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: DNA gyrase inhibitor YacG



Gene: yacG Accession Numbers: EG12314 (EcoCyc), b0101, ECK0101

Regulation Summary Diagram: ?

Summary:
DNA gyrase inhibitor YacG blocks DNA binding by DNA gyrase, inhibiting its function.

YacG inhibits the supercoiling activity of DNA gyrase, as well as partially inhibiting its intrinsic ATPase activity as well. It does so via direct binding to the GyrB component of the gyrase holoenzyme that disrupts DNA binding by the enzyme. This inhibition is specific to gyrase, as neither topoisomerase I nor topoisomerase IV are affected by the presence of YacG [Sengupta08].

The structure of YacG has been analyzed via NMR. It appears to contain a classic zinc finger domain, including a tetrahedrally coordinated Zn2+ [Ramelot02].

Based on a deletion analysis, yacG appears to be dispensible for normal growth in minimal and rich medium [Hare01]. Overexpression of yacG leads to growth inhibition and abnormally low levels of DNA supercoiling [Sengupta08].

Gene Citations: [Zaslaver06]

Locations: cytosol

Map Position: [111,649 <- 111,846] (2.41 centisomes)
Length: 198 bp / 65 aa

Molecular Weight of Polypeptide: 7.306 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000351 , DIP:DIP-48126N , EchoBASE:EB2220 , EcoGene:EG12314 , EcoliWiki:b0101 , Mint:MINT-1228215 , ModBase:P0A8H8 , OU-Microarray:b0101 , PortEco:yacG , Pride:P0A8H8 , Protein Model Portal:P0A8H8 , RefSeq:NP_414643 , RegulonDB:EG12314 , SMR:P0A8H8 , String:511145.b0101 , UniProt:P0A8H8

Relationship Links: InterPro:IN-FAMILY:IPR005584 , InterPro:IN-FAMILY:IPR013088 , PDB:Structure:1LV3 , Pfam:IN-FAMILY:PF03884

GO Terms:

Biological Process: GO:2000372 - negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity Inferred by computational analysis Inferred from experiment [Sengupta08, GOA06]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Ramelot02]
GO:0008657 - DNA topoisomerase (ATP-hydrolyzing) inhibitor activity Inferred from experiment Inferred by computational analysis [GOA06, Sengupta08]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation posttranscriptional inhibition / activation of enzymes

Essentiality data for yacG 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-Sep-2008 by Shearer A , SRI International


Sequence Features

Feature Class Location Common Name Attached Group Citations Comment
Metal-Binding-Site 9    
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 9, 12, 28, 32 Zinc binding site Zn2+
[Ramelot02]
 
Metal-Binding-Site 12    
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 28    
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 32    
[UniProt10a]
UniProt: Zinc;


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 ].
10/20/97 Gene b0101 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12314; 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

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."

Hare01: Hare RS, Walker SS, Dorman TE, Greene JR, Guzman LM, Kenney TJ, Sulavik MC, Baradaran K, Houseweart C, Yu H, Foldes Z, Motzer A, Walbridge M, Shimer GH, Shaw KJ (2001). "Genetic footprinting in bacteria." J Bacteriol 183(5);1694-706. PMID: 11160101

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

Ramelot02: Ramelot TA, Cort JR, Yee AA, Semesi A, Edwards AM, Arrowsmith CH, Kennedy MA (2002). "NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins." Proteins 49(2);289-93. PMID: 12211008

Sengupta08: Sengupta S, Nagaraja V (2008). "YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase." Nucleic Acids Res 36(13);4310-6. PMID: 18586829

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

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

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

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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 Thu Dec 18, 2014, BIOCYC14B.