1tae: Difference between revisions

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-[[Image:1tae.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1tae", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1tae|  PDB=1tae  |  SCENE=  }}
-'''Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal'''
+==Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal==
+<StructureSection load='1tae' size='340' side='right'caption='[[1tae]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-TAE is a [[Single protein]] structure of 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].
+</div>
+<div class="pdbe-citations 1tae" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal., Gajiwala KS, Pinko C, Structure. 2004 Aug;12(8):1449-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15296738 15296738]
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
-[[Category: Enterococcus faecalis v583]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Gajiwala, K S.]]
+__TOC__
-[[Category: Pinko, C.]]
+</StructureSection>
-[[Category: Nucleotidyl transferase fold]]
+[[Category: Enterococcus faecalis V583]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:44:26 2008''
+[[Category: Large Structures]]
+[[Category: Gajiwala KS]]
+[[Category: Pinko C]]