2zm7: Difference between revisions
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==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/G181D Mutant Complexed with 6-Aminohexanoate-dimer== | ==Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/G181D Mutant Complexed with 6-Aminohexanoate-dimer== | ||
<StructureSection load='2zm7' size='340' side='right' caption='[[2zm7]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='2zm7' size='340' side='right'caption='[[2zm7]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2zm7]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2zm7]] 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=2ZM7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</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=2zm7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm7 OCA], [https://pdbe.org/2zm7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm7 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm7 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zm7_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zm7_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2zm7 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 27: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2zm7" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[6-aminohexanoate-dimer hydrolase|6-aminohexanoate-dimer hydrolase]] | *[[6-aminohexanoate-dimer hydrolase 3D structures|6-aminohexanoate-dimer hydrolase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Flavobacterium sp]] | [[Category: Flavobacterium sp]] | ||
[[Category: Higuchi | [[Category: Large Structures]] | ||
[[Category: Kato | [[Category: Higuchi Y]] | ||
[[Category: Kawashima | [[Category: Kato D]] | ||
[[Category: Negoro | [[Category: Kawashima Y]] | ||
[[Category: Ohki | [[Category: Negoro S]] | ||
[[Category: Shibata | [[Category: Ohki T]] | ||
[[Category: Takeo | [[Category: Shibata N]] | ||
[[Category: Takeo M]] | |||
Latest revision as of 16:43, 1 November 2023
Structure of 6-Aminohexanoate-dimer Hydrolase, S112A/G181D Mutant Complexed with 6-Aminohexanoate-dimerStructure of 6-Aminohexanoate-dimer Hydrolase, S112A/G181D Mutant Complexed with 6-Aminohexanoate-dimer
Structural highlights
FunctionNYLB2_FLASK Involved in nylon oligomer degradation.[1] [2] NYLB_FLASK Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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