3BWG

The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168

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	d3bwga1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	GntR-like transcriptional regulators	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d3bwga2	Alpha and beta proteins (a+b)	Chorismate lyase-like	Chorismate lyase-like	UTRA domain	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d3bwgb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	GntR-like transcriptional regulators	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d3bwgb2	Alpha and beta proteins (a+b)	Chorismate lyase-like	Chorismate lyase-like	UTRA domain	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d3bwgc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	GntR-like transcriptional regulators	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d3bwgc2	Alpha and beta proteins (a+b)	Chorismate lyase-like	Chorismate lyase-like	UTRA domain	Transcriptional regulator YydK	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Chorismate lyase-like	8002709	3000072	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8017598	3000034	SCOP2B (2022-06-29)
B	SCOP2 Family	GntR-like transcriptional regulators	8002705	4000155	SCOP2 (2022-06-29)
B	SCOP2 Family	UTRA domain	8002707	4000314	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Winged helix DNA-binding domain	8017598	3000034	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Chorismate lyase-like	8002709	3000072	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8017598	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Chorismate lyase-like	8002709	3000072	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	GntR	e3bwgA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: GntR	ECOD (1.6)
A	UTRA	e3bwgA2	A: a+b two layers	X: Chorismate lyase (From Topology)	H: Chorismate lyase (From Topology)	T: Chorismate lyase	F: UTRA	ECOD (1.6)
B	GntR	e3bwgB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: GntR	ECOD (1.6)
B	UTRA	e3bwgB2	A: a+b two layers	X: Chorismate lyase (From Topology)	H: Chorismate lyase (From Topology)	T: Chorismate lyase	F: UTRA	ECOD (1.6)
C	GntR	e3bwgC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: GntR	ECOD (1.6)
C	UTRA	e3bwgC2	A: a+b two layers	X: Chorismate lyase (From Topology)	H: Chorismate lyase (From Topology)	T: Chorismate lyase	F: UTRA	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	3.40.1410.10	Alpha Beta	3-Layer(aba) Sandwich	Chorismate lyase	Chorismate lyase-like	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	3.40.1410.10	Alpha Beta	3-Layer(aba) Sandwich	Chorismate lyase	Chorismate lyase-like	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	3.40.1410.10	Alpha Beta	3-Layer(aba) Sandwich	Chorismate lyase	Chorismate lyase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00392	Bacterial regulatory proteins, gntR family (GntR)	Bacterial regulatory proteins, gntR family	This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-fam ...	This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [1-2][4][5]. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships [3]. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor [5].	Domain
A, B, C	PF07702	UTRA domain (UTRA)	UTRA domain	The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to Pfam:PF04345 [1]. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules ...	The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to Pfam:PF04345 [1]. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules [1] sugar phosphates and urocanate, 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	Uncharacterized HTH-type transcriptional regulator yydK	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR050679	Bacterial HTH-type transcriptional regulator	Family
A, B, C	IPR011663	UbiC transcription regulator-associated	Domain
A, B, C	IPR028978	Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily	Homologous Superfamily
A, B, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C	IPR000524	Transcription regulator HTH, GntR	Domain
A, B, C	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 R01GM157729.