2w3x: Difference between revisions
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<StructureSection load='2w3x' size='340' side='right' caption='[[2w3x]], [[Resolution|resolution]] 1.75Å' scene=''> | ==Crystal structure of a bifunctional hotdog fold thioesterase in enediyne biosynthesis, CalE7== | ||
<StructureSection load='2w3x' size='340' side='right'caption='[[2w3x]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2w3x]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2w3x]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_echinospora Micromonospora echinospora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W3X FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JEF:O-(O-(2-AMINOPROPYL)-O-(2-METHOXYETHYL)POLYPROPYLENE+GLYCOL+500)'>JEF</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></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]] 1.75Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JEF:O-(O-(2-AMINOPROPYL)-O-(2-METHOXYETHYL)POLYPROPYLENE+GLYCOL+500)'>JEF</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=2w3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w3x OCA], [https://pdbe.org/2w3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w3x RCSB], [https://www.ebi.ac.uk/pdbsum/2w3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w3x ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8KNG2_MICEC Q8KNG2_MICEC] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w3/2w3x_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w3/2w3x_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2w3x ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2w3x" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Micromonospora echinospora]] | [[Category: Micromonospora echinospora]] | ||
[[Category: Cheung | [[Category: Cheung P]] | ||
[[Category: Goh | [[Category: Goh LP]] | ||
[[Category: Ho | [[Category: Ho QS]] | ||
[[Category: Kong | [[Category: Kong R]] | ||
[[Category: Kotaka | [[Category: Kotaka M]] | ||
[[Category: Lescar | [[Category: Lescar J]] | ||
[[Category: Liang | [[Category: Liang ZX]] | ||
[[Category: Liew | [[Category: Liew CW]] | ||
[[Category: Mu | [[Category: Mu Y]] | ||
[[Category: Qureshi | [[Category: Qureshi I]] | ||
[[Category: Sun | [[Category: Sun H]] | ||
Latest revision as of 18:43, 13 December 2023
Crystal structure of a bifunctional hotdog fold thioesterase in enediyne biosynthesis, CalE7Crystal structure of a bifunctional hotdog fold thioesterase in enediyne biosynthesis, CalE7
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe biosynthesis of the enediyne moiety of the antitumor natural product calicheamicin involves an iterative polyketide synthase (CalE8) and other ancillary enzymes. In the proposed mechanism for the early stage of 10-membered enediyne biosynthesis, CalE8 produces a carbonyl-conjugated polyene with the assistance of a putative thioesterase (CalE7). We have determined the x-ray crystal structure of CalE7 and found that the subunit adopts a hotdog fold with an elongated and kinked substrate-binding channel embedded between two subunits. The 1.75-A crystal structure revealed that CalE7 does not contain a critical catalytic residue (Glu or Asp) conserved in other hotdog fold thioesterases. Based on biochemical and site-directed mutagenesis studies, we proposed a catalytic mechanism in which the conserved Arg(37) plays a crucial role in the hydrolysis of the thioester bond, and that Tyr(29) and a hydrogen-bonded water network assist the decarboxylation of the beta-ketocarboxylic acid intermediate. Moreover, computational docking suggested that the substrate-binding channel binds a polyene substrate that contains a single cis double bond at the C4/C5 position, raising the possibility that the C4=C5 double bond in the enediyne moiety could be generated by the iterative polyketide synthase. Together, the results revealed a hotdog fold thioesterase distinct from the common type I and type II thioesterases associated with polyketide biosynthesis and provided interesting insight into the enediyne biosynthetic mechanism. Structure and catalytic mechanism of the thioesterase CalE7 in enediyne biosynthesis.,Kotaka M, Kong R, Qureshi I, Ho QS, Sun H, Liew CW, Goh LP, Cheung P, Mu Y, Lescar J, Liang ZX J Biol Chem. 2009 Jun 5;284(23):15739-49. Epub 2009 Apr 8. PMID:19357082[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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