1RFY

Crystal Structure of Quorum-Sensing Antiactivator TraM

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	d1rfya_	All alpha proteins	Long alpha-hairpin	Transcriptional repressor TraM	Transcriptional repressor TraM	Transcriptional repressor TraM	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
B	d1rfyb_	All alpha proteins	Long alpha-hairpin	Transcriptional repressor TraM	Transcriptional repressor TraM	Transcriptional repressor TraM	(Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Transcriptional repressor TraM	8029863	4002233	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tram-like	8042242	3000130	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Tram-like	8042242	3000130	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	Prok-TraM	e1rfyA1	A: alpha bundles	X: Long alpha-hairpin	H: Transcriptional repressor TraM (From Topology)	T: Transcriptional repressor TraM	F: Prok-TraM	ECOD (1.6)
B	Prok-TraM	e1rfyB1	A: alpha bundles	X: Long alpha-hairpin	H: Transcriptional repressor TraM (From Topology)	T: Transcriptional repressor TraM	F: Prok-TraM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.160	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	HR1 repeat	CATH (4.3.0)
B	1.10.287.160	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	HR1 repeat	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09228	Prokaryotic Transcriptional repressor TraM (Prok-TraM)	Prokaryotic Transcriptional repressor TraM	Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regu ...	Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Transcriptional repressor traM	-	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036336	Transcriptional repressor TraM superfamily	Homologous Superfamily
A, B	IPR015309	Transcriptional repressor TraM	Family

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.