5k87: Difference between revisions
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==crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis== | ==crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis== | ||
<StructureSection load='5k87' size='340' side='right' caption='[[5k87]], [[Resolution|resolution]] 1.22Å' scene=''> | <StructureSection load='5k87' size='340' side='right'caption='[[5k87]], [[Resolution|resolution]] 1.22Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5k87]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5k87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K87 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.219Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=5k87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k87 OCA], [https://pdbe.org/5k87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k87 RCSB], [https://www.ebi.ac.uk/pdbsum/5k87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k87 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/PRPF_SHEON PRPF_SHEON] Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle II (propionate degradation route). PrpF catalyzes the cis-trans isomerization of 2-methyl-aconitate through a base-catalyzed proton abstraction coupled with a rotation about C2-C3 bond of 2-methyl-aconitate.<ref>PMID:14702315</ref> <ref>PMID:17567742</ref> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The 2-methylcitric acid cycle (2-MCC) is a common route of propionate catabolism in microorganisms. In Salmonella enterica, the prpBCDE operon encodes most of the 2-MCC enzymes. In other organisms, e.g., Shewanella oneidensis MR-1, two genes, acnD and prpF replace prpD, which encodes 2-methylcitrate dehydratase. We showed that together, S. oneidensis AcnD and PrpF (SoAcnD, SoPrpF) compensated for the absence of PrpD in a S. enterica prpD strain. We also showed that SoAcnD had 2-methylcitrate dehydratase activity and that PrpF has aconitate isomerase activity. Here we report in vitro evidence that the product of the SoAcnD reaction is an isomer of 2-methyl-cis-aconitate (2-MCA], the product of the SePrpD reaction. We show that the SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product (2-MCA], a known substrate of the housekeeping aconitase (AcnB]. Given that SoPrpF is an isomerase, that SoAcnD is a dehydratase, and the results from in vivo and in vitro experiments reported here, it is likely that 4-methylaconitate is the product of the AcnD enzyme. Results from in vivo studies using a S. enterica prpD strain show that SoPrpF variants with substitutions of residues K73 or C107 failed to support growth with propionate as the sole source of carbon and energy. High-resolution (1.22 A) three-dimensional crystal structures of PrpFK73E in complex with trans-aconitate or malonate provide insights into the mechanism of catalysis of the wild-type protein. | |||
The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle.,Rocco CJ, Wetterhorn KM, Garvey GS, Rayment I, Escalante-Semerena JC PLoS One. 2017 Nov 16;12(11):e0188130. doi: 10.1371/journal.pone.0188130., eCollection 2017. PMID:29145506<ref>PMID:29145506</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5k87" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Shewanella oneidensis MR-1]] | ||
[[Category: | [[Category: Rayment I]] | ||
[[Category: | [[Category: Wetterhorn K]] | ||
