3DPJ | pdb_00003dpj

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)
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)
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)
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)
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)
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)
A	FeoA	e3dpjA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: FeoA	ECOD (v294.1)
B	Lipocalin	e3dpjB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
C	Lipocalin	e3dpjC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
D	Lipocalin	e3dpjD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
E	Lipocalin	e3dpjE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
F	Lipocalin	e3dpjF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
G	Lipocalin	e3dpjG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)
H	Lipocalin	e3dpjH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Lipocalin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
D	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)
F	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 nucleic acid binding	-	-

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