1dgs
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<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> | <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> | ||
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <tr id=' | + | <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> |
<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> | <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> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [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> | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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]. | </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]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | 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: 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1dgs" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
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[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: Thermus filiformis]] | [[Category: Thermus filiformis]] | ||
| - | [[Category: Chang | + | [[Category: Chang C]] |
| - | [[Category: Kwon | + | [[Category: Kwon ST]] |
| - | [[Category: Lee | + | [[Category: Lee JY]] |
| - | [[Category: Song | + | [[Category: Song HK]] |
| - | [[Category: Suh | + | [[Category: Suh SW]] |
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Revision as of 09:50, 20 March 2024
CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS
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