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| | ==Structure of the REP associates tyrosine transposase bound to a REP hairpin== | | ==Structure of the REP associates tyrosine transposase bound to a REP hairpin== |
| - | <StructureSection load='4er8' size='340' side='right' caption='[[4er8]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='4er8' size='340' side='right'caption='[[4er8]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4er8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ER8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ER8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4er8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ER8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ER8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0228, JW0218, tnparep, yafM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4er8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4er8 OCA], [https://pdbe.org/4er8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4er8 RCSB], [https://www.ebi.ac.uk/pdbsum/4er8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4er8 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4er8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4er8 OCA], [http://pdbe.org/4er8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4er8 RCSB], [http://www.ebi.ac.uk/pdbsum/4er8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4er8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RAYT_ECOLI RAYT_ECOLI] Transposase that is always flanked by repeated extragenic palindrome (REP) sequences, which are clustered in structures called bacterial interspersed mosaic elements (BIMEs). RayT catalyzes cleavage and recombination of BIMEs. Binds REP sequences and cleaves BIMEs both upstream and downstream of the REP sequence. Could be important in the creation of BIME variability and amplification.<ref>PMID:20085626</ref> <ref>PMID:22199259</ref> <ref>PMID:22885300</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Chandler, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Dyda, F]] | + | [[Category: Chandler M]] |
| - | [[Category: Ghirlando, R]] | + | [[Category: Dyda F]] |
| - | [[Category: Hickman, A B]] | + | [[Category: Ghirlando R]] |
| - | [[Category: Messing, S A.J]] | + | [[Category: Hickman AB]] |
| - | [[Category: Ton-Hoang, B]] | + | [[Category: Messing SAJ]] |
| - | [[Category: Catalytic tyrosine]]
| + | [[Category: Ton-Hoang B]] |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Guide sequence]]
| + | |
| - | [[Category: Huh motif]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Rna recognition motif]]
| + | |
| - | [[Category: Transposase]]
| + | |
| Structural highlights
Function
RAYT_ECOLI Transposase that is always flanked by repeated extragenic palindrome (REP) sequences, which are clustered in structures called bacterial interspersed mosaic elements (BIMEs). RayT catalyzes cleavage and recombination of BIMEs. Binds REP sequences and cleaves BIMEs both upstream and downstream of the REP sequence. Could be important in the creation of BIME variability and amplification.[1] [2] [3]
Publication Abstract from PubMed
Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation of certain bacterial functions, such as Integration Host Factor recruitment and mRNA turnover. Although a new clade of putative transposases (RAYTs or TnpA(REP)) is often associated with an increase in these repeats, it is not clear how these proteins might have directed amplification of REPs. We report here the structure to 2.6 A of TnpA(REP) from Escherichia coli MG1655 bound to a REP. Sequence analysis showed that TnpA(REP) is highly related to the IS200/IS605 family, but in contrast to IS200/IS605 transposases, TnpA(REP) is a monomer, is auto-inhibited and is active only in manganese. These features suggest that, relative to IS200/IS605 transposases, it has evolved a different mechanism for the movement of discrete segments of DNA and has been severely down-regulated, perhaps to prevent REPs from sweeping through genomes.
The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease.,Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F Nucleic Acids Res. 2012 Aug 9. PMID:22885300[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nunvar J, Huckova T, Licha I. Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. BMC Genomics. 2010 Jan 19;11:44. doi: 10.1186/1471-2164-11-44. PMID:20085626 doi:http://dx.doi.org/10.1186/1471-2164-11-44
- ↑ Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G, Chandler M. Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences. Nucleic Acids Res. 2012 Apr;40(8):3596-609. doi: 10.1093/nar/gkr1198. Epub 2011, Dec 22. PMID:22199259 doi:http://dx.doi.org/10.1093/nar/gkr1198
- ↑ Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease. Nucleic Acids Res. 2012 Aug 9. PMID:22885300 doi:10.1093/nar/gks741
- ↑ Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease. Nucleic Acids Res. 2012 Aug 9. PMID:22885300 doi:10.1093/nar/gks741
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