1v9p

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[[Image:1v9p.gif|left|200px]]
 
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{{Structure
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==Crystal Structure Of Nad+-Dependent DNA Ligase==
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|PDB= 1v9p |SIZE=350|CAPTION= <scene name='initialview01'>1v9p</scene>, resolution 2.90&Aring;
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<StructureSection load='1v9p' size='340' side='right'caption='[[1v9p]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=AMP:ADENOSINE MONOPHOSPHATE'>AMP</scene>
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<table><tr><td colspan='2'>[[1v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dgt 1dgt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9P FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2]
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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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|GENE= LIGA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=276 Thermus filiformis])
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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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}}
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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=1v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9p OCA], [https://pdbe.org/1v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9p RCSB], [https://www.ebi.ac.uk/pdbsum/1v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9p 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/v9/1v9p_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1v9p 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'''
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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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<div class="pdbe-citations 1v9p" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1V9P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_filiformis Thermus filiformis]. This structure supersedes the now removed PDB entry 1DGT. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9P OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/10698952 10698952]
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[[Category: DNA ligase (NAD(+))]]
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[[Category: Single protein]]
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[[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: Kim, H K.]]
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[[Category: Kim HK]]
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[[Category: Kwon, S K.]]
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[[Category: Kwon SK]]
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[[Category: Lee, J Y.]]
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[[Category: Lee JY]]
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[[Category: Moon, J.]]
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[[Category: Moon J]]
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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: Yang, J K.]]
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[[Category: Yang JK]]
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[[Category: AMP]]
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[[Category: ZN]]
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[[Category: nad+-dependent dna ligase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:42:41 2008''
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Current revision

Crystal Structure Of Nad+-Dependent DNA Ligase

PDB ID 1v9p

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