4XK4

E. coli transcriptional regulator RUTR with dihydrouracil

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	d4xk4a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Tetracyclin repressor-like, N-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4xk4a2	All alpha proteins	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4xk4b1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Tetracyclin repressor-like, N-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4xk4b2	All alpha proteins	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4xk4c1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Tetracyclin repressor-like, N-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4xk4c2	All alpha proteins	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4xk4d1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Tetracyclin repressor-like, N-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4xk4d2	All alpha proteins	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Tetracyclin repressor-like, C-terminal domain	Hypothetical transcriptional regulator YcdC	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	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	PF00440	e4xk4A2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00440	ECOD (1.6)
A	PF08362	e4xk4A3	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: PF08362	ECOD (1.6)
B	PF00440	e4xk4B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00440	ECOD (1.6)
B	PF08362	e4xk4B2	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: PF08362	ECOD (1.6)
C	PF00440	e4xk4C2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00440	ECOD (1.6)
C	PF08362	e4xk4C1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: PF08362	ECOD (1.6)
D	PF00440	e4xk4D1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00440	ECOD (1.6)
D	PF08362	e4xk4D2	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: PF08362	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
A	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
B	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
B	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
C	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
C	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
D	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
D	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08362	YcdC-like protein, C-terminal region (TetR_C_3)	YcdC-like protein, C-terminal region	This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC (Swiss:P75899), a putative HTH-containing protein. This family features the C-terminal region of these sequences, whi ...	This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC (Swiss:P75899), a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix.	Domain
A, B, C, D	PF00440	Bacterial regulatory proteins, tetR family (TetR_N)	Bacterial regulatory proteins, tetR family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	HTH-type transcriptional regulator RutR	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	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 positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013573	Transcription regulator YcdC, C-terminal	Domain
A, B, C, D	IPR019915	Transcription regulator, pyrimidine utilisation, RutR	Family
A, B, C, D	IPR001647	DNA-binding HTH domain, TetR-type	Domain
A, B, C, D	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR009057	Homeobox-like 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.