2ezi: Difference between revisions

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-{{Seed}}
-[[Image:2ezi.png|left|200px]]
-<!--
+==SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF MU PHAGE TRANSPOSASE, 30 STRUCTURES==
-The line below this paragraph, containing "STRUCTURE_2ezi", creates the "Structure Box" on the page.
+<StructureSection load='2ezi' size='340' side='right'caption='[[2ezi]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ezi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Mu Escherichia virus Mu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2ezi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ezi OCA], [https://pdbe.org/2ezi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ezi RCSB], [https://www.ebi.ac.uk/pdbsum/2ezi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ezi ProSAT]</span></td></tr>
-{{STRUCTURE_2ezi|  PDB=2ezi  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TNPA_BPMU TNPA_BPMU] Responsible for viral genome integration into the host chromosome. During integration of the incoming virus, DDE-recombinase A cleaves both viral DNA ends and the resulting 3'-OH perform a nucleophilic attack of the host DNA. The 5' flanking DNA attached to the ends of the viral genome (flaps) are resected by the DDE-recombinase A endonuclease activity, with the help of host chaperone ClpX. The gaps created in the host chromosome by the viral genome insertion are repaired by the host primary machinery for double-strand break repair.  Responsible for replication of the viral genome by replicative transposition. During replicative transposition, DDE-recombinase A is part of the transpososome complex. DDE-recombinase A cleaves the viral DNA and the resulting 3'-OH performs a nucleophilic attack of the host DNA. The 5' flanking DNA is not resected and an intermediary structure is formed. This structure is resolved by target-primed replication leading to two copies of the viral genome (the original one and the copied one). Host ClpX and translation initiation factor IF2 play an essential transpososome-remodeling role by releasing the block between transposition and DNA replication. Successive rounds of replicative transposition can lead up to 100 copies of the viral genome.  Promotes replication and thereby lytic development by competing with repressor c (Repc) for binding to the internal activation sequence (IAS) in the enhancer/operator region. The outcome of this competition determines if the virus enters latency or starts replication.
+== 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/ez/2ezi_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=2ezi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The MuA transposase of phase Mu is a large modular protein that plays a central role in transposition. We show that the Mu end DNA-binding domain, I beta gamma, which is responsible for binding the DNA attachment sites at each end of the Mu genome, comprises two subdomains, I beta and I gamma, that are structurally autonomous and do not interact with each other in the absence of DNA. The solution structure of the I gamma subdomain has been determined by multidimensional NMR spectroscopy. The structure of I gamma comprises a four helix bundle and, despite the absence of any significant sequence identity, the topology of the first three helices is very similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins. The helix-turn-helix motif of I gamma, however, differs from that of the homeodomains in so far as the loop is longer and the second helix is shorter, reminiscent of that in the POU-specific domain.
-===SOLUTION NMR STRUCTURE OF THE IGAMMA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF MU PHAGE TRANSPOSASE, 30 STRUCTURES===
+Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase.,Clubb RT, Schumacher S, Mizuuchi K, Gronenborn AM, Clore GM J Mol Biol. 1997 Oct 17;273(1):19-25. PMID:9367742<ref>PMID:9367742</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ezi" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9367742}}, adds the Publication Abstract to the page
+*[[Transposase 3D structures|Transposase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9367742 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9367742}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus Mu]]
-EZI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_mu Enterobacteria phage mu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EZI OCA].
+[[Category: Large Structures]]
+[[Category: Clore GM]]
-==Reference==
+[[Category: Clubb RT]]
-Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase., Clubb RT, Schumacher S, Mizuuchi K, Gronenborn AM, Clore GM, J Mol Biol. 1997 Oct 17;273(1):19-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9367742 9367742]
+[[Category: Gronenborn AM]]
-[[Category: Enterobacteria phage mu]]
+[[Category: Schumaker S]]
-[[Category: Single protein]]
-[[Category: Clore, G M.]]
-[[Category: Clubb, R T.]]
-[[Category: Gronenborn, A M.]]
-[[Category: Schumaker, S.]]
-[[Category: Dna-binding protein]]
-[[Category: Transposition]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:45:02 2008''