1mm8: Difference between revisions

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OCA

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-[[Image:1mm8.gif|left|200px]]<br /><applet load="1mm8" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1mm8, resolution 2.8&Aring;" />
-'''Crystal structure of Tn5 Transposase complexed with ME DNA'''<br />
-==Overview==
+==Crystal structure of Tn5 Transposase complexed with ME DNA==
-In this study, evidence of novel, important interactions between a, hyperactive Tn5 transposon recognition end sequence and hyperactive Tn5, transposase (Tnp) are presented. A hyperactive Tn5 end sequence, the, mosaic end (ME), was isolated previously. The ME and a wild-type end, sequence, the outside end (OE), differ at only three positions, yet, transposition on the ME is tenfold higher than on the OE in vivo. Also, transposition on the ME is much more efficient than transposition on the, OE in vitro. Here, we show that the decreased activity observed for the OE, is caused by a defect in paired ends complex (PEC) formation resulting, from the orientation of the A-T base-pair at position 4 of this end., Efficient PEC formation requires an interaction between the C5-methyl, group (C5-Me) on the non-transferred strand thymine base at position 4, (T4) and Tnp. PEC formation on nicked substrates is much less affected by, the orientation of the A-T base-pair at position 4, indicating that the, C5-Me group is important only for steps preceding nicking. A recently, determined co-crystal structure of Tn5 Tnp with the ME is discussed and a, model explaining possible roles for the base-pair at position 4 is, explored.
+<StructureSection load='1mm8' size='340' side='right'caption='[[1mm8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1mm8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MM8 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1mm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mm8 OCA], [https://pdbe.org/1mm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mm8 RCSB], [https://www.ebi.ac.uk/pdbsum/1mm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mm8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TN5P_ECOLX TN5P_ECOLX] Mediates transposition of transposon Tn5 by a 'cut and paste' mechanism. First, the monomeric transposase binds the 19 bp inverted DNA repeats flanking the transposon. Then, dimerization of the DNA-bound transposase creates a synaptic DNA complex. After nicking of the first DNA strand, excision of the transposon proceeds through a series of intermediates. The transposase then mediates the insertion of the transposon at a new site by strand transfer. The activity of the wild-type transposase is very low, and is further inhibited by dimerization with the transposase inhibitor (inh).<ref>PMID:6260374</ref> <ref>PMID:6291786</ref> <ref>PMID:6303899</ref> <ref>PMID:1310499</ref> <ref>PMID:8226636</ref> <ref>PMID:8871560</ref> <ref>PMID:11877443</ref> <ref>PMID:12367522</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mm/1mm8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mm8 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-MM8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MM8 OCA].
+*[[Transposase 3D structures|Transposase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Evidence for "unseen" transposase--DNA contacts., Steiniger-White M, Bhasin A, Lovell S, Rayment I, Reznikoff WS, J Mol Biol. 2002 Oct 4;322(5):971-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12367522 12367522]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bhasin, A.]]
+[[Category: Bhasin A]]
-[[Category: Lovell, S.]]
+[[Category: Lovell S]]
-[[Category: Rayment, I.]]
+[[Category: Rayment I]]
-[[Category: Reznikoff, W.S.]]
+[[Category: Reznikoff WS]]
-[[Category: Steiniger-White, M.]]
+[[Category: Steiniger-White M]]
-[[Category: MN]]
-[[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:20:11 2007''