4er8: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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='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'>[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>
</table>
</table>
== Function ==
== 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>  
[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;">
== 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<ref>PMID:22885300</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4er8" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 11:05, 1 March 2024

Structure of the REP associates tyrosine transposase bound to a REP hairpin

4er8, resolution 2.60Å

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