1FX7

CRYSTAL STRUCTURE OF THE IRON-DEPENDENT REGULATOR (IDER) FROM MYCOBACTERIUM TUBERCULOSIS

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)
A	d1fx7a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1fx7a2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1fx7a3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1fx7b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1fx7b2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1fx7b3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1fx7c1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1fx7c2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1fx7c3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1fx7d1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1fx7d2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent regulator	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d1fx7d3	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	FeoA-like	Iron-dependent regulator IdeR	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DtxR regulatory element-like	8003195	4000231	SCOP2 (2021-05-27)
A	SCOP2 Family	FeoA-like	8003196	4000199	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8017619	3000034	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	DtxR dimerization domain-like	8017622	3000063	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Transcriptional regulator domain	8017617	3000121	SCOP2 (2021-05-27)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8017619	3000034	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	DtxR dimerization domain-like	8017622	3000063	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Transcriptional regulator domain	8017617	3000121	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8017619	3000034	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	DtxR dimerization domain-like	8017622	3000063	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Transcriptional regulator domain	8017617	3000121	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8017619	3000034	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	Transcriptional regulator domain	8017617	3000121	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	DtxR dimerization domain-like	8017622	3000063	SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF18357	e1fx7A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18357	ECOD (1.6)
A	PF01325	e1fx7A2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF01325	ECOD (1.6)
A	PF02742	e1fx7A3	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: PF02742	ECOD (1.6)
B	PF18357	e1fx7B1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18357	ECOD (1.6)
B	PF01325	e1fx7B2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF01325	ECOD (1.6)
B	PF02742	e1fx7B3	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: PF02742	ECOD (1.6)
C	PF18357	e1fx7C1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18357	ECOD (1.6)
C	PF01325	e1fx7C2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF01325	ECOD (1.6)
C	PF02742	e1fx7C3	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: PF02742	ECOD (1.6)
D	PF18357	e1fx7D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18357	ECOD (1.6)
D	PF01325	e1fx7D2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF01325	ECOD (1.6)
D	PF02742	e1fx7D3	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: PF02742	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
A	2.30.30.90	Mainly Beta	Roll	SH3 type barrels.	Ferrous iron transport protein A (FeoA)	CATH (4.3.0)
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)
B	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
B	2.30.30.90	Mainly Beta	Roll	SH3 type barrels.	Ferrous iron transport protein A (FeoA)	CATH (4.3.0)
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)
C	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
C	2.30.30.90	Mainly Beta	Roll	SH3 type barrels.	Ferrous iron transport protein A (FeoA)	CATH (4.3.0)
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)
D	1.10.60.10	Mainly Alpha	Orthogonal Bundle	Diphtheria Toxin Repressor	domain 2	CATH (4.3.0)
D	2.30.30.90	Mainly Beta	Roll	SH3 type barrels.	Ferrous iron transport protein A (FeoA)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, 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
A, B, C, 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
A, B, C, 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, B, C, D	IRON-DEPENDENT REPRESSOR IDER	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding nickel cation binding iron ion binding ferrous iron binding manganese ion binding transcription regulator activity DNA-binding transcription factor activity DNA binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding nickel cation binding iron ion binding ferrous iron binding manganese ion binding transcription regulator activity DNA-binding transcription factor activity DNA binding organic cyclic compound binding nucleic acid binding cadmium ion binding zinc ion binding protein binding protein dimerization activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic 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 catechol-containing siderophore biosynthetic process organic hydroxy compound metabolic process catechol-containing compound metabolic process secondary metabolic process siderophore biosynthetic process peptide biosynthetic process secondary metabolite biosynthetic process siderophore metabolic process organic hydroxy compound biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process catechol-containing compound biosynthetic process nonribosomal peptide biosynthetic process peptide metabolic process response to oxidative stress response to stimulus response to stress	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036421	Iron dependent repressor, metal binding and dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR022687	DTXR-type HTH domain	Domain
A, B, C, D	IPR001367	Iron dependent repressor, metal binding and dimerisation domain	Domain
A, B, C, D	IPR022689	Iron dependent repressor	Family
A, B, C, D	IPR007167	Ferrous iron transporter FeoA-like domain	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR038157	Ferrous iron transporter, core domain	Homologous Superfamily
A, B, C, D	IPR008988	Transcriptional repressor, C-terminal	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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 R01GM133198.