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| | <StructureSection load='2zm9' size='340' side='right'caption='[[2zm9]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='2zm9' size='340' side='right'caption='[[2zm9]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zm9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"corynebacterium_creatinovorans"_dubos_and_miller_1937 "corynebacterium creatinovorans" dubos and miller 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zm9]] 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=2ZM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM9 FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wyb|1wyb]], [[1wyc|1wyc]], [[2dcf|2dcf]], [[2e8i|2e8i]], [[2zm7|2zm7]], [[2zm8|2zm8]], [[2zma|2zma]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nylB, nylB' ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37931 "Corynebacterium creatinovorans" Dubos and Miller 1937])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </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=2zm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm9 OCA], [https://pdbe.org/2zm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm9 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm9 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=2zm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm9 OCA], [https://pdbe.org/2zm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm9 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm9 ProSAT]</span></td></tr> |
| | </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]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Corynebacterium creatinovorans dubos and miller 1937]] | + | [[Category: Flavobacterium sp]] |
| - | [[Category: 6-aminohexanoate-dimer hydrolase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Higuchi, Y]] | + | [[Category: Higuchi Y]] |
| - | [[Category: Kato, D]] | + | [[Category: Kato D]] |
| - | [[Category: Kawashima, Y]] | + | [[Category: Kawashima Y]] |
| - | [[Category: Negoro, S]] | + | [[Category: Negoro S]] |
| - | [[Category: Ohki, T]] | + | [[Category: Ohki T]] |
| - | [[Category: Shibata, N]] | + | [[Category: Shibata N]] |
| - | [[Category: Takeo, M]] | + | [[Category: Takeo M]] |
| - | [[Category: Alpha-beta]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nylon degradation]]
| + | |
| Structural highlights
Function
NYLB2_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 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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Negoro S, Nakamura S, Kimura H, Fujiyama K, Zhang YZ, Kanzaki N, Okada H. Construction of hybrid genes of 6-aminohexanoic acid-oligomer hydrolase and its analogous enzyme. Estimation of the intramolecular regions important for the enzyme evolution. J Biol Chem. 1984 Nov 25;259(22):13648-51 PMID:6389532
- ↑ Okada H, Negoro S, Kimura H, Nakamura S. Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature. 1983 Nov 10-16;306(5939):203-6. PMID:6646204 doi:10.1038/306203a0
- ↑ Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S. 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. Protein Sci. 2009 Aug;18(8):1662-73. PMID:19521995 doi:10.1002/pro.185
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