2zly: Difference between revisions
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New page: '''Unreleased structure''' The entry 2zly is ON HOLD until Paper Publication Authors: Ohki, T., Shibata, N., Higuchi, Y., Kawashima, Y., Takeo, M., Kato, D., Negoro, S. Description: St... |
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==Structure of 6-aminohexanoate-dimer hydrolase, D370Y mutant== | |||
<StructureSection load='2zly' size='340' side='right'caption='[[2zly]], [[Resolution|resolution]] 1.58Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2zly]] 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=2ZLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZLY 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]] 1.58Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2zly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zly OCA], [https://pdbe.org/2zly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zly RCSB], [https://www.ebi.ac.uk/pdbsum/2zly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zly 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/zl/2zly_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=2zly ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Promiscuous 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity originally obtained in a carboxylesterase with a beta-lactamase fold was enhanced about 80-fold by directed evolution using error-prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb-S4M94) demonstrated that the enzyme had acquired an increased affinity (K(m) = 15 mM) and turnover (k(cat) = 3.1 s(-1)) for Ald, and that a catalytic center suitable for nylon-6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb-S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen-bonding/hydrophobic interactions between the Ald--COOH and Tyr370, a hydrogen-bonding network from Ser187 to Ald--NH(3) (+), and interaction between Ald--NH(3) (+) and Gln27-O(epsilon) derived from another subunit in the homo-dimeric structure. In wild-type Ald-hydrolase (NylB), Ald-hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with Ald--NH(3) (+) (Kawashima et al., FEBS J 2009; 276:2547-2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a beta-lactamase fold. | |||
Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.,Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S Protein Sci. 2009 Aug;18(8):1662-73. PMID:19521995<ref>PMID:19521995</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2zly" 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: Kato D]] | |||
[[Category: Kawashima Y]] | |||
[[Category: Negoro S]] | |||
[[Category: Ohki T]] | |||
[[Category: Shibata N]] | |||
[[Category: Takeo M]] | |||
Latest revision as of 13:42, 1 November 2023
Structure of 6-aminohexanoate-dimer hydrolase, D370Y mutant
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