1vyb: Difference between revisions

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{{Seed}}
[[Image:1vyb.png|left|200px]]


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==Endonuclease domain of human LINE1 ORF2p==
The line below this paragraph, containing "STRUCTURE_1vyb", creates the "Structure Box" on the page.
<StructureSection load='1vyb' size='340' side='right'caption='[[1vyb]], [[Resolution|resolution]] 1.80&Aring;' 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'>[[1vyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VYB 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">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1vyb|  PDB=1vyb  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vyb OCA], [https://pdbe.org/1vyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vyb RCSB], [https://www.ebi.ac.uk/pdbsum/1vyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vyb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LORF2_HUMAN LORF2_HUMAN] Has a reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Has also an endonuclease activity that allows the introduction of nicks in the chromosomal target DNA. Cleaves DNA in AT-rich regions between a 5' stretch of purines and a 3' stretch of pyrimidines, corresponding to sites of LINE-1 integration in the genome.<ref>PMID:7516468</ref> <ref>PMID:8945517</ref> <ref>PMID:9140393</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/vy/1vyb_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=1vyb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The human L1 endonuclease (L1-EN) is encoded by the non-LTR retrotransposon LINE-1 (L1). L1 is responsible for more than 1.5 million retrotransposition events in the history of the human genome, contributing more than a quarter to human genomic DNA (L1 and Alu elements). L1-EN is related to the well-understood human DNA repair endonuclease APE1, and its nicking specificity is a major determinant for retrotransposon integration site selection. The crystal structure of human L1 endonuclease is the first of a retrotransposon-encoded protein and a prototype for retrotransposon-encoded endonucleases involved in target-primed reverse transcription. Structure-based endonuclease alignments reveal a conserved threonine in addition to previously identified invariant residues and suggest that DNA recognition proceeds via the accommodation of an extrahelical nucleotide within a pocket of the enzyme. The present analysis will help to refine phylogenetic and functional relationships among metal-dependent phosphohydrolases and provides a basis for manipulating non-LTR retrotransposon integration site selection.


===ENDONUCLEASE DOMAIN OF HUMAN LINE1 ORF2P===
Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.,Weichenrieder O, Repanas K, Perrakis A Structure. 2004 Jun;12(6):975-86. PMID:15274918<ref>PMID:15274918</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_15274918}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1vyb" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15274918 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15274918}}
__TOC__
 
</StructureSection>
==About this Structure==
1VYB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VYB OCA].
 
==Reference==
<ref group="xtra">PMID:15274918</ref><references group="xtra"/>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Perrakis, A.]]
[[Category: Large Structures]]
[[Category: Repanas, K.]]
[[Category: Perrakis A]]
[[Category: Weichenrieder, O.]]
[[Category: Repanas K]]
[[Category: Ape-1 type]]
[[Category: Weichenrieder O]]
[[Category: Endonuclease]]
[[Category: Retrotransposition]]
[[Category: Retrotransposon]]
[[Category: Rna-directed dna polymerase]]
[[Category: Transferase]]
 
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Retrieved from "https://proteopedia.org/1vyb"