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| | ==Structure of 6-aminohexanoate cyclic dimer hydrolase complexed with substrate== | | ==Structure of 6-aminohexanoate cyclic dimer hydrolase complexed with substrate== |
| - | <StructureSection load='3a2q' size='340' side='right' caption='[[3a2q]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='3a2q' size='340' side='right'caption='[[3a2q]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a2q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp._ki72 Arthrobacter sp. ki72]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A2Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a2q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_ureafaciens Paenarthrobacter ureafaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2Q 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></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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a2p|3a2p]]</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></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-cyclic-dimer_hydrolase 6-aminohexanoate-cyclic-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.12 3.5.2.12] </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=3a2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2q OCA], [https://pdbe.org/3a2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2q RCSB], [https://www.ebi.ac.uk/pdbsum/3a2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2q ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3a2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2q OCA], [http://pdbe.org/3a2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a2q RCSB], [http://www.ebi.ac.uk/pdbsum/3a2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NYLA_FLASK NYLA_FLASK]] Specifically catalyzes the hydrolysis of 6-aminohexanoic acid cyclic dimer (1,8-diazacyclotetradecane-2,9-dione) to form the linear dimer 6-aminohexanoyl-6-aminohexanoic acid. Is inactive on 6-aminohexanoic acid oligomers (degree of polymerization 2 to 6), various other cyclic amides, cyclic diamides, linear amides, oligopeptides, and casein. Allows the bacterium to grow on a medium containing 6-aminohexanoic acid cyclic dimer as the sole carbon and nitrogen sources.<ref>PMID:923591</ref> | + | [https://www.uniprot.org/uniprot/NYLA_FLASK NYLA_FLASK] Specifically catalyzes the hydrolysis of 6-aminohexanoic acid cyclic dimer (1,8-diazacyclotetradecane-2,9-dione) to form the linear dimer 6-aminohexanoyl-6-aminohexanoic acid. Is inactive on 6-aminohexanoic acid oligomers (degree of polymerization 2 to 6), various other cyclic amides, cyclic diamides, linear amides, oligopeptides, and casein. Allows the bacterium to grow on a medium containing 6-aminohexanoic acid cyclic dimer as the sole carbon and nitrogen sources.<ref>PMID:923591</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==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: 6-aminohexanoate-cyclic-dimer hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Arthrobacter sp. ki72]] | + | [[Category: Paenarthrobacter ureafaciens]] |
| - | [[Category: Shibata, N]] | + | [[Category: Shibata N]] |
| - | [[Category: Alpha/beta fold]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nylon degradation]]
| + | |
| Structural highlights
Function
NYLA_FLASK Specifically catalyzes the hydrolysis of 6-aminohexanoic acid cyclic dimer (1,8-diazacyclotetradecane-2,9-dione) to form the linear dimer 6-aminohexanoyl-6-aminohexanoic acid. Is inactive on 6-aminohexanoic acid oligomers (degree of polymerization 2 to 6), various other cyclic amides, cyclic diamides, linear amides, oligopeptides, and casein. Allows the bacterium to grow on a medium containing 6-aminohexanoic acid cyclic dimer as the sole carbon and nitrogen sources.[1]
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 the 6-aminohexanoate cyclic dimer (Acd) hydrolase (NylA) from Arthrobacter sp., an enzyme responsible for the degradation of the nylon-6 industry byproduct. The fold adopted by the 472-amino acid polypeptide generated a compact mixed alpha/beta fold, typically found in the amidase signature superfamily; this fold was especially similar to the fold of glutamyl-tRNA(Gln) amidotransferase subunit A (z score, 49.4) and malonamidase E2 (z score, 44.8). Irrespective of the high degree of structural similarity to the typical amidase signature superfamily enzymes, the specific activity of NylA for glutamine, malonamide, and indoleacetamide was found to be lower than 0.5% of that for Acd. However, NylA possessed carboxylesterase activity nearly equivalent to the Acd hydrolytic activity. Structural analysis of the inactive complex between the activity-deficient S174A mutant of NylA and Acd, performed at 1.8 A resolution, suggested the following enzyme/substrate interactions: a Ser(174)-cis-Ser(150)-Lys(72) triad constitutes the catalytic center; the backbone N in Ala(171) and Ala(172) are involved in oxyanion stabilization; Cys(316)-S(gamma) forms a hydrogen bond with nitrogen (Acd-N(7)) at the uncleaved amide bond in two equivalent amide bonds of Acd. A single S174A, S150A, or K72A substitution in NylA by site-directed mutagenesis decreased the Acd hydrolytic and esterolytic activities to undetectable levels, indicating that Ser(174)-cis-Ser(150)-Lys(72) is essential for catalysis. In contrast, substitutions at position 316 specifically affected Acd hydrolytic activity, suggesting that Cys(316) is responsible for Acd binding. On the basis of the structure and functional analysis, we discussed the catalytic mechanisms and evolution of NylA in comparison with other Ser-reactive hydrolases.
X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.,Yasuhira K, Shibata N, Mongami G, Uedo Y, Atsumi Y, Kawashima Y, Hibino A, Tanaka Y, Lee YH, Kato D, Takeo M, Higuchi Y, Negoro S J Biol Chem. 2010 Jan 8;285(2):1239-48. Epub 2009 Nov 3. PMID:19889645[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kinoshita S, Negoro S, Muramatsu M, Bisaria VS, Sawada S, Okada H. 6-Aminohexanoic acid cyclic dimer hydrolase. A new cyclic amide hydrolase produced by Achromobacter guttatus KI74. Eur J Biochem. 1977 Nov 1;80(2):489-95. PMID:923591
- ↑ Yasuhira K, Shibata N, Mongami G, Uedo Y, Atsumi Y, Kawashima Y, Hibino A, Tanaka Y, Lee YH, Kato D, Takeo M, Higuchi Y, Negoro S. X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation. J Biol Chem. 2010 Jan 8;285(2):1239-48. Epub 2009 Nov 3. PMID:19889645 doi:10.1074/jbc.M109.041285
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