8C7S

Transcriptional pleiotropic repressor CodY from Staphylococcus aureus in complex with Ile, GTP, and a 30-bp DNA fragment encompassing two overlapping binding sites

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	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
C [auth A], D [auth B]	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 [auth M]	DNA (30-MER)	-	-	-
C [auth A], D [auth B]	Global transcriptional regulator CodY (Fragment)	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity 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 DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity 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	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
B [auth N]	DNA (30-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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