3axg

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<StructureSection load='3axg' size='340' side='right'caption='[[3axg]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3axg' size='340' side='right'caption='[[3axg]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3axg]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Agromyces_sp._ky5r Agromyces sp. ky5r]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXG FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3axg]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Agromyces_sp._KY5R Agromyces sp. KY5R]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXG FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nylC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=388924 Agromyces sp. KY5R])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=3axg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axg OCA], [https://pdbe.org/3axg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axg RCSB], [https://www.ebi.ac.uk/pdbsum/3axg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axg 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=3axg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axg OCA], [https://pdbe.org/3axg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axg RCSB], [https://www.ebi.ac.uk/pdbsum/3axg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axg ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/NYLC_AGRS5 NYLC_AGRS5] Involved in the degradation of nylon-6 oligomers. Degrades cyclic and linear oligomers of 6-aminohexanoate (Ahx) with a degree of polymerization greater than three by an endo-type mode. Cannot use Ahx cyclic dimer or the Ahx linear dimer.<ref>PMID:17827307</ref>
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We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 A-resolution. This enzyme is a member of the N-terminal nucleophile hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct. We observed four identical heterodimers (27 kDa + 9 kDa), which resulted from the autoprocessing of the precursor protein (36 kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr-267 of the 9-kDa subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked alphabetabetaalpha core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130Y/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T(m) = 52 degrees C, enhanced the protein thermostability by 36 degrees C (T(m) = 88 degrees C), whereas a single mutation (G111S or L137A) decreased the stability by approximately 10 degrees C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60 degrees C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.
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Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis.,Negoro S, Shibata N, Tanaka Y, Yasuhira K, Shibata H, Hashimoto H, Lee YH, Oshima S, Santa R, Oshima S, Mochiji K, Goto Y, Ikegami T, Nagai K, Kato D, Takeo M, Higuchi Y J Biol Chem. 2012 Feb 10;287(7):5079-90. doi: 10.1074/jbc.M111.321992. Epub 2011 , Dec 19. PMID:22187439<ref>PMID:22187439</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3axg" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Agromyces sp. ky5r]]
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[[Category: Agromyces sp. KY5R]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Goto, Y]]
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[[Category: Goto Y]]
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[[Category: Hashimoto, H]]
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[[Category: Hashimoto H]]
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[[Category: Higuchi, Y]]
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[[Category: Higuchi Y]]
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[[Category: Ikegami, T]]
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[[Category: Ikegami T]]
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[[Category: Kato, D]]
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[[Category: Kato D]]
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[[Category: Lee, Y H]]
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[[Category: Lee YH]]
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[[Category: Mochiji, K]]
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[[Category: Mochiji K]]
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[[Category: Nagai, K]]
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[[Category: Nagai K]]
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[[Category: Negoro, S]]
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[[Category: Negoro S]]
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[[Category: Ohshima, S]]
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[[Category: Ohshima S]]
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[[Category: Santa, R]]
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[[Category: Santa R]]
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[[Category: Shibata, H]]
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[[Category: Shibata H]]
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[[Category: Shibata, N]]
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[[Category: Shibata N]]
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[[Category: Takeo, M]]
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[[Category: Takeo M]]
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[[Category: Tanaka, Y]]
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[[Category: Tanaka Y]]
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[[Category: Yasuhira, K]]
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[[Category: Yasuhira K]]
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[[Category: Hydrolase]]
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[[Category: Nylon oligomer]]
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Current revision

Structure of 6-aminohexanoate-oligomer hydrolase

PDB ID 3axg

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