6da6: Difference between revisions
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==Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)== | ==Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)== | ||
<StructureSection load='6da6' size='340' side='right' caption='[[6da6]], [[Resolution|resolution]] 2.59Å' scene=''> | <StructureSection load='6da6' size='340' side='right'caption='[[6da6]], [[Resolution|resolution]] 2.59Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6da6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DA6 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6da6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseochromogenes Streptomyces griseochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DA6 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.59Å</td></tr> | ||
<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6da6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6da6 OCA], [https://pdbe.org/6da6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6da6 RCSB], [https://www.ebi.ac.uk/pdbsum/6da6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6da6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/C6ZCR8_9ACTN C6ZCR8_9ACTN] Catalyzes the reversible decarboxylation of aromatic carboxylic acids.[HAMAP-Rule:MF_01983] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 23: | Line 23: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Streptomyces griseochromogenes]] | ||
[[Category: | [[Category: Chang C-Y]] | ||
[[Category: | [[Category: Han L]] | ||
[[Category: | [[Category: Miller MD]] | ||
[[Category: | [[Category: Phillips Jr GN]] | ||
[[Category: | [[Category: Rudolf JD]] | ||
[[Category: | [[Category: Shen B]] | ||
[[Category: | [[Category: Soman J]] | ||
Latest revision as of 18:20, 4 October 2023
Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)
Structural highlights
FunctionC6ZCR8_9ACTN Catalyzes the reversible decarboxylation of aromatic carboxylic acids.[HAMAP-Rule:MF_01983] Publication Abstract from PubMedTautomycetin (TTN) is a polyketide natural product featuring a terminal alkene. Functional characterization of the genes within the ttn gene cluster from Streptomyces griseochromogenes established the biosynthesis of the TTN polyketide backbone, its dialkylmaleic anhydride moiety, the coupling of the two moieties to form the nascent intermediate TTN F-1, and the tailoring steps converting TTN F-1 to TTN. Here, we report biochemical and structural characterization of TtnD, a prenylated FMN (prFMN)-dependent decarboxylase belonging to the UbiD family that catalyzes the penultimate step of TTN biosynthesis. TtnD catalyzes decarboxylation of TTN D-1 to TTN I-1, utilizing prFMN as a cofactor generated by the TtnC flavin prenyltransferase; both TtnD and TtnC are encoded within the ttn biosynthetic gene cluster. TtnD exhibits substrate promiscuity but accepts only TTN D-1 congeners that feature an alpha,beta-unsaturated acid, supporting the [3+2] cycloaddition mechanism during catalysis that requires the double bond of an alpha,beta-unsaturated acid substrate. TtnD shares a similar overall structure with other members of the UbiD family but forms a homotetramer in solution. Each protomer is composed of three domains with the active site located between the middle and C-terminal domains; R169-E272-E277, constituting the catalytic triad, and E228, involved in Mn(II)-mediated binding of prFMN, were confirmed by site-directed mutagenesis. TtnD represents the first example of a prFMN-dependent decarboxylase involved in polyketide biosynthesis, expanding the substrate scope of the UbiD family of decarboxylases beyond simple aromatic and cinnamic acids. TtnD and its homologues are widespread in nature and could be exploited as biocatalysts for organic synthesis. Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway.,Annaval T, Han L, Rudolf JD, Xie G, Yang D, Chang CY, Ma M, Crnovcic I, Miller MD, Soman J, Xu W, Phillips GN Jr, Shen B ACS Chem Biol. 2018 Sep 21;13(9):2728-2738. doi: 10.1021/acschembio.8b00673. Epub, 2018 Sep 10. PMID:30152678[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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