View source for 2ezk


==SOLUTION NMR STRUCTURE OF THE IBETA SUBDOMAIN OF THE MU END DNA BINDING DOMAIN OF PHAGE MU TRANSPOSASE, REGULARIZED MEAN STRUCTURE==
<StructureSection load='2ezk' size='340' side='right'caption='[[2ezk]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ezk]] 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=2EZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EZK FirstGlance]. <br>
</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=2ezk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ezk OCA], [https://pdbe.org/2ezk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ezk RCSB], [https://www.ebi.ac.uk/pdbsum/2ezk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ezk ProSAT]</span></td></tr>
</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/2ezk_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=2ezk ConSurf].
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== Publication Abstract from PubMed ==
The phage Mu transposase (MuA) binds to the ends of the Mu genome during the assembly of higher order nucleoprotein complexes. We investigate the structure and function of the MuA end-binding domain (Ibetagamma). The three-dimensional solution structure of the Ibeta subdomain (residues 77-174) has been determined using multidimensional NMR spectroscopy. It comprises five alpha-helices, including a helix-turn-helix (HTH) DNA-binding motif formed by helices 3 and 4, and can be subdivided into two interacting structural elements. The structure has an elongated disc-like appearance from which protrudes the recognition helix of the HTH motif. The topology of helices 2-4 is very similar to that of helices 1-3 of the previously determined solution structure of the MuA Igamma subdomain and to that of the homeodomain family of HTH DNA-binding proteins. We show that each of the two subdomains binds to one half of the 22 bp recognition sequence, Ibeta to the more conserved Mu end distal half (beta subsite) and Igamma to the Mu end proximal half (gamma subsite) of the consensus Mu end-binding site. The complete Ibetagamma domain binds the recognition sequence with a 100- to 1000-fold higher affinity than the two subdomains independently, indicating a cooperative effect. Our results show that the Mu end DNA-binding domain of MuA has a modular organization, with each module acting on a specific part of the 22 bp binding site. Based on the present binding data and the structures of the Ibeta and Igamma subdomains, a model for the interaction of the complete Ibetagamma domain with DNA is proposed.

Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.,Schumacher S, Clubb RT, Cai M, Mizuuchi K, Clore GM, Gronenborn AM EMBO J. 1997 Dec 15;16(24):7532-41. PMID:9405381<ref>PMID:9405381</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2ezk" style="background-color:#fffaf0;"></div>

==See Also==
*[[Transposase 3D structures|Transposase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia virus Mu]]
[[Category: Large Structures]]
[[Category: Clore GM]]
[[Category: Clubb RT]]
[[Category: Gronenborn AM]]
[[Category: Schumaker S]]