1F9N | pdb_00001f9n

CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS

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	d1f9na1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1f9na2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1f9nb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1f9nb2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1f9nc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1f9nc2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1f9nd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1f9nd2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1f9ne1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1f9ne2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1f9nf1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	Arginine repressor (ArgR), N-terminal DNA-binding domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1f9nf2	Alpha and beta proteins (a+b)	DCoH-like	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	C-terminal domain of arginine repressor	(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	SCOP2 Family	ArgR-like	8058557	4000153	SCOP2 (2022-06-29)
A	SCOP2 Family	C-terminal domain of arginine repressor	8091642	4001468	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ArgR regulatory domain-like	8058559	3000096	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ArgR regulatory domain-like	8058559	3000096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ArgR regulatory domain-like	8058559	3000096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ArgR regulatory domain-like	8058559	3000096	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ArgR regulatory domain-like	8058559	3000096	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8058558	3000034	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ArgR regulatory domain-like	8058559	3000096	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	Arg_repressor	e1f9nA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
A	Arg_repressor_C	e1f9nA2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_C	ECOD (1.6)
B	Arg_repressor	e1f9nB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
B	Arg_repressor_C	e1f9nB2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_C	ECOD (1.6)
C	Arg_repressor	e1f9nC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
C	Arg_repressor_C	e1f9nC2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_C	ECOD (1.6)
D	Arg_repressor	e1f9nD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
D	Arg_repressor_C	e1f9nD2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_C	ECOD (1.6)
E	Arg_repressor	e1f9nE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
E	Arg_repressor_C	e1f9nE2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_C	ECOD (1.6)
F	Arg_repressor	e1f9nF1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Arg_repressor	ECOD (1.6)
F	Arg_repressor_C	e1f9nF2	A: a+b two layers	X: Glucose permease domain IIB-like	H: arginine repressor C terminal domain-related	T: C-terminal domain of arginine repressor	F: Arg_repressor_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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
E	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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
F	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	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01316	Arginine repressor, DNA binding domain (Arg_repressor)	Arginine repressor, DNA binding domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF02863	Arginine repressor, C-terminal domain (Arg_repressor_C)	Arginine repressor, C-terminal domain	This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization [1,2]. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.o ...	This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization [1,2]. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	ARGININE REPRESSOR/ACTIVATOR PROTEIN	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding organic acid binding ion binding anion binding amino acid binding carboxylic acid binding arginine binding small molecule binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process glutamine family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process glutamine family amino acid biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process arginine metabolic process small molecule metabolic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process alpha-amino acid biosynthetic process ornithine metabolic process arginine catabolic process to ornithine catabolic process glutamine family amino acid catabolic process arginine catabolic process organic acid catabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process amino acid catabolic process L-amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process regulation of cellular process regulation of arginine biosynthetic process regulation of amino acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of arginine metabolic process regulation of amino acid metabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of metabolic process regulation of glutamine family amino acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001669	Arginine repressor	Family
A, B, C, D, E A, B, C, D, E, F	IPR020899	Arginine repressor, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR020900	Arginine repressor, DNA-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036251	Arginine repressor, C-terminal 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 R01GM157729.