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3nyr

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Current revision (10:02, 14 February 2024) (edit) (undo)
 
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<StructureSection load='3nyr' size='340' side='right'caption='[[3nyr]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='3nyr' size='340' side='right'caption='[[3nyr]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3nyr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3nyr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NYR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLC:MALONYL-COENZYME+A'>MLC</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nyq|3nyq]], [[3ite|3ite]], [[3e7w|3e7w]], [[1t5d|1t5d]], [[2d1r|2d1r]], [[1ry2|1ry2]], [[1pg3|1pg3]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MLC:MALONYL-COENZYME+A'>MLC</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MatB, SCC24.15, SCO2444 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyr OCA], [https://pdbe.org/3nyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyr RCSB], [https://www.ebi.ac.uk/pdbsum/3nyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyr ProSAT]</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=3nyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nyr OCA], [https://pdbe.org/3nyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nyr RCSB], [https://www.ebi.ac.uk/pdbsum/3nyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nyr ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9L0A2_STRCO Q9L0A2_STRCO]
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In vitro experiments with modular polyketide synthases (PKSs) are often limited by the availability of polyketide extender units. To determine the polyketide extender units that can be biocatalytically accessed via promiscuous malonyl-CoA ligases, structural and functional studies were conducted on Streptomyces coelicolor MatB. We demonstrate that this adenylate-forming enzyme is capable of producing most CoA-linked polyketide extender units as well as pantetheine- and N-acetylcysteamine-linked analogs useful for in vitro PKS studies. Two ternary product complex structures, one containing malonyl-CoA and AMP and the other containing (2R)-methylmalonyl-CoA and AMP, were solved to 1.45 A and 1.43 A resolution, respectively. MatB crystallized in the thioester-forming conformation, making extensive interactions with the bound extender unit products. This first structural characterization of an adenylate-forming enzyme that activates diacids reveals the molecular details for how malonate and its derivatives are accepted. The orientation of the alpha-methyl group of bound (2R)-methylmalonyl-CoA, indicates that it is necessary to epimerize alpha-substituted extender units formed by MatB before they can be accepted by PKS acyltransferase domains. We demonstrate the in vitro incorporation of methylmalonyl groups ligated by MatB to CoA, pantetheine, or N-acetylcysteamine into a triketide pyrone by the terminal module of the 6-deoxyerythronolide B synthase. Additionally, a means for quantitatively monitoring certain in vitro PKS reactions using MatB is presented.
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Enzymatic extender unit generation for in vitro polyketide synthase reactions: structural and functional showcasing of Streptomyces coelicolor MatB.,Hughes AJ, Keatinge-Clay A Chem Biol. 2011 Feb 25;18(2):165-76. PMID:21338915<ref>PMID:21338915</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3nyr" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Hughes, A J]]
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[[Category: Streptomyces coelicolor]]
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[[Category: Keatinge-Clay, A T]]
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[[Category: Hughes AJ]]
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[[Category: A/b topology ababa sandwich beta-barrel]]
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[[Category: Keatinge-Clay AT]]
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[[Category: Adenylate-forming enzyme fold]]
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[[Category: Ligase]]
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Current revision

Malonyl-CoA Ligase Ternary Product Complex with Malonyl-CoA and AMP bound

PDB ID 3nyr

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