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Escherichia coli K-12 substr. MG1655 Polypeptide: protein that protects iron-sulfur proteins against oxidative damage



Gene: yggX Accession Numbers: G7532 (EcoCyc), b2962, ECK2957

Regulation Summary Diagram: ?

Summary:
YggX is proposed to play a role in oxidation resistance of iron-sulfur clusters [Pomposiello03]. YggX is found at high abundance in vivo [Link97].

A solution structure of YggX has been determined [Osborne05]. C7 of YggX is redox-sensitive [Leichert08].

A yggX mutant shows paraquat sensitivity, a paraquat-induced aconitase defect [Pomposiello03] and increased sensitivity to redox stress [Leichert08]. Multicopy yggX expression results in elevated aconitase activity, compared to wild type [Pomposiello03].

Transcription of yggX is induced by SoxS overproduction or by oxidative stress [Pomposiello03]. YggX is upregulated under glucose-limited fed-batch conditions [Raman05].

Gene Citations: [Gifford99]

Locations: cytosol

Map Position: [3,102,115 -> 3,102,390] (66.86 centisomes)
Length: 276 bp / 91 aa

Molecular Weight of Polypeptide: 10.953 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009722 , EchoBASE:EB2809 , EcoGene:EG12984 , EcoliWiki:b2962 , Mint:MINT-1253097 , OU-Microarray:b2962 , PortEco:yggX , Pride:P0A8P3 , Protein Model Portal:P0A8P3 , RefSeq:NP_417437 , RegulonDB:G7532 , SMR:P0A8P3 , String:511145.b2962 , UniProt:P0A8P3

Relationship Links: InterPro:IN-FAMILY:IPR007457 , PDB:Structure:1YHD , Pfam:IN-FAMILY:PF04362 , ProDom:IN-FAMILY:PD029191

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0034599 - cellular response to oxidative stress Inferred from experiment [Pomposiello03, Leichert08]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005506 - iron ion binding Inferred by computational analysis [GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)

Essentiality data for yggX knockouts: ?

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

Credits:
Last-Curated ? 12-Apr-2011 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Wasinger98, Link97, UniProt10a, Wasinger98]
UniProt: Removed;
Chain 2 -> 91
[UniProt09]
UniProt: Probable Fe(2+)-trafficking protein;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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

Gifford99: Gifford CM, Wallace SS (1999). "The genes encoding formamidopyrimidine and MutY DNA glycosylases in Escherichia coli are transcribed as part of complex operons." J Bacteriol 181(14);4223-36. PMID: 10400579

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Leichert08: Leichert LI, Gehrke F, Gudiseva HV, Blackwell T, Ilbert M, Walker AK, Strahler JR, Andrews PC, Jakob U (2008). "Quantifying changes in the thiol redox proteome upon oxidative stress in vivo." Proc Natl Acad Sci U S A 105(24);8197-202. PMID: 18287020

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Osborne05: Osborne MJ, Siddiqui N, Landgraf D, Pomposiello PJ, Gehring K (2005). "The solution structure of the oxidative stress-related protein YggX from Escherichia coli." Protein Sci 14(6);1673-8. PMID: 15883188

Pomposiello03: Pomposiello PJ, Koutsolioutsou A, Carrasco D, Demple B (2003). "SoxRS-regulated expression and genetic analysis of the yggX gene of Escherichia coli." J Bacteriol 185(22);6624-32. PMID: 14594836

Raman05: Raman B, Nandakumar MP, Muthuvijayan V, Marten MR (2005). "Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions." Biotechnol Bioeng 92(3);384-92. PMID: 16180237

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Wasinger98: Wasinger VC, Humphery-Smith I (1998). "Small genes/gene-products in Escherichia coli K-12." FEMS Microbiol Lett 169(2);375-82. PMID: 9868784

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


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.