2PE5

Crystal Structure of the Lac Repressor bound to ONPG in repressed state

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 [auth A]	d2pe5a1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Lac repressor (LacR), N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth A]	d2pe5a2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Lac-repressor (lacR) core (C-terminal domain)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth B]	d2pe5b1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Lac repressor (LacR), N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth B]	d2pe5b2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Lac-repressor (lacR) core (C-terminal domain)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth C]	d2pe5c1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	GalR/LacI-like bacterial regulator	Lac repressor (LacR), N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth C]	d2pe5c2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Lac-repressor (lacR) core (C-terminal domain)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037209	3000119	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Type 1 solute binding protein-like	8037462	3000125	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037209	3000119	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Type 1 solute binding protein-like	8037462	3000125	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8037209	3000119	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Type 1 solute binding protein-like	8037462	3000125	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 [auth A]	LacI	e2pe5A3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
D [auth A]	Peripla_BP_3	e2pe5A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
D [auth A]	Peripla_BP_1_1st_1	e2pe5A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
E [auth B]	LacI	e2pe5B3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
E [auth B]	Peripla_BP_3	e2pe5B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
E [auth B]	Peripla_BP_1_1st_1	e2pe5B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)
F [auth C]	LacI	e2pe5C3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: LacI	ECOD (1.6)
F [auth C]	Peripla_BP_3	e2pe5C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_3	ECOD (1.6)
F [auth C]	Peripla_BP_1_1st_1	e2pe5C2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_1_1st_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
D [auth A]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E [auth B]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F [auth C]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
F [auth C]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C]	PF13377	Periplasmic binding protein-like domain (Peripla_BP_3)	Periplasmic binding protein-like domain	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule liga ...	This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
D [auth A], E [auth B], F [auth C]	PF00356	Bacterial regulatory proteins, lacI family (LacI)	Bacterial regulatory proteins, lacI family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth A], E [auth B], F [auth C]	Lactose operon repressor	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 cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity identical protein binding protein binding 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 cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity identical protein binding protein binding DNA-binding transcription repressor 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth D], B [auth E], C [auth F]	DNA (5'-D(DAPDAPDTPDTPDGPDTPDGPDAPDGPDCPDGPDCPDTPDCPDAPDCPDAPDAPDTPDT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C]	IPR046335	Transcriptional regulator LacI/GalR-like, sensor domain	Domain
D [auth A], E [auth B], F [auth C]	IPR000843	LacI-type HTH domain	Domain
D [auth A], E [auth B], F [auth C]	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR010982	Lambda repressor-like, DNA-binding 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.