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| - | [[Image:1wyc.gif|left|200px]] | |
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| - | <!--
| + | ==Structure of 6-aminohexanoate-dimer hydrolase, DN mutant== |
| - | The line below this paragraph, containing "STRUCTURE_1wyc", creates the "Structure Box" on the page.
| + | <StructureSection load='1wyc' size='340' side='right'caption='[[1wyc]], [[Resolution|resolution]] 1.58Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1wyc]] 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=1WYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYC FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyc OCA], [https://pdbe.org/1wyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyc RCSB], [https://www.ebi.ac.uk/pdbsum/1wyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyc ProSAT]</span></td></tr> |
| - | {{STRUCTURE_1wyc| PDB=1wyc | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NYLB2_PAEUR NYLB2_PAEUR] Involved in nylon oligomer degradation.<ref>PMID:6389532</ref> <ref>PMID:6646204</ref> |
| | + | == 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/wy/1wyc_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=1wyc ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase (Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN) and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution, respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between Asn167 and Val177. This state is the so-called open form, allowing its substrate to bind in the space between the loop and catalytic residues. Upon substrate binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In addition, electrostatic interaction between Asp181-O(delta) and the amino group in Ald stabilizes the substrate binding. We propose here that the enzyme catalysis proceeds according to the following steps: (i) Ald-induced transition from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and transition to open form, (iv) deacylation. Amino acid substitutions reducing the enzyme/Ald interaction at positions 181 or 170 drastically decreased the Ald-hydrolytic activity, but had very little effect on esterolytic activity, suggesting that esterolytic reaction proceeds regardless of conversion. Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions. |
| | | | |
| - | '''Structure of 6-aminohexanoate-dimer hydrolase, DN mutant'''
| + | Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase.,Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:17512009<ref>PMID:17512009</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase (Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN) and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution, respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between Asn167 and Val177. This state is the so-called open form, allowing its substrate to bind in the space between the loop and catalytic residues. Upon substrate binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In addition, electrostatic interaction between Asp181-O(delta) and the amino group in Ald stabilizes the substrate binding. We propose here that the enzyme catalysis proceeds according to the following steps: (i) Ald-induced transition from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and transition to open form, (iv) deacylation. Amino acid substitutions reducing the enzyme/Ald interaction at positions 181 or 170 drastically decreased the Ald-hydrolytic activity, but had very little effect on esterolytic activity, suggesting that esterolytic reaction proceeds regardless of conversion. Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 1WYC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYC OCA].
| + | </div> |
| | + | <div class="pdbe-citations 1wyc" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase., Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y, J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17512009 17512009]
| + | *[[6-aminohexanoate-dimer hydrolase 3D structures|6-aminohexanoate-dimer hydrolase 3D structures]] |
| - | [[Category: 6-aminohexanoate-dimer hydrolase]]
| + | == References == |
| - | [[Category: Flavobacterium sp.]] | + | <references/> |
| - | [[Category: Single protein]] | + | __TOC__ |
| - | [[Category: Higuchi, Y.]] | + | </StructureSection> |
| - | [[Category: Kawamoto, I.]] | + | [[Category: Flavobacterium sp]] |
| - | [[Category: Matsumoto, K.]] | + | [[Category: Large Structures]] |
| - | [[Category: Mizuno, N.]] | + | [[Category: Higuchi Y]] |
| - | [[Category: Negoro, S.]] | + | [[Category: Kawamoto I]] |
| - | [[Category: Ohki, T.]] | + | [[Category: Matsumoto K]] |
| - | [[Category: Shibata, N.]] | + | [[Category: Mizuno N]] |
| - | [[Category: Takeo, M.]] | + | [[Category: Negoro S]] |
| - | [[Category: Tsurukame, J.]] | + | [[Category: Ohki T]] |
| - | [[Category: Wakitani, Y.]] | + | [[Category: Shibata N]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Takeo M]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 28 09:27:01 2008''
| + | [[Category: Tsurukame J]] |
| | + | [[Category: Wakitani Y]] |
| Structural highlights
Function
NYLB2_PAEUR Involved in nylon oligomer degradation.[1] [2]
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
We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase (Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN) and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution, respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between Asn167 and Val177. This state is the so-called open form, allowing its substrate to bind in the space between the loop and catalytic residues. Upon substrate binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In addition, electrostatic interaction between Asp181-O(delta) and the amino group in Ald stabilizes the substrate binding. We propose here that the enzyme catalysis proceeds according to the following steps: (i) Ald-induced transition from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and transition to open form, (iv) deacylation. Amino acid substitutions reducing the enzyme/Ald interaction at positions 181 or 170 drastically decreased the Ald-hydrolytic activity, but had very little effect on esterolytic activity, suggesting that esterolytic reaction proceeds regardless of conversion. Present models illustrate why new activity against the nylon oligomer has evolved in an esterase with beta-lactamase folds, while retaining the original esterolytic functions.
Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase.,Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:17512009[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
- ↑ Negoro S, Ohki T, Shibata N, Sasa K, Hayashi H, Nakano H, Yasuhira K, Kato D, Takeo M, Higuchi Y. Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase. J Mol Biol. 2007 Jun 29;370(1):142-56. Epub 2007 Apr 24. PMID:17512009 doi:http://dx.doi.org/10.1016/j.jmb.2007.04.043
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