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Escherichia coli K-12 substr. MG1655 Polypeptide: REP-associated tyrosine transposase



Gene: rayT Accession Numbers: G6112 (EcoCyc), b0228, ECK0229

Synonyms: yafM, TnpAREP

Regulation Summary Diagram: ?

Summary:
TnpAREP (RayT) is closely related to IS200/IS605 transposases and is associated with a repetitive extragenic palindromic (REP) sequence [Nunvar10, TonHoang12]. It catalyses cleavage and recombination of bacterial interspersed mosaic elements (BIMEs) in vitro [TonHoang12].

TnpAREP binds single-stranded REP sequences containing the conserved 5' GATG tetranucleotide and catalyses BIME cleavage both upstream and downstream of the REP sequence [TonHoang12]. A crystal structure of TnpAREP bound to a REP has been solved at 2.6 Å resolution. Unlike the IS200/IS605 transposases, TnpAREP is momoneric and specifically requires Mn2+ for cleavage and the formation of a covalent intermediate [Messing12].

RayT: "REP-associated tyrosine transposase" [Nunvar10]

Citations: [Bertels11]

Map Position: [247,637 -> 248,134] (5.34 centisomes)
Length: 498 bp / 165 aa

Molecular Weight of Polypeptide: 20.042 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000779 , DIP:DIP-11217N , EchoBASE:EB2944 , EcoGene:EG13150 , EcoliWiki:b0228 , OU-Microarray:b0228 , PortEco:yafM , Pride:Q47152 , Protein Model Portal:Q47152 , RefSeq:NP_414763 , RegulonDB:G6112 , SMR:Q47152 , String:511145.b0228 , UniProt:Q47152

Relationship Links: InterPro:IN-FAMILY:IPR002686 , PDB:Structure:4ER8 , Pfam:IN-FAMILY:PF07605

GO Terms:

Biological Process: GO:0006310 - DNA recombination Inferred from experiment [TonHoang12]
GO:0006313 - transposition, DNA-mediated Inferred by computational analysis [GOA01]
Molecular Function: GO:0043565 - sequence-specific DNA binding Inferred from experiment [TonHoang12, Messing12]
GO:0043566 - structure-specific DNA binding Inferred from experiment [TonHoang12, Messing12]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01]
GO:0004803 - transposase activity Inferred by computational analysis [GOA01]

MultiFun Terms: extrachromosomal transposon related

Essentiality data for rayT 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]

Credits:
Last-Curated ? 30-Aug-2012 by Keseler I , SRI International


Gene Local Context (not to scale): ?

Transcription Unit:

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

Bertels11: Bertels F, Rainey PB (2011). "Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria." PLoS Genet 7(6);e1002132. PMID: 21698139

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

Messing12: Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F (2012). "The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease." Nucleic Acids Res. PMID: 22885300

Nunvar10: Nunvar J, Huckova T, Licha I (2010). "Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes." BMC Genomics 11;44. PMID: 20085626

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

TonHoang12: Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G, Chandler M (2012). "Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences." Nucleic Acids Res 40(8);3596-609. PMID: 22199259


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, biocyc13.