Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: PrpR DNA-binding transcriptional dual regulator



Gene: prpR Accession Numbers: G6195 (EcoCyc), b0330, ECK0328

Synonyms: yahP

Regulation Summary Diagram: ?

Component of: PrpR-2-methylcitrate DNA-binding transcriptional dual regulator (summary available)

Locations: cytosol

Map Position: [346,081 <- 347,667] (7.46 centisomes)
Length: 1587 bp / 528 aa

Molecular Weight of Polypeptide: 58.649 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001133 , DIP:DIP-10582N , EchoBASE:EB3369 , EcoGene:EG13600 , EcoliWiki:b0330 , ModBase:P77743 , OU-Microarray:b0330 , PortEco:prpR , PR:PRO_000023610 , Pride:P77743 , Protein Model Portal:P77743 , RefSeq:NP_414864 , RegulonDB:G6195 , SMR:P77743 , String:511145.b0330 , Swiss-Model:P77743 , UniProt:P77743

Relationship Links: InterPro:IN-FAMILY:IPR002078 , InterPro:IN-FAMILY:IPR002197 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR010524 , InterPro:IN-FAMILY:IPR012704 , InterPro:IN-FAMILY:IPR025943 , InterPro:IN-FAMILY:IPR025944 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2PJU , Pfam:IN-FAMILY:PF00158 , Pfam:IN-FAMILY:PF02954 , Pfam:IN-FAMILY:PF06506 , Prosite:IN-FAMILY:PS00675 , Prosite:IN-FAMILY:PS00676 , Prosite:IN-FAMILY:PS00688 , Prosite:IN-FAMILY:PS50045 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 105 (10 members)

In Reactions of unknown directionality:

Not in pathways:
PrpR + (2S,3S)-2-methylcitrate = PrpR DNA-binding transcriptional dual regulator

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Lee05]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Lee05]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0019629 - propionate catabolic process, 2-methylcitrate cycle Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment [Lee05]
GO:0000156 - phosphorelay response regulator activity Inferred by computational analysis [GOA01a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008134 - transcription factor binding Inferred by computational analysis [GOA01a]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization fatty acids
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Essentiality data for prpR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: PrpR-2-methylcitrate DNA-binding transcriptional dual regulator

Synonyms: B0330, YahP, PrpR

Subunit composition of PrpR-2-methylcitrate DNA-binding transcriptional dual regulator = [PrpR][(2S,3S)-2-methylcitrate]
         PrpR DNA-binding transcriptional dual regulator = PrpR

Summary:
The "Propionate Regulator," PrpR, is a transcription factor that controls expression of genes involved in catabolism of propionate [Lee05]. It is negatively autoregulated, sensitive to catabolite control, and coordinately activates transcription of a divergent operon related to propionate catabolism [Lee05]. Synthesis of this operon is induced when E. coli is grown in the absence of glucose or glycerol.

PrpR belongs to the NtrC family of activators, which interact directly with the RpoN RNA polymerase [Merrick93]. PrpR is a σ54-dependent activator and belongs to the AAA+ superfamily of mechano-chemical ATPases. It consists of three domains, an amino-terminal domain involved in effector recognition, a catalytic domain, and a carboxy-terminal DNA-binding domain [Palacios04]. This regulator binds to a palindromic sequence (5'-GTTTCAT-10n-ATGAAAC-3') that overlaps prpRp [Lee05].

Sequence Length: 528 AAs

Relationship Links: Pfam:IN-FAMILY:PF06506

In Reactions of unknown directionality:

Not in pathways:
PrpR + (2S,3S)-2-methylcitrate = PrpR DNA-binding transcriptional dual regulator

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization fatty acids
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 24 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: GTTTCAtTnaAcgttTnAtGaAAc

Regulated Transcription Units (2 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 218 -> 461
[UniProt09]
UniProt: Sigma-54 factor interaction;
Nucleotide-Phosphate-Binding-Region 318 -> 327
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;
DNA-Binding-Region 508 -> 527
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lee05: Lee SK, Newman JD, Keasling JD (2005). "Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein." J Bacteriol 187(8);2793-800. PMID: 15805526

Merrick93: Merrick MJ (1993). "In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N)." Mol Microbiol 10(5);903-9. PMID: 7934866

Palacios04: Palacios S, Escalante-Semerena JC (2004). "2-Methylcitrate-dependent activation of the propionate catabolic operon (prpBCDE) of Salmonella enterica by the PrpR protein." Microbiology 150(Pt 11);3877-87. PMID: 15528672

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Hawley83: Hawley DK, McClure WR (1983). "Compilation and analysis of Escherichia coli promoter DNA sequences." Nucleic Acids Res 11(8);2237-55. PMID: 6344016

Ishida09: Ishida Y, Kori A, Ishihama A (2009). "Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon." J Bacteriol 191(19);6136-44. PMID: 19633077

Yang12: Yang C, Huang TW, Wen SY, Chang CY, Tsai SF, Wu WF, Chang CH (2012). "Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli." PLoS One 7(10);e47314. PMID: 23071782


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, biocyc14.