1O3Q

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1o3qa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	CAP C-terminal domain-like	Catabolite gene activator protein (CAP), C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d1o3qa2	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	cAMP-binding domain	Catabolite gene activator protein, N-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)
C [auth A]	SCOP2B Superfamily	cAMP-binding domain-like	8002726	3000084	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8002723	3000034	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)
C [auth A]	cNMP_binding	e1o3qA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: cNMP_binding	ECOD (1.6)
C [auth A]	Crp	e1o3qA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Crp	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
C [auth A]	ARO:3000518	CRP	CRP is a global regulator that represses MdtEF multidrug efflux pump expression.	CARD (3.2.9)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
C [auth A]	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic, fluoroquinolone antibiotic, penam	antibiotic efflux	CARD (3.2.9)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF13545	Crp-like helix-turn-helix domain (HTH_Crp_2)	Crp-like helix-turn-helix domain	This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.	Domain
C [auth A]	PF00027	Cyclic nucleotide-binding domain (cNMP_binding)	Cyclic nucleotide-binding domain	This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	5'-D(APAPAPAPAPTPGPTPGPAP*T)-3'	-	-	-
B [auth C]	5'-D(CPTPAPGPAPTPCPAPCPAPTPTPTPTP*T)-3'	-	-	-
C [auth A]	CATABOLITE GENE ACTIVATOR PROTEIN	binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA secondary structure binding DNA binding nucleic acid binding minor groove of adenine-thymine-rich DNA binding DNA binding, bending transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding identical protein binding protein binding	cellular response to stimulus regulation of cellular process response to stimulus negative regulation of biological process negative regulation of nitrogen compound metabolic process carbon catabolite regulation of transcription negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process cell communication nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process cellular response to stimulus regulation of cellular process response to stimulus negative regulation of biological process negative regulation of nitrogen compound metabolic process carbon catabolite regulation of transcription negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process cell communication nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process response to external stimulus catabolite repression negative regulation of cellular biosynthetic process carbon catabolite repression organic cyclic compound metabolic process regulation of gene expression cellular response to nutrient levels biosynthetic process aromatic compound biosynthetic process negative regulation of macromolecule biosynthetic process response to chemical organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to extracellular stimulus response to nutrient levels cellular biosynthetic process RNA metabolic process RNA biosynthetic process carbon catabolite repression of transcription nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process cellular response to external stimulus regulation of biosynthetic process biological regulation response to nutrient regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process cellular response to chemical stimulus negative regulation of biosynthetic process cellular process cellular response to nutrient cellular response to extracellular stimulus cellular aromatic compound metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of nitrogen compound metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR000595	Cyclic nucleotide-binding domain	Domain
C [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR012318	Crp-type HTH domain	Domain
C [auth A]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
C [auth A]	IPR018488	Cyclic nucleotide-binding, conserved site	Conserved Site
C [auth A]	IPR018335	Transcription regulator HTH, Crp-type, conserved site	Conserved Site
C [auth A]	IPR018490	Cyclic nucleotide-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.