3lzc: Difference between revisions

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 ==Crystal structure of Dph2 from Pyrococcus horikoshii==
-<StructureSection load='3lzc' size='340' side='right' caption='[[3lzc]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+<StructureSection load='3lzc' size='340' side='right'caption='[[3lzc]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lzc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LZC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LZC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lzc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LZC FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lzd|3lzd]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.261&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lzc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lzc RCSB], [http://www.ebi.ac.uk/pdbsum/3lzc PDBsum]</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=3lzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lzc OCA], [https://pdbe.org/3lzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lzc RCSB], [https://www.ebi.ac.uk/pdbsum/3lzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lzc ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPH2_PYRHO DPH2_PYRHO] Catalyzes the first step of diphthamide biosynthesis, i.e. the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the C2 position of the imidazole ring of the target histidine residue in translation elongation factor 2 (EF-2).<ref>PMID:20559380</ref>
 == 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/lz/3lzc_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lz/3lzc_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/chain_selection.php?pdb_ID=2ata 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=3lzc ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Archaeal and eukaryotic translation elongation factor 2 contain a unique post-translationally modified histidine residue called diphthamide, which is the target of diphtheria toxin. The biosynthesis of diphthamide was proposed to involve three steps, with the first being the formation of a C-C bond between the histidine residue and the 3-amino-3-carboxypropyl group of S-adenosyl-l-methionine (SAM). However, further details of the biosynthesis remain unknown. Here we present structural and biochemical evidence showing that the first step of diphthamide biosynthesis in the archaeon Pyrococcus horikoshii uses a novel iron-sulphur-cluster enzyme, Dph2. Dph2 is a homodimer and each of its monomers can bind a [4Fe-4S] cluster. Biochemical data suggest that unlike the enzymes in the radical SAM superfamily, Dph2 does not form the canonical 5'-deoxyadenosyl radical. Instead, it breaks the C(gamma,Met)-S bond of SAM and generates a 3-amino-3-carboxypropyl radical. Our results suggest that P. horikoshii Dph2 represents a previously unknown, SAM-dependent, [4Fe-4S]-containing enzyme that catalyses unprecedented chemistry.
-Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.,Zhang Y, Zhu X, Torelli AT, Lee M, Dzikovski B, Koralewski RM, Wang E, Freed J, Krebs C, Ealick SE, Lin H Nature. 2010 Jun 17;465(7300):891-6. PMID:20559380<ref>PMID:20559380</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Dzikovski, B]]
+[[Category: Dzikovski B]]
-[[Category: Ealick, S E]]
+[[Category: Ealick SE]]
-[[Category: Freed, J]]
+[[Category: Freed J]]
-[[Category: Koralewski, R M]]
+[[Category: Koralewski RM]]
-[[Category: Krebs, C]]
+[[Category: Krebs C]]
-[[Category: Lee, M]]
+[[Category: Lee M]]
-[[Category: Lin, H]]
+[[Category: Lin H]]
-[[Category: Torelli, A T]]
+[[Category: Torelli AT]]
-[[Category: Wang, E]]
+[[Category: Wang E]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Zhu, X]]
+[[Category: Zhu X]]
-[[Category: Biosynthetic protein]]
-[[Category: Diphthamide biosynthesis]]
-[[Category: Gene triplication]]
-[[Category: Radical sam enzyme]]