auth C]	6.10.140.1920	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
F [auth D]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F [auth D]	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
F [auth D]	6.10.140.1920	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B], E [auth C], F [auth D]	PF18357	Diphteria toxin repressor SH3 domain (DtxR)	Diphteria toxin repressor SH3 domain	This is an SH3 domain which can be found in diphtheria toxin repressor (DtxR) proteins. DtxR) from Corynebacterium diphtheriae regulates the expression of the gene on corynebacteriophages that encodes diphtheria toxin (DT). Other genes regulated by D ...	This is an SH3 domain which can be found in diphtheria toxin repressor (DtxR) proteins. DtxR) from Corynebacterium diphtheriae regulates the expression of the gene on corynebacteriophages that encodes diphtheria toxin (DT). Other genes regulated by DtxR include those that encode proteins involved in siderophore-mediated iron uptake [1].	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	PF02742	Iron dependent repressor, metal binding and dimerisation domain (Fe_dep_repr_C)	Iron dependent repressor, metal binding and dimerisation domain	This family includes the Diphtheria toxin repressor [1]. It acts as an iron-binding repressor of diphtheria toxin gene expression and may serve as a global regulator of gene expression. DTXR comprises an N-terminal DNA-binding domain, an interface do ...	This family includes the Diphtheria toxin repressor [1]. It acts as an iron-binding repressor of diphtheria toxin gene expression and may serve as a global regulator of gene expression. DTXR comprises an N-terminal DNA-binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible C-terminal domain. The second domain is responsible for dimerization and metal binding. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [2]. This domain can also bind Cd(II), Ca(II) and Cu(II) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	PF01325	Iron dependent repressor, N-terminal DNA binding domain (Fe_dep_repress)	Iron dependent repressor, N-terminal DNA binding domain	This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E]	DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPCPCPTPAPCPCPCPTPAPAP*T)-3')	-	-	-
B [auth F]	DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPGPCPTPAPCPCPCPTPAPAP*T)-3')	-	-	-
C [auth A], D [auth B], E [auth C], F [auth D]	DIPHTHERIA TOXIN REPRESSOR	SH3 domain binding protein binding binding protein domain specific binding DNA binding nucleic acid binding cation binding transition metal ion binding ion binding metal ion binding small molecule binding transcription regulator activity DNA-binding transcription factor activity protein dimerization activity SH3 domain binding protein binding binding protein domain specific binding DNA binding nucleic acid binding cation binding transition metal ion binding ion binding metal ion binding small molecule binding transcription regulator activity DNA-binding transcription factor activity protein dimerization activity identical 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B], E [auth C], F [auth D]	IPR036421	Iron dependent repressor, metal binding and dimerisation domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR022687	DTXR-type HTH domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR022689	Iron dependent repressor	Family
C [auth A], D [auth B], E [auth C], F [auth D]	IPR001367	Iron dependent repressor, metal binding and dimerisation domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR007167	Ferrous iron transporter FeoA-like domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR038157	Ferrous iron transporter, core domain	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR050536	DtxR/MntR Metal-Dependent Regulators	Family
C [auth A], D [auth B], E [auth C], F [auth D]	IPR008988	Transcriptional repressor, C-terminal	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR040767	Diphteria toxin repressor/Iron-dependent repressor IdeR, SH3 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.