1dgs

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[[Image:1dgs.png|left|200px]]
 
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==CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS==
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The line below this paragraph, containing "STRUCTURE_1dgs", creates the "Structure Box" on the page.
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<StructureSection load='1dgs' size='340' side='right'caption='[[1dgs]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dgs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. The July 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Ligase'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_7 10.2210/rcsb_pdb/mom_2004_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DGS FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1dgs| PDB=1dgs | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dgs OCA], [https://pdbe.org/1dgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dgs RCSB], [https://www.ebi.ac.uk/pdbsum/1dgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dgs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DNLJ_THEFI DNLJ_THEFI] DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.<ref>PMID:15268945</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dg/1dgs_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1dgs ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.
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===CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS===
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Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.,Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952<ref>PMID:10698952</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_10698952}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1dgs" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 10698952 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10698952}}
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==About this Structure==
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[[1dgs]] is a 2 chain structure of [[DNA ligase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. The July 2004 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Ligase'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2004_7 10.2210/rcsb_pdb/mom_2004_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DGS OCA].
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==See Also==
==See Also==
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*[[DNA ligase|DNA ligase]]
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*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:010698952</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: DNA Ligase]]
[[Category: DNA Ligase]]
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[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Thermus filiformis]]
[[Category: Thermus filiformis]]
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[[Category: Chang, C.]]
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[[Category: Chang C]]
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[[Category: Kwon, S T.]]
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[[Category: Kwon ST]]
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[[Category: Lee, J Y.]]
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[[Category: Lee JY]]
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[[Category: Song, H K.]]
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[[Category: Song HK]]
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[[Category: Suh, S W.]]
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[[Category: Suh SW]]
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[[Category: Amp complex]]
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[[Category: Ligase]]
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[[Category: Nad+-dependent]]
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Current revision

CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

PDB ID 1dgs

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