1tae: Difference between revisions

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-[[Image:1tae.png|left|200px]]
-<!--
+==Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal==
-The line below this paragraph, containing "STRUCTURE_1tae", creates the "Structure Box" on the page.
+<StructureSection load='1tae' size='340' side='right'caption='[[1tae]], [[Resolution|resolution]] 2.70&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'>[[1tae]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis_V583 Enterococcus faecalis V583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TAE 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]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1tae|  PDB=1tae  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tae OCA], [https://pdbe.org/1tae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tae RCSB], [https://www.ebi.ac.uk/pdbsum/1tae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tae ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNLJ_ENTFA DNLJ_ENTFA] 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 (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/ta/1tae_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=1tae ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction.
-===Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal===
+Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.,Gajiwala KS, Pinko C Structure. 2004 Aug;12(8):1449-59. PMID:15296738<ref>PMID:15296738</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15296738}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1tae" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15296738 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15296738}}
-==About this Structure==
-[[1tae]] is a 4 chain structure of [[DNA ligase]] with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis_v583 Enterococcus faecalis v583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAE OCA].
 ==See Also==
-*[[DNA ligase]]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:15296738</ref><references group="xtra"/>
+__TOC__
-[[Category: Enterococcus faecalis v583]]
+</StructureSection>
-[[Category: Gajiwala, K S.]]
+[[Category: Enterococcus faecalis V583]]
-[[Category: Pinko, C.]]
+[[Category: Large Structures]]
-[[Category: Ligase]]
+[[Category: Gajiwala KS]]
-[[Category: Nucleotidyl transferase fold]]
+[[Category: Pinko C]]