3qm1: Difference between revisions

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<StructureSection load='3qm1' size='340' side='right'caption='[[3qm1]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='3qm1' size='340' side='right'caption='[[3qm1]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qm1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33200 Atcc 33200]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QM1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qm1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_johnsonii Lactobacillus johnsonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QM1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZYC:ETHYL+(2E)-3-(4-HYDROXY-3-METHOXYPHENYL)PROP-2-ENOATE'>ZYC</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]] 1.817&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pf8|3pf8]], [[3pf9|3pf9]], [[3pfa|3pfa]], [[3pfb|3pfb]], [[3pfc|3pfc]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZYC:ETHYL+(2E)-3-(4-HYDROXY-3-METHOXYPHENYL)PROP-2-ENOATE'>ZYC</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LJ0536 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33959 ATCC 33200])</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=3qm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qm1 OCA], [https://pdbe.org/3qm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3qm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qm1 ProSAT]</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=3qm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qm1 OCA], [https://pdbe.org/3qm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3qm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qm1 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/D3YEX6_LACJH D3YEX6_LACJH]
BACKGROUND: Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. METHODOLOGY/PRINCIPAL FINDINGS: We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical alpha/beta fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser(106), His(225), and Asp(197), while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted alpha/beta subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. CONCLUSIONS: The binding mechanism characterized (involving the inserted alpha/beta subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases.
 
An inserted alpha/beta subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase.,Lai KK, Stogios PJ, Vu C, Xu X, Cui H, Molloy S, Savchenko A, Yakunin A, Gonzalez CF PLoS One. 2011;6(8):e23269. Epub 2011 Aug 18. PMID:21876742<ref>PMID:21876742</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qm1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 33200]]
[[Category: Lactobacillus johnsonii]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cui, H]]
[[Category: Cui H]]
[[Category: Gonzalez, C F]]
[[Category: Gonzalez CF]]
[[Category: Lai, K K]]
[[Category: Lai KK]]
[[Category: Molloy, S]]
[[Category: Molloy S]]
[[Category: Savchenko, A]]
[[Category: Savchenko A]]
[[Category: Stogios, P J]]
[[Category: Stogios PJ]]
[[Category: Vu, C]]
[[Category: Vu C]]
[[Category: Xu, X]]
[[Category: Xu X]]
[[Category: Yakunin, A]]
[[Category: Yakunin A]]
[[Category: Alpha/beta hydrolase fold]]
[[Category: Cinnamoyl/feruloyl esterase]]
[[Category: Hydrolase]]
[[Category: Hydroxycinammate]]

Latest revision as of 11:50, 14 March 2024

CRYSTAL STRUCTURE OF THE LACTOBACILLUS JOHNSONII CINNAMOYL ESTERASE LJ0536 S106A MUTANT IN COMPLEX WITH ETHYLFERULATE, Form II

3qm1, resolution 1.82Å

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