6kxf: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry~~ 6kxf is ~~ON HOLD until Sep 10 2021~~

==The ishigamide ketosynthase/chain length factor==

== Structural highlights ==

<table><tr><td colspan='2'>[[6kxf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._msc090213je08 Streptomyces sp. msc090213je08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KXF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KXF FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DYF:[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl]+dihydrogen+phosphate'>DYF</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">iga11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08]), iga12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08]), iga10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08])</td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kxf OCA], [http://pdbe.org/6kxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kxf RCSB], [http://www.ebi.ac.uk/pdbsum/6kxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kxf ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

In type II polyketide synthases (PKSs), the ketosynthase-chain length factor (KS-CLF) complex catalyzes polyketide chain elongation with the acyl carrier protein (ACP). Highly reducing type II PKSs, represented by IgaPKS, produce polyene structures instead of the well-known aromatic skeletons. Here, we report the crystal structures of the Iga11-Iga12 (KS-CLF) heterodimer and the covalently cross-linked Iga10=Iga11-Iga12 (ACP=KS-CLF) tripartite complex. The latter structure revealed the molecular basis of the interaction between Iga10 and Iga11-Iga12, which differs from that between the ACP and KS of Escherichia coli fatty acid synthase. Furthermore, the reaction pocket structure and site-directed mutagenesis revealed that the negative charge of Asp 113 of Iga11 prevents further condensation using a beta-ketoacyl product as a substrate, which distinguishes IgaPKS from typical type II PKSs. This work will facilitate the future rational design of PKSs.

~~Authors~~:

Structural basis for selectivity in a highly reducing type II polyketide synthase.,Du D, Katsuyama Y, Horiuchi M, Fushinobu S, Chen A, Davis TD, Burkart MD, Ohnishi Y Nat Chem Biol. 2020 May 4. pii: 10.1038/s41589-020-0530-0. doi:, 10.1038/s41589-020-0530-0. PMID:32367018<ref>PMID:32367018</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Streptomyces sp. msc090213je08]]

[[Category: Burkart, M]]

[[Category: Chen, A]]

[[Category: Davis, T]]

[[Category: Du, D]]

[[Category: Fushinobu, S]]

[[Category: Horiuchi, M]]

[[Category: Katsuyama, Y]]

[[Category: Ohnishi, Y]]

[[Category: Polyketide synthase]]

[[Category: Transferase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6kxf is ON HOLD  until Sep 10 2021
+==The ishigamide ketosynthase/chain length factor==
+<StructureSection load='6kxf' size='340' side='right'caption='[[6kxf]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6kxf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._msc090213je08 Streptomyces sp. msc090213je08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KXF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KXF FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DYF:[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl]+dihydrogen+phosphate'>DYF</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">iga11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08]), iga12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08]), iga10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1670457 Streptomyces sp. MSC090213JE08])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kxf OCA], [http://pdbe.org/6kxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kxf RCSB], [http://www.ebi.ac.uk/pdbsum/6kxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kxf ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In type II polyketide synthases (PKSs), the ketosynthase-chain length factor (KS-CLF) complex catalyzes polyketide chain elongation with the acyl carrier protein (ACP). Highly reducing type II PKSs, represented by IgaPKS, produce polyene structures instead of the well-known aromatic skeletons. Here, we report the crystal structures of the Iga11-Iga12 (KS-CLF) heterodimer and the covalently cross-linked Iga10=Iga11-Iga12 (ACP=KS-CLF) tripartite complex. The latter structure revealed the molecular basis of the interaction between Iga10 and Iga11-Iga12, which differs from that between the ACP and KS of Escherichia coli fatty acid synthase. Furthermore, the reaction pocket structure and site-directed mutagenesis revealed that the negative charge of Asp 113 of Iga11 prevents further condensation using a beta-ketoacyl product as a substrate, which distinguishes IgaPKS from typical type II PKSs. This work will facilitate the future rational design of PKSs.
-Authors:
+Structural basis for selectivity in a highly reducing type II polyketide synthase.,Du D, Katsuyama Y, Horiuchi M, Fushinobu S, Chen A, Davis TD, Burkart MD, Ohnishi Y Nat Chem Biol. 2020 May 4. pii: 10.1038/s41589-020-0530-0. doi:, 10.1038/s41589-020-0530-0. PMID:32367018<ref>PMID:32367018</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6kxf" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Streptomyces sp. msc090213je08]]
+[[Category: Burkart, M]]
+[[Category: Chen, A]]
+[[Category: Davis, T]]
+[[Category: Du, D]]
+[[Category: Fushinobu, S]]
+[[Category: Horiuchi, M]]
+[[Category: Katsuyama, Y]]
+[[Category: Ohnishi, Y]]
+[[Category: Polyketide synthase]]
+[[Category: Transferase]]