3LOC | pdb_00003loc

Crystal structure of putative transcriptional regulator ycdc

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)
D	d3locd1	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	d3locd2	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	d3locc1	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	d3locc2	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	d3locb1	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	d3locb2	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)
A	d3loca1	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	d3loca2	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)
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)
C	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8056463	3000001	SCOP2B (2022-06-29)
A	SCOP2 Family	Tetracyclin repressor-like	8056462	4000333	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TetR C-terminal domain-like	8056464	3000086	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Homeodomain-like	8056463	3000001	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	RVP	e3locD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
D	DctP	e3locD2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: DctP	ECOD (v294.1)
C	RVP	e3locC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
C	DctP	e3locC2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: DctP	ECOD (v294.1)
B	RVP	e3locB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B	DctP	e3locB2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: DctP	ECOD (v294.1)
A	TetR_N	e3locA1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: TetR_N	ECOD (v294.1)
A	HemS	e3locA2	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F: HemS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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 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 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 positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
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	IPR050109	HTH-type, TetR-like transcriptional regulator	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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.