View source for 3gde


==The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus==
<StructureSection load='3gde' size='340' side='right'caption='[[3gde]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3gde]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDE 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]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3gde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gde OCA], [https://pdbe.org/3gde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gde RCSB], [https://www.ebi.ac.uk/pdbsum/3gde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gde ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DNLI_ARCFU DNLI_ARCFU] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair (By similarity).
== 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/gd/3gde_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=3gde ConSurf].
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== Publication Abstract from PubMed ==
DNA ligases join the breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 3'-hydroxyl and 5'-phosphate termini. They fall into two classes that require either ATP or NAD(+) as the source of an AMP group that is covalently attached to a strictly conserved lysine. Conformational flexibility is essential for the function of multi-domain DNA ligases because they must undergo large conformational changes involving domain rearrangements during the course of the reaction. In the absence of the nicked DNA substrate, both open and closed conformations have been observed for the ATP-dependent DNA ligases from Sulfolobus solfataricus and Pyrococcus furiosus. Here, the crystal structure of an ATP-dependent DNA ligase from Archaeoglobus fulgidus has been determined in the DNA-unbound unadenylated state. It resembles the closed conformation of P. furiosus DNA ligase but was even more closed, thus enhancing our understanding of the conformational variability of these enzymes.

ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation.,Kim do J, Kim O, Kim HW, Kim HS, Lee SJ, Suh SW Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt, 6):544-50. Epub 2009 May 22. PMID:19478428<ref>PMID:19478428</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 3gde" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Large Structures]]
[[Category: Kim DJ]]
[[Category: Kim H-W]]
[[Category: Kim HS]]
[[Category: Kim O]]
[[Category: Lee SJ]]
[[Category: Suh SW]]