3IWZ | pdb_00003iwz

The c-di-GMP Responsive Global Regulator CLP Links Cell-Cell Signaling to Virulence Gene Expression in Xanthomonas campestris

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)
D	d3iwzd2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
D	d3iwzd1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
C	d3iwzc2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
C	d3iwzc1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
B	d3iwzb2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
B	d3iwzb1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
A	d3iwza2	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)
A	d3iwza1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Xanthomonas campestris pv. campestris ) [TaxId: 340 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	C1-set	e3iwzD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
C	C1-set	e3iwzC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
B	C1-set	e3iwzB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: C1-set	ECOD (v294.1)
A	Lectin_C	e3iwzA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: Lectin_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
D	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)
C	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C	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)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B	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)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00325	Bacterial regulatory proteins, crp family (Crp)	Bacterial regulatory proteins, crp family		Domain
A, B, C, D	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, B, C, D	Catabolite activation-like protein	DNA binding binding nucleic acid binding guanyl nucleotide binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding DNA binding binding nucleic acid binding guanyl nucleotide binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity transcription regulator activity DNA-binding transcription factor activity protein binding protein dimerization 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050397	Global Transcriptional Regulators in Environmental Response	Family
A, B, C, D	IPR000595	Cyclic nucleotide-binding domain	Domain
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
A, B, C, D	IPR012318	Crp-type HTH domain	Domain
A, B, C, D	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A, B, C, D	IPR018335	Transcription regulator HTH, Crp-type, conserved site	Conserved Site
A, B, C, D	IPR018490	Cyclic nucleotide-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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.