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Escherichia coli K-12 substr. MG1655 Protein: IdnR-5-ketogluconate DNA-binding transcriptional dual regulator
Inferred from experiment



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

Synonyms: gntS?, gntH, yjgS

Regulation Summary Diagram

Regulation summary diagram for idnR

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

Map Position: [4,490,141 <- 4,491,139] (96.74 centisomes, 348°)
Length: 999 bp / 332 aa

Molecular Weight: 37.567 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013966, EchoBASE:EB2427, EcoGene:EG12538, OU-Microarray:b4264, PortEco:idnR, RegulonDB:G7891, String:511145.b4264

Relationship Links: Pfam:IN-FAMILY:PF00356

In Paralogous Gene Group: 30 (25 members)

Reactions known to both consume and produce the compound:

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

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for idnR


GO Terms:
Biological Process:
Inferred from experimentGO:0045893 - positive regulation of transcription, DNA-templated [Bausch98]

MultiFun Terms: information transferRNA relatedTranscription related
metabolismcarbon utilizationcarbon compounds
regulationgenetic unit regulatedoperon
regulationtype of regulationtranscriptional levelactivator
regulationtype of regulationtranscriptional levelrepressor

DNA binding site length: 16 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: atGTTACgcgTAACat

Regulated Transcription Units (3 total):

Notes:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Subunit of IdnR-5-ketogluconate DNA-binding transcriptional dual regulator: IdnR transcriptional regulator

Synonyms: GntH, YjgS, IdnR

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

Locations: cytosol

Sequence Length: 332 AAs

Molecular Weight: 37.567 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0019521 - D-gluconate metabolic process [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0003700 - transcription factor activity, sequence-specific DNA binding [GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: information transferRNA relatedTranscription related
metabolismcarbon utilizationcarbon compounds
regulationgenetic unit regulatedoperon
regulationtype of regulationtranscriptional levelactivator
regulationtype of regulationtranscriptional levelrepressor

Unification Links: EcoliWiki:b4264, ModBase:P39343, PR:PRO_000022996, Protein Model Portal:P39343, RefSeq:NP_418685, SMR:P39343, UniProt:P39343

Relationship Links: InterPro:IN-FAMILY:IPR000843, InterPro:IN-FAMILY:IPR010982, InterPro:IN-FAMILY:IPR028082, Pfam:IN-FAMILY:PF00356, Pfam:IN-FAMILY:PF13377, Prosite:IN-FAMILY:PS00356, Prosite:IN-FAMILY:PS50932, Smart:IN-FAMILY:SM00354

Reactions known to both consume and produce the compound:

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

Citations: [Isturiz01]

Essentiality data for idnR knockouts:

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

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

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

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

Isturiz01: Isturiz T, Diaz-Benjumea R, Rodriguez N, Porco A (2001). "Involvement of gntS in the control of GntI, the main system for gluconate metabolism in Escherichia coli." J Basic Microbiol 41(2);75-83. PMID: 11441462

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

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

Suvorova15: Suvorova IA, Korostelev YD, Gelfand MS (2015). "GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution." PLoS One 10(7);e0132618. PMID: 26151451

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by Pathway Tools version 20.0 (software by SRI International) on Fri May 6, 2016, BIOCYC14.