2PQQ | pdb_00002pqq

Structural Genomics, the crystal structure of the N-terminal domain of a transcriptional regulator from Streptomyces coelicolor A3(2)

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	d2pqqd1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
D	d2pqqd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
C	d2pqqc1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
C	d2pqqc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
B	d2pqqb1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
B	d2pqqb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
A	d2pqqa1	All beta proteins	Double-stranded beta-helix	cAMP-binding domain-like	automated matches	automated matches	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
A	d2pqqa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	SCOPe (2.08)
A	d2pqqa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptomyces coelicolor A3(2) ) [TaxId: 100226 ],	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		e2pqqD2	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Cupin_2	F:	ECOD (20:10:01)
C		e2pqqC2	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Cupin_2	F:	ECOD (20:10:01)
B		e2pqqB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: DAO, NAD_binding_8	F:	ECOD (20:10:01)
A		e2pqqA1	A: Profilin-like	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: DUF1507	F:	ECOD (20:10:01)

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)
C	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	Putative transcriptional regulator	DNA binding binding nucleic acid binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding DNA binding binding nucleic acid binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding transcription regulator activity DNA-binding transcription factor activity	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 positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic 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	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.