Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: ZraR transcriptional activator



Gene: zraR Accession Numbers: EG10482 (EcoCyc), b4004, ECK3996

Synonyms: hydG, ZraR response regulator

Regulation Summary Diagram: ?

Alternative forms of ZraR transcriptional activator: ZraR-Phosphorylated DNA-binding transcriptional activator (extended summary available)

Citations: [Pao95, Parkinson92, Stock90, Parkinson93]

Gene Citations: [Stoker89]

Locations: cytosol

Map Position: [4,201,343 -> 4,202,668] (90.55 centisomes)
Length: 1326 bp / 441 aa

Molecular Weight of Polypeptide: 48.395 kD (from nucleotide sequence)

pI: 5.68

Unification Links: ASAP:ABE-0013093 , CGSC:34252 , DIP:DIP-9980N , EchoBASE:EB0477 , EcoGene:EG10482 , EcoliWiki:b4004 , ModBase:P14375 , OU-Microarray:b4004 , PortEco:zraR , PR:PRO_000024256 , Pride:P14375 , Protein Model Portal:P14375 , RegulonDB:EG10482 , SMR:P14375 , String:511145.b4004 , Swiss-Model:P14375 , UniProt:P14375

Relationship Links: InterPro:IN-FAMILY:IPR001789 , InterPro:IN-FAMILY:IPR002078 , InterPro:IN-FAMILY:IPR002197 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR011006 , InterPro:IN-FAMILY:IPR025662 , InterPro:IN-FAMILY:IPR025943 , InterPro:IN-FAMILY:IPR025944 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00072 , Pfam:IN-FAMILY:PF00158 , Pfam:IN-FAMILY:PF02954 , Prints:IN-FAMILY:PR01590 , Prosite:IN-FAMILY:PS00675 , Prosite:IN-FAMILY:PS00676 , Prosite:IN-FAMILY:PS00688 , Prosite:IN-FAMILY:PS50045 , Prosite:IN-FAMILY:PS50110 , Smart:IN-FAMILY:SM00382 , Smart:IN-FAMILY:SM00448

In Paralogous Gene Group: 121 (40 members)

Reactions known to consume the compound:

ZraSR Two-Component Signal Transduction System :
ZraR + ZraS-Phis254[inner membrane] → ZraR-Pasp56 + ZraS[inner membrane]

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Yamamoto05]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0000156 - phosphorelay response regulator activity Inferred from experiment [Yamamoto05]
GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Leonhartsberger01]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008134 - transcription factor binding Inferred by computational analysis [GOA01]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon fermentation
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Transcription Units regulated by related protein ZraR-Phosphorylated DNA-binding transcriptional activator (2 total):

Essentiality data for zraR 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 State
Conserved-Region 7 -> 121
[UniProt09]
UniProt: Response regulatory;
 
4-aspartylphosphate-Modification 56
[UniProt11a]
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.
Unmodified
Sequence-Conflict 117 -> 122
[Stoker89, UniProt10]
Alternate sequence: LEKALA → WKKRS; UniProt: (in Ref. 1; AAA24004);
 
Conserved-Region 141 -> 370
[UniProt09]
UniProt: Sigma-54 factor interaction;
 
Sequence-Conflict 161
[Stoker89, UniProt10]
Alternate sequence: S → C; UniProt: (in Ref. 1; AAA24004);
 
Nucleotide-Phosphate-Binding-Region 169 -> 176
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: potential;
 
Sequence-Conflict 172 -> 174
[Stoker89, UniProt10]
Alternate sequence: GTG → AR; UniProt: (in Ref. 1; AAA24004);
 
Sequence-Conflict 181 -> 182
[Stoker89, UniProt10]
Alternate sequence: AI → GL; UniProt: (in Ref. 1; AAA24004);
 
Sequence-Conflict 228
[Stoker89, UniProt10]
Alternate sequence: R → P; UniProt: (in Ref. 1; AAA24004);
 
Nucleotide-Phosphate-Binding-Region 232 -> 241
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: potential;
 
Sequence-Conflict 237 -> 238
[Stoker89, UniProt10]
Alternate sequence: LF → C; UniProt: (in Ref. 1; AAA24004);
 
Sequence-Conflict 336 -> 346
[Stoker89, UniProt10]
Alternate sequence: KAVKGFTPQAM → RGKRFYAPGL; UniProt: (in Ref. 1; AAA24004);
 
Sequence-Conflict 385
[Stoker89, UniProt10]
Alternate sequence: A → G; UniProt: (in Ref. 1; AAA24004);
 
DNA-Binding-Region 421 -> 440
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
 


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4004 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10482; confirmed by SwissProt match.


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

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

Leonhartsberger01: Leonhartsberger S, Huber A, Lottspeich F, Bock A (2001). "The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system." J Mol Biol 2001;307(1);93-105. PMID: 11243806

Pao95: Pao GM, Saier MH (1995). "Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution." J Mol Evol 1995;40(2);136-54. PMID: 7699720

Parkinson92: Parkinson JS, Kofoid EC (1992). "Communication modules in bacterial signaling proteins." Annu Rev Genet 1992;26;71-112. PMID: 1482126

Parkinson93: Parkinson JS (1993). "Signal transduction schemes of bacteria." Cell 1993;73(5);857-71. PMID: 8098993

Stock90: Stock JB, Stock AM, Mottonen JM (1990). "Signal transduction in bacteria." Nature 1990;344(6265);395-400. PMID: 2157156

Stoker89: Stoker K, Reijnders WN, Oltmann LF, Stouthamer AH (1989). "Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12." J Bacteriol 1989;171(8);4448-56. PMID: 2666400

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Yamamoto05: Yamamoto K, Hirao K, Oshima T, Aiba H, Utsumi R, Ishihama A (2005). "Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli." J Biol Chem 280(2);1448-56. PMID: 15522865

Other References Related to Gene Regulation

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

Reitzer01: Reitzer L, Schneider BL (2001). "Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli." Microbiol Mol Biol Rev 65(3);422-44, table of contents. PMID: 11528004

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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 Sun Dec 21, 2014, biocyc14.