2HYF

The Structure of apo-MntR from Bacillus subtilis, selenomethionine derivative

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2hyfa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2hyfa2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2hyfd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2hyfd2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2hyfb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2hyfb2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2hyfc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Iron-dependent repressor protein	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2hyfc2	All alpha proteins	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Iron-dependent repressor protein, dimerization domain	Manganese transport regulator MntR	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8058120	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DtxR dimerization domain-like	8058121	3000063	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DtxR dimerization domain-like	8058121	3000063	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8058120	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8058120	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DtxR dimerization domain-like	8058121	3000063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DtxR dimerization domain-like	8058121	3000063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8058120	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)
A	Fe_dep_repress	e2hyfA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
A	Fe_dep_repr_C	e2hyfA2	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	Fe_dep_repress	e2hyfD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
D	Fe_dep_repr_C	e2hyfD2	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)
B	Fe_dep_repress	e2hyfB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
B	Fe_dep_repr_C	e2hyfB2	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)
C	Fe_dep_repress	e2hyfC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Fe_dep_repress	ECOD (1.6)
C	Fe_dep_repr_C	e2hyfC2	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)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	Transcriptional regulator mntR	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding transcription regulator activity DNA-binding transcription factor activity protein binding protein dimerization activity	inorganic ion homeostasis homeostatic process manganese ion homeostasis intracellular manganese ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR022897	HTH-type transcription regulator MntR	Family
A, B, C, D	IPR022689	Iron dependent repressor	Family
A, B, C, D	IPR001367	Iron dependent repressor, metal binding and dimerisation domain	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.