3DPJ

The crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
F	SCOP2 Family	Tetracyclin repressor-like	8088734	4000333	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Homeodomain-like	8090196	3000001	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Homeodomain-like	8090196	3000001	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	TetR C-terminal domain-like	8090197	3000086	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Homeodomain-like	8090196	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)
D	TetR_N	e3dpjD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
D	TetR_C_13	e3dpjD2	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: TetR_C_13	ECOD (1.6)
F	TetR_N	e3dpjF1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
F	TetR_C_13	e3dpjF2	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: TetR_C_13	ECOD (1.6)
A	TetR_N	e3dpjA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
A	TetR_C_13	e3dpjA2	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: TetR_C_13	ECOD (1.6)
B	TetR_N	e3dpjB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
B	TetR_C_13	e3dpjB2	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: TetR_C_13	ECOD (1.6)
C	TetR_N	e3dpjC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
C	TetR_C_13	e3dpjC2	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: TetR_C_13	ECOD (1.6)
E	TetR_N	e3dpjE1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
E	TetR_C_13	e3dpjE2	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: TetR_C_13	ECOD (1.6)
G	TetR_N	e3dpjG1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
G	TetR_C_13	e3dpjG2	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: TetR_C_13	ECOD (1.6)
H	TetR_N	e3dpjH1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
H	TetR_C_13	e3dpjH2	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: TetR_C_13	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
F	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
A	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
B	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
C	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
E	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
G	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
H	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, E A, B, C, D, E, F, G, H	PF21993	Transcriptional regulator LmrA/YxaF-like, C-terminal domain (TetR_C_13_2)	Transcriptional regulator LmrA/YxaF-like, C-terminal domain	This entry represents the C-terminal domain found in a group of TetR transcription regulators, including YxaF (also known as T1414) [1] and LmrA from Bacillus subtilis, which are paralogous to each other [2]. LmrA and YxaF are repressors that bind sp ...	This entry represents the C-terminal domain found in a group of TetR transcription regulators, including YxaF (also known as T1414) [1] and LmrA from Bacillus subtilis, which are paralogous to each other [2]. LmrA and YxaF are repressors that bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon [2].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	Transcription regulator, TetR family	DNA binding binding organic cyclic compound binding nucleic acid binding	regulation of biosynthetic process regulation of biological process regulation of cellular process biosynthetic process biological regulation cellular process metabolic process regulation of metabolic process primary metabolic process regulation of primary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR054156	Transcriptional regulator LmrA/YxaF-like, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001647	DNA-binding HTH domain, TetR-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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.