2O3F

Structural Genomics, the crystal structure of the N-terminal domain of the putative transcriptional regulator ybbH 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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2o3fa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	RpiR-like	Putative transcriptional regulator YbbH	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2o3fb_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	RpiR-like	Putative transcriptional regulator YbbH	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2o3fc_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	RpiR-like	Putative transcriptional regulator YbbH	(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	RpiR-like	8002266	4000148	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Homeodomain-like	8002267	3000001	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8002267	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8002267	3000001	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	PF01418	e2o3fA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF01418	ECOD (1.6)
B	PF01418	e2o3fB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF01418	ECOD (1.6)
C	PF01418	e2o3fC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF01418	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01418	Helix-turn-helix domain, rpiR family (HTH_6)	Helix-turn-helix domain, rpiR family	This domain contains a helix-turn-helix motif [1]. The best characterised member of this family is Swiss:P39266. RpiR is a regulator of the expression of rpiB gene.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Putative HTH-type transcriptional regulator ybbH	DNA binding binding organic cyclic compound binding nucleic acid binding carbohydrate derivative binding transcription regulator activity DNA-binding transcription factor activity	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular 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 regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process carbohydrate derivative metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR046348	SIS domain superfamily	Homologous Superfamily
A, B, C	IPR035472	RpiR-like, SIS domain	Domain
A, B, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C	IPR047640	HTH-type transcriptional regulator RpiR-like	Family
A, B, C	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
A, B, C	IPR000281	Helix-turn-helix protein RpiR	Domain
A, B, C	IPR001347	SIS domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
A, B, C	MSE	Parent Component: MET RESID: AA0075

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.