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3wl3

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==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==
==N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii==
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<StructureSection load='3wl3' size='340' side='right' caption='[[3wl3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='3wl3' size='340' side='right'caption='[[3wl3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3wl3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WL3 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wl4|3wl4]], [[3we7|3we7]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [http://www.ebi.ac.uk/pdbsum/3wl3 PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wl3 OCA], [https://pdbe.org/3wl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wl3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wl3 ProSAT]</span></td></tr>
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<table>
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</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/O58235_PYRHO O58235_PYRHO]
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In order to develop a structure-based understanding of the chitinolytic pathway in hyperthermophilic Pyrococcus species, we performed crystallographic studies on N,N'-diacetylchitobiose deacetylases (Dacs) from Pyrococcus horikoshii (Ph-Dac) and Pyrococcus furiosus (Pf-Dac). Neither Ph-Dac nor Pf-Dac was expressed in the soluble fraction of Escherichia coli harboring the expression plasmid. However, insertion of the target genes into the chromosome of E. coli yielded the soluble recombinant protein. The purified Pyrococcus Dacs were active and thermostable up to 85 degrees C. The crystal structures of Ph-Dac and Pf-Dac were determined at resolutions of 2.0 A and 1.54 A, respectively. The Pyrococcus Dac forms a hexamer composed of two trimers. These Dacs are characterized by an intermolecular cleft, which is formed by two polypeptides in the trimeric assembly. In Ph-Dac, catalytic Zn situated at the end of the cleft is coordinated by three side chain ligands from His44, Asp47, and His155, and by a phosphate ion derived from the crystallization reservoir solution. We considered that the bound phosphate mimicked the tetrahedral oxyanion, which is an intermediate of hydrolysis of the N-acetyl group, and proposed an appropriate reaction mechanism. In the proposed mechanism, the Nepsilon atom of His264 (from the adjacent polypeptide in the Ph-Dac sequence) is directly involved in the stabilization of the oxyanion intermediate. Mutation analysis also indicated that His264 was essential to the catalysis. These factors give the archaeal Dacs an unprecedented active site architecture a Zn-dependent deacetylases. DATABASE: Structural data are available in the Protein Data Bank database under accession numbers 3WL3, 3WL4, and 3WE7. STRUCTURED DIGITAL ABSTRACT: Ph-Dac and Ph-Dac bind by x-ray crystallography (View interaction) Pf-Dac and Pf-Dac bind by x-ray crystallography (View interaction).
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Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase.,Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T FEBS J. 2014 Apr 7. doi: 10.1111/febs.12805. PMID:24702737<ref>PMID:24702737</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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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Hashimoto, W.]]
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[[Category: Large Structures]]
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[[Category: Nakamura, T.]]
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Niiyama, M.]]
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[[Category: Hashimoto W]]
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[[Category: Uegaki, K.]]
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[[Category: Nakamura T]]
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[[Category: Hydrolase]]
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[[Category: Niiyama M]]
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[[Category: Zn-dependent deacetylase]]
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[[Category: Uegaki K]]

Current revision

N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii

PDB ID 3wl3

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