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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Protein: IdnR-5-ketogluconate DNA-binding transcriptional dual regulator



Gene: idnR Accession Numbers: G7891 (EcoCyc), b4264, ECK4257

Synonyms: gntS?, gntH, yjgS

Regulation Summary Diagram: ?

Subunit composition of IdnR-5-ketogluconate DNA-binding transcriptional dual regulator = [IdnR]
         IdnR transcriptional regulator = IdnR

Summary:
"l-idonate regulator," IdnR, is a transcription factor that regulates genes involved in l-idonate metabolism, which are organized in two coordinately regulated transcription units [Bausch98, Bausch04]. This regulator is positively autoregulated and co-regulates with CRP, a global transcriptional regulator; these regulators bind cooperatively to activate transcription of an operon related to transport and catabolism of l-idonate [Bausch04]. Synthesis of this operon is induced when Escherichia coli is grown on l-idonate/5KG in the absence of glucose and gluconate. In addition, this regulator represses transcription of genes related to gluconate metabolism [Bausch98].

In the presence of l-idonate, IdnR binds to 16-nucleotide-long DNA-target sites in the idnK/idnDOTR intergenic region to coordinately activate transcription of idnKp and idnDp [Bausch04].

IdnR exhibits a high similarity to GntR (53%) and belongs to the LacI/GalR family of transcriptional regulators [Rodionov00]. It is part of the idnDOTR operon, yet it can also be transcribed as an independent (idnR) transcription unit [Bausch04].

Gene Citations: [Tsunedomi03]

Locations: cytosol

Map Position: [4,488,164 <- 4,489,162] (96.73 centisomes)
Length: 999 bp / 332 aa

Molecular Weight of Polypeptide: 37.567 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013966 , EchoBASE:EB2427 , EcoGene:EG12538 , EcoliWiki:b4264 , ModBase:P39343 , OU-Microarray:b4264 , PortEco:idnR , PR:PRO_000022996 , Protein Model Portal:P39343 , RefSeq:NP_418685 , RegulonDB:G7891 , SMR:P39343 , String:511145.b4264 , UniProt:P39343

Relationship Links: InterPro:IN-FAMILY:IPR000843 , InterPro:IN-FAMILY:IPR010982 , InterPro:IN-FAMILY:IPR028082 , Pfam:IN-FAMILY:PF00356 , Prosite:IN-FAMILY:PS00356 , Prosite:IN-FAMILY:PS50932 , Smart:IN-FAMILY:SM00354

In Paralogous Gene Group: 30 (25 members)

In Reactions of unknown directionality:

Not in pathways:
IdnR + 5-dehydro-D-gluconate = IdnR transcriptional regulator

In Reactions of unknown directionality:

Not in pathways:
IdnR + 5-dehydro-D-gluconate = IdnR transcriptional regulator

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Bausch98]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0019521 - D-gluconate metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

DNA binding site length: 16 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: atGTTACgcgTAACat

Regulated Transcription Units (1 total): ?

Notes:

Regulated Transcription Units (3 total): ?

Notes:

Essentiality data for idnR 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]

Sequence Features

Feature Class Location Citations Comment
Conserved-Region 6 -> 60
[UniProt09]
UniProt: HTH lacI-type;
DNA-Binding-Region 8 -> 27
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


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

Bausch04: Bausch C, Ramsey M, Conway T (2004). "Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli." J Bacteriol 186(5);1388-97. PMID: 14973046

Bausch98: Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T (1998). "Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli." J Bacteriol 1998;180(14);3704-10. PMID: 9658018

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

GOA01: 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

Rodionov00: Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS (2000). "Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria." Mol Microbiol 38(4);673-83. PMID: 11115104

Tsunedomi03: Tsunedomi R, Izu H, Kawai T, Matsushita K, Ferenci T, Yamada M (2003). "The activator of GntII genes for gluconate metabolism, GntH, exerts negative control of GntR-regulated GntI genes in Escherichia coli." J Bacteriol 185(6);1783-95. PMID: 12618441

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

Tsunedomi03a: Tsunedomi R, Izu H, Kawai T, Yamada M (2003). "Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli." J Mol Microbiol Biotechnol 6(1);41-56. PMID: 14593252


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 Sat Dec 20, 2014, BIOCYC13A.