8dk0: Difference between revisions
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New page: '''Unreleased structure''' The entry 8dk0 is ON HOLD Authors: Description: Category: Unreleased Structures |
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==Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound (S)gamma-valerolactone== | |||
<StructureSection load='8dk0' size='340' side='right'caption='[[8dk0]], [[Resolution|resolution]] 1.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8dk0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas palustris CGA009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DK0 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=YVR:GAMMA-VALEROLACTONE'>YVR</scene></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=8dk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dk0 OCA], [https://pdbe.org/8dk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dk0 RCSB], [https://www.ebi.ac.uk/pdbsum/8dk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dk0 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6N3R9_RHOPA Q6N3R9_RHOPA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, gamma-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca(2+)-dependent enzyme from Rhodopseudomonas palustris (Rpa3624) and showed that it can hydrolyze aliphatic and aromatic lactones and esters, including GVL. Maximum-likelihood phylogenetic analysis of other related lactonases with experimentally determined substrate preferences shows that Rpa3624 separates by sequence motifs into a subclade with preference for hydrophobic substrates. Additionally, we solved crystal structures of this beta-propeller enzyme separately with either phosphate, an inhibitor, or a mixture of GVL and products to define an active site where calcium-bound water and calcium-bound aspartic and glutamic acid residues make close contact with substrate and product. Our kinetic characterization of wild type and mutant enzymes combined with structural insights inform a reaction mechanism that centers around activation of a calcium-bound water molecule promoted by general base catalysis and close contacts with substrate and a potential intermediate. Similarity of Rpa3624 with other beta-propeller lactonases suggests this mechanism may be relevant for other members of this emerging class of versatile catalysts. | |||
A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone.,Hall BW, Bingman CA, Fox BG, Noguera DR, Donohue TJ J Biol Chem. 2022 Dec 8:102782. doi: 10.1016/j.jbc.2022.102782. PMID:36502920<ref>PMID:36502920</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8dk0" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhodopseudomonas palustris CGA009]] | |||
[[Category: Bingman CA]] | |||
[[Category: Donohue TJ]] | |||
[[Category: Fox BG]] | |||
[[Category: Hall BW]] | |||
[[Category: Smith RW]] | |||
