5LOE | pdb_00005loe

Structure of full length Cody from Bacillus subtilis in complex with Ile

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Winged helix DNA-binding domain	8003364	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GAF domain-like	8003369	3000080	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAF domain-like	8003369	3000080	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8003364	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAF domain-like	8003369	3000080	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8003364	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8003364	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAF domain-like	8003369	3000080	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	HTH_CodY	e5loeD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_CodY	ECOD (1.6)
D	CodY	e5loeD2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: CodY	ECOD (1.6)
C	HTH_CodY	e5loeC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_CodY	ECOD (1.6)
C	CodY	e5loeC2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: CodY	ECOD (1.6)
B	HTH_CodY	e5loeB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_CodY	ECOD (1.6)
B	CodY	e5loeB2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: CodY	ECOD (1.6)
A	HTH_CodY	e5loeA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_CodY	ECOD (1.6)
A	CodY	e5loeA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: CodY	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08222	CodY helix-turn-helix domain (HTH_CodY)	CodY helix-turn-helix domain	This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nut ...	This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions [1]. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [2].	Domain
A, B, C, D	PF06018	CodY GAF-like domain (CodY)	CodY GAF-like domain	This domain is a GAF-like domain found at the N-terminus of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. This domain is involved in GTP binding and also branched chain amino acids (Matilla et. al., FEMS Microbiol ...	This domain is a GAF-like domain found at the N-terminus of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. This domain is involved in GTP binding and also branched chain amino acids (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions [1]. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GTP-sensing transcriptional pleiotropic repressor CodY	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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding 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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	protein-containing complex protein-DNA complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010312	Global transcriptional regulator CodY, N-terminal	Domain
A, B, C, D	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013198	Global transcriptional regulator CodY, C-terminal	Domain
A, B, C, D	IPR014154	Global transcriptional regulator CodY	Family
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix 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.