2zma: Difference between revisions
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New page: '''Unreleased structure''' The entry 2zma is ON HOLD until Paper Publication Authors: Ohki, T., Shibata, N., Higuchi, Y., Takeo, M., Negoro, S. Description: Crystal Structure of 6-Amin... |
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==Crystal Structure of 6-Aminohexanoate-dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate== | |||
<StructureSection load='2zma' size='340' side='right'caption='[[2zma]], [[Resolution|resolution]] 1.51Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2zma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMA 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]] 1.51Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2zma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zma OCA], [https://pdbe.org/2zma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zma RCSB], [https://www.ebi.ac.uk/pdbsum/2zma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zma ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NYLB2_FLASK NYLB2_FLASK] Involved in nylon oligomer degradation.<ref>PMID:6389532</ref> <ref>PMID:6646204</ref> [https://www.uniprot.org/uniprot/NYLB_FLASK NYLB_FLASK] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zma_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zma ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A carboxylesterase with a beta-lactamase fold from Arthrobacter possesses a low level of hydrolytic activity (0.023 mumol.min(-1).mg(-1)) when acting on a 6-aminohexanoate linear dimer byproduct of the nylon-6 industry (Ald). G181D/H266N/D370Y triple mutations in the parental esterase increased the Ald-hydrolytic activity 160-fold. Kinetic studies showed that the triple mutant possesses higher affinity for the substrate Ald (K(m) = 2.0 mm) than the wild-type Ald hydrolase from Arthrobacter (K(m) = 21 mm). In addition, the k(cat)/K(m) of the mutant (1.58 s(-1).mm(-1)) was superior to that of the wild-type enzyme (0.43 s(-1).mm(-1)), demonstrating that the mutant efficiently converts the unnatural amide compounds even at low substrate concentrations, and potentially possesses an advantage for biotechnological applications. X-ray crystallographic analyses of the G181D/H266N/D370Y enzyme and the inactive S112A-mutant-Ald complex revealed that Ald binding induces rotation of Tyr370/His375, movement of the loop region (N167-V177), and flip-flop of Tyr170, resulting in the transition from open to closed forms. From the comparison of the three-dimensional structures of various mutant enzymes and site-directed mutagenesis at positions 266 and 370, we now conclude that Asn266 makes suitable contacts with Ald and improves the electrostatic environment at the N-terminal region of Ald cooperatively with Asp181, and that Tyr370 stabilizes Ald binding by hydrogen-bonding/hydrophobic interactions at the C-terminal region of Ald. | |||
Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.,Kawashima Y, Ohki T, Shibata N, Higuchi Y, Wakitani Y, Matsuura Y, Nakata Y, Takeo M, Kato D, Negoro S FEBS J. 2009 May;276(9):2547-56. Epub 2009 Mar 18. PMID:19476493<ref>PMID:19476493</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2zma" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[6-aminohexanoate-dimer hydrolase 3D structures|6-aminohexanoate-dimer hydrolase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Flavobacterium sp]] | |||
[[Category: Large Structures]] | |||
[[Category: Higuchi Y]] | |||
[[Category: Negoro S]] | |||
[[Category: Ohki T]] | |||
[[Category: Shibata N]] | |||
[[Category: Takeo M]] | |||
