1muh: Difference between revisions

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 ==CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH TRANSPOSON END DNA==
-<StructureSection load='1muh' size='340' side='right' caption='[[1muh]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1muh' size='340' side='right'caption='[[1muh]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1muh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1f3i 1f3i]. The December 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Transposase''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_12 10.2210/rcsb_pdb/mom_2006_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MUH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MUH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1muh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1f3i 1f3i]. The December 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Transposase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_12 10.2210/rcsb_pdb/mom_2006_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MUH FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><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]] 2.3&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1muh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1muh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1muh RCSB], [http://www.ebi.ac.uk/pdbsum/1muh PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1muh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1muh OCA], [https://pdbe.org/1muh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1muh RCSB], [https://www.ebi.ac.uk/pdbsum/1muh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1muh 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/mu/1muh_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mu/1muh_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1muh ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.
-Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.,Davies DR, Goryshin IY, Reznikoff WS, Rayment I Science. 2000 Jul 7;289(5476):77-85. PMID:10884228<ref>PMID:10884228</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Transposase|Transposase]]
+*[[Transposase 3D structures|Transposase 3D structures]]
 == References ==
 <references/>
@@ Line 32: / Line 28: @@
 </StructureSection>
 [[Category: Escherichia coli]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Transposase]]
-[[Category: Davies, D R.]]
+[[Category: Davies DR]]
-[[Category: Goryshin, I Y.]]
+[[Category: Goryshin IY]]
-[[Category: Holden, H M.]]
+[[Category: Holden HM]]
-[[Category: Rayment, I.]]
+[[Category: Rayment I]]
-[[Category: Reznikoff, W S.]]
+[[Category: Reznikoff WS]]
-[[Category: Thoden, J B.]]
+[[Category: Thoden JB]]
-[[Category: Protein-dna complex]]
-[[Category: Ribonuclease h-like motif]]
-[[Category: Synaptic complex]]
-[[Category: Transcription-dna complex]]
-[[Category: Transposase]]