7ris: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 7ris is ~~ON HOLD until Paper~~ Publication

==Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound phosphate==

== Structural highlights ==

<table><tr><td colspan='2'>[[7ris]] 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=7RIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RIS FirstGlance]. <br>

</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=PO4:PHOSPHATE+ION'>PO4</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=7ris FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ris OCA], [https://pdbe.org/7ris PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ris RCSB], [https://www.ebi.ac.uk/pdbsum/7ris PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ris ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q6N3R9_RHOPA Q6N3R9_RHOPA]

== 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.

~~Authors~~:

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>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== 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]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7ris is ON HOLD  until Paper Publication
+==Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound phosphate==
+<StructureSection load='7ris' size='340' side='right'caption='[[7ris]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7ris]] 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=7RIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RIS FirstGlance]. <br>
+</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=PO4:PHOSPHATE+ION'>PO4</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=7ris FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ris OCA], [https://pdbe.org/7ris PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ris RCSB], [https://www.ebi.ac.uk/pdbsum/7ris PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ris 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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7ris" 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]]