2PJU | pdb_00002pju

Crystal structure of propionate catabolism operon regulatory protein prpR

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)
A	d2pjua1	Alpha and beta proteins (a/b)	Chelatase-like	PrpR receptor domain-like	PrpR receptor domain-like	Propionate catabolism operon regulatory protein PrpR	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2pjub_	Alpha and beta proteins (a/b)	Chelatase-like	PrpR receptor domain-like	PrpR receptor domain-like	Propionate catabolism operon regulatory protein PrpR	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2pjuc_	Alpha and beta proteins (a/b)	Chelatase-like	PrpR receptor domain-like	PrpR receptor domain-like	Propionate catabolism operon regulatory protein PrpR	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2pjud1	Alpha and beta proteins (a/b)	Chelatase-like	PrpR receptor domain-like	PrpR receptor domain-like	Propionate catabolism operon regulatory protein PrpR	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2pjud2	Artifacts	Tags	Tags	Tags	C-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)
A	SCOP2 Family	PrpR receptor domain-like	8023383	4002461	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PrpR receptor domain-like	8035763	3001278	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PrpR receptor domain-like	8035763	3001278	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PrpR receptor domain-like	8035763	3001278	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PrpR receptor domain-like	8035763	3001278	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)
A	PrpR_N	e2pjuA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: PrpR receptor domain-like	F: PrpR_N	ECOD (1.6)
B	PrpR_N	e2pjuB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: PrpR receptor domain-like	F: PrpR_N	ECOD (1.6)
C	PrpR_N	e2pjuC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: PrpR receptor domain-like	F: PrpR_N	ECOD (1.6)
D	PrpR_N	e2pjuD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: PrpR receptor domain-like	F: PrpR_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.2.0)
A	3.40.50.10660	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	PrpR receptor domain-like	CATH (4.2.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.2.0)
B	3.40.50.10660	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	PrpR receptor domain-like	CATH (4.2.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.2.0)
C	3.40.50.10660	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	PrpR receptor domain-like	CATH (4.2.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.2.0)
D	3.40.50.10660	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	PrpR receptor domain-like	CATH (4.2.0)
D	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06506	Propionate catabolism activator (PrpR_N)	Propionate catabolism activator	This domain is found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Propionate catabolism operon regulatory protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity molecular transducer activity phosphorelay response regulator 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 response to stimulus response to radiation response to abiotic stimulus fatty acid metabolic process short-chain fatty acid catabolic process lipid catabolic process catabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process fatty acid catabolic process propionate catabolic process propionate catabolic process, 2-methylcitrate cycle monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process lipid metabolic process propionate metabolic process	protein-containing complex protein-DNA complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR010524	Signal transduction response regulator, propionate catabolism activator, N-terminal	Domain
A, B, C, D	IPR002197	DNA binding HTH domain, Fis-type	Domain
A, B, C, D	IPR002078	RNA polymerase sigma factor 54 interaction domain	Domain
A, B, C, D	IPR025944	Sigma-54 interaction domain, conserved site	Conserved Site
A, B, C, D	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D	IPR012704	Signal transduction response regulator, propionate catabolism, transcriptional regulator PrpR	Family
A, B, C, D	IPR025943	Sigma-54 interaction domain, ATP-binding site 2	Binding Site
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.