3lzd: Difference between revisions

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-{{STRUCTURE_3lzd|  PDB=3lzd  |  SCENE=  }}
+==Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster==
-===Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster===
+<StructureSection load='3lzd' size='340' side='right' caption='[[3lzd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-{{ABSTRACT_PUBMED_20559380}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3lzd]] 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=3LZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LZD FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lzc|3lzc]]</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=3lzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lzd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lzd RCSB], [http://www.ebi.ac.uk/pdbsum/3lzd PDBsum]</span></td></tr>
+</table>
+== 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/3lzd_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].
+<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.
-==Function==
+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>
-[[http://www.uniprot.org/uniprot/O58832_PYRHO O58832_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>
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[3lzd]] 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=3LZD OCA].
+</div>
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020559380</ref><references group="xtra"/><references/>
+__TOC__
+</StructureSection>
 [[Category: Pyrococcus horikoshii]]
-[[Category: Dzikovski, B.]]
+[[Category: Dzikovski, B]]
-[[Category: Ealick, S E.]]
+[[Category: Ealick, S E]]
-[[Category: Freed, J.]]
+[[Category: Freed, J]]
-[[Category: Koralewski, R M.]]
+[[Category: Koralewski, R M]]
-[[Category: Krebs, C.]]
+[[Category: Krebs, C]]
-[[Category: Lee, M.]]
+[[Category: Lee, M]]
-[[Category: Lin, H.]]
+[[Category: Lin, H]]
-[[Category: Torelli, A T.]]
+[[Category: Torelli, A T]]
-[[Category: Wang, E.]]
+[[Category: Wang, E]]
-[[Category: Zhang, Y.]]
+[[Category: Zhang, Y]]
-[[Category: Zhu, X.]]
+[[Category: Zhu, X]]
 [[Category: Biosynthetic protein]]
 [[Category: Diphthamide biosynthesis]]