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| | <StructureSection load='3we7' size='340' side='right'caption='[[3we7]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='3we7' size='340' side='right'caption='[[3we7]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3we7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WE7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3we7]] 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=3WE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WE7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wl4|3wl4]], [[3wl3|3wl3]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0499 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=3we7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3we7 OCA], [https://pdbe.org/3we7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3we7 RCSB], [https://www.ebi.ac.uk/pdbsum/3we7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3we7 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=3we7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3we7 OCA], [https://pdbe.org/3we7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3we7 RCSB], [https://www.ebi.ac.uk/pdbsum/3we7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3we7 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/O58235_PYRHO O58235_PYRHO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Fukuda, Y]] | + | [[Category: Fukuda Y]] |
| - | [[Category: Inoue, T]] | + | [[Category: Inoue T]] |
| - | [[Category: Mine, S]] | + | [[Category: Mine S]] |
| - | [[Category: Nakamura, T]] | + | [[Category: Nakamura T]] |
| - | [[Category: Sato, T]] | + | [[Category: Sato T]] |
| - | [[Category: Uegaki, K]] | + | [[Category: Uegaki K]] |
| - | [[Category: Deacetylation]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Zinc binding]]
| + | |
| Structural highlights
3we7 is a 3 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.55Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
O58235_PYRHO
Publication Abstract from PubMed
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).
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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. Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase. FEBS J. 2014 Apr 7. doi: 10.1111/febs.12805. PMID:24702737 doi:http://dx.doi.org/10.1111/febs.12805
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