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5xsw

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==Crystal structure of an archaeal chitinase in the substrate-complex form (P63)==
==Crystal structure of an archaeal chitinase in the substrate-complex form (P63)==
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<StructureSection load='5xsw' size='340' side='right' caption='[[5xsw]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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<StructureSection load='5xsw' size='340' side='right'caption='[[5xsw]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xsw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_10152 Dsm 10152]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XSW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xsw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_chitonophagus Thermococcus chitonophagus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XSW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.95&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chiD, CHITON_1119 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54262 DSM 10152])</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </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=5xsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsw OCA], [https://pdbe.org/5xsw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xsw RCSB], [https://www.ebi.ac.uk/pdbsum/5xsw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsw ProSAT]</span></td></tr>
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<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=5xsw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsw OCA], [http://pdbe.org/5xsw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsw RCSB], [http://www.ebi.ac.uk/pdbsum/5xsw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsw ProSAT]</span></td></tr>
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</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/A0A161KIT4_9EURY A0A161KIT4_9EURY]
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Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95 degrees C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(DeltaBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.
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Crystal structures of an archaeal chitinase ChiD and its ligand complexes.,Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K Glycobiology. 2018 Jun 1;28(6):418-426. doi: 10.1093/glycob/cwy024. PMID:29800365<ref>PMID:29800365</ref>
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==See Also==
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*[[Chitinase 3D structures|Chitinase 3D structures]]
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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 5xsw" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Chitinase]]
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[[Category: Large Structures]]
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[[Category: Dsm 10152]]
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[[Category: Thermococcus chitonophagus]]
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[[Category: Miki, K]]
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[[Category: Miki K]]
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[[Category: Nishitani, Y]]
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[[Category: Nishitani Y]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of an archaeal chitinase in the substrate-complex form (P63)

PDB ID 5xsw

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