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| | ==Crystal structure of the thioesterase domain of deoxyerythronolide B synthase== | | ==Crystal structure of the thioesterase domain of deoxyerythronolide B synthase== |
| - | <StructureSection load='5d3k' size='340' side='right' caption='[[5d3k]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='5d3k' size='340' side='right'caption='[[5d3k]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5d3k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D3K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5d3k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D3K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d2r|5d2r]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=5d3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d3k OCA], [https://pdbe.org/5d3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d3k RCSB], [https://www.ebi.ac.uk/pdbsum/5d3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d3k ProSAT]</span></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=5d3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d3k OCA], [http://pdbe.org/5d3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d3k RCSB], [http://www.ebi.ac.uk/pdbsum/5d3k PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ERYA3_SACER ERYA3_SACER] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5d3k" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5d3k" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[6-deoxyerythronolide B synthase 3D structures|6-deoxyerythronolide B synthase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 6-deoxyerythronolide-B synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Argyropoulos, P]] | + | [[Category: Saccharopolyspora erythraea]] |
| - | [[Category: Bergeret, F]] | + | [[Category: Argyropoulos P]] |
| - | [[Category: Boddy, C N]] | + | [[Category: Bergeret F]] |
| - | [[Category: Schmeing, T M]] | + | [[Category: Boddy CN]] |
| - | [[Category: Hydrolase]] | + | [[Category: Schmeing TM]] |
| - | [[Category: Thioesterase domaine alpha / beta hydrolase fold deoxyerythronolide b synthase]]
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| Structural highlights
Function
ERYA3_SACER
Publication Abstract from PubMed
Type I polyketide synthases (PKSs) are giant multidomain proteins that synthesize many therapeutics and other natural products. The synthesis proceeds by a thiotemplate mechanism whereby intermediates are covalently attached to the PKS. The release of the final polyketide is catalyzed by the terminal thioesterase (TE) domain through hydrolysis, transesterification, or macrocyclization. The PKS 6-deoxyerythronolide B synthase (DEBS) produces the 14-membered macrolide core of the clinically important antibiotic erythromycin. The TE domain of DEBS (DEBS TE) has well-established, empirically-defined specificities for hydrolysis or macrocyclization of native and modified substrates. We present efforts towards understanding the structural basis for the specificity of the thioesterase reaction in DEBS TE using a set of novel diphenyl alkylphosphonates, which mimic substrates that are specifically cyclized or hydrolyzed by DEBS TE. We have determined structures of a new construct of DEBS TE alone at 1.7A, and DEBS TE bound with a simple allylphosphonate at 2.1A resolution. Other, more complex diphenyl alkylphosphonates inhibit DEBS TE, but we were unable to visualize these faithful cyclization analogs in complex with DEBS TE. This work represents a first step towards using DEBS TE complexed with sophisticated substrate analogs to decipher the specificity determinants in this important reaction.
Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis.,Argyropoulos P, Bergeret F, Pardin C, Reimer JM, Pinto A, Boddy CN, Martin Schmeing T Biochim Biophys Acta. 2015 Nov 22. pii: S0304-4165(15)00324-4. doi:, 10.1016/j.bbagen.2015.11.007. PMID:26592346[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Argyropoulos P, Bergeret F, Pardin C, Reimer JM, Pinto A, Boddy CN, Martin Schmeing T. Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis. Biochim Biophys Acta. 2015 Nov 22. pii: S0304-4165(15)00324-4. doi:, 10.1016/j.bbagen.2015.11.007. PMID:26592346 doi:http://dx.doi.org/10.1016/j.bbagen.2015.11.007
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