3KJX

Crystal structure of a transcriptional regulator, Lacl family protein from Silicibacter pomeroyi

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3kjxa1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
A	d3kjxa2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
B	d3kjxb1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
B	d3kjxb2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
C	d3kjxc1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
C	d3kjxc2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
D	d3kjxd1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)
D	d3kjxd2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	automated matches	automated matches	(Ruegeria pomeroyi ) [TaxId: 89184 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00356	e3kjxA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF00356	ECOD (1.6)
A	PF00532	e3kjxA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF00532	ECOD (1.6)
B	PF00356	e3kjxB3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF00356	ECOD (1.6)
B	PF00532	e3kjxB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF00532	ECOD (1.6)
C	PF00356	e3kjxC3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF00356	ECOD (1.6)
C	PF00532	e3kjxC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF00532	ECOD (1.6)
D	PF00356	e3kjxD3	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF00356	ECOD (1.6)
D	PF00532	e3kjxD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: PF00532	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
D	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
A, B, C, D	PF00356	Bacterial regulatory proteins, lacI family (LacI)	Bacterial regulatory proteins, lacI family	-	Domain
A, B, C, D	PF00532	Periplasmic binding proteins and sugar binding domain of LacI family (Peripla_BP_1)	Periplasmic binding proteins and sugar binding domain of LacI family	This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins ...	This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (Pfam:PF00356).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Transcriptional regulator, LacI family	DNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000843	LacI-type HTH domain	Domain
A, B, C, D	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A, B, C, D	IPR001761	Periplasmic binding protein/LacI sugar binding domain	Domain
A, B, C, D	IPR010982	Lambda repressor-like, DNA-binding 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.