2O9A | pdb_00002o9a

The crystal structure of the E.coli IclR C-terminal fragment in complex with pyruvate.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d2o9ad2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	IclR ligand-binding domain-like	Transcriptional regulator IclR, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2o9ad3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2o9ac2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	IclR ligand-binding domain-like	Transcriptional regulator IclR, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2o9ac4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2o9ac3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2o9ab2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	IclR ligand-binding domain-like	Transcriptional regulator IclR, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2o9ab3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2o9aa2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	IclR ligand-binding domain-like	Transcriptional regulator IclR, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2o9aa4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2o9aa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
D	SCOP2B Superfamily	GAF domain-like	8043426	3000080	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAF domain-like	8043426	3000080	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAF domain-like	8043426	3000080	SCOP2B (2022-06-29)
A	SCOP2 Family	IclR ligand-binding domain-like	8031048	4000191	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAF domain-like	8043426	3000080	SCOP2 (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		e2o9aD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
C		e2o9aC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
B		e2o9aB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: tRNA-synt_2	F:	ECOD (20:10:01)
A		e2o9aA1	A: Profilin-like	X: sensor domains	H: sensor domains	T: IclR	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
C	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
B	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
A	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01614	Bacterial transcriptional regulator IclR C-terminal (IclR_C)	Bacterial transcriptional regulator IclR C-terminal	This entry includes bacterial transcriptional regulators, such as glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family [1,2]. These proteins have a Helix-Turn-Helix motif at the N-terminus. Howe ...	This entry includes bacterial transcriptional regulators, such as glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family [1,2]. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this domain covers the C-terminal region that binds to regulatory substrates including Glyoxylate, allantoin/ate, indole, aromatic hydrocarbons, sugar acids, succinic semialdehyde, benzoate derivatives, ascorbic acid, glycerol-3-phosphate, glyceraldehyde-3-phosphate and pyruvate [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Acetate operon repressor	DNA binding binding nucleic acid 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 carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid 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	IPR050707	HTH-type Transcriptional Regulators in Metabolic Pathways	Family
A, B, C, D	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR005471	Transcription regulator IclR, N-terminal	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	IPR014757	Transcription regulator IclR, C-terminal	Domain

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.