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6eom

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==Structure of DPP III from Caldithrix abyssi==
==Structure of DPP III from Caldithrix abyssi==
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<StructureSection load='6eom' size='340' side='right' caption='[[6eom]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='6eom' size='340' side='right'caption='[[6eom]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6eom]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EOM FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6eom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldithrix_abyssi_DSM_13497 Caldithrix abyssi DSM 13497]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EOM 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=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.103&#8491;</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=6eom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eom OCA], [http://pdbe.org/6eom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eom RCSB], [http://www.ebi.ac.uk/pdbsum/6eom PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eom ProSAT]</span></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=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6eom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eom OCA], [https://pdbe.org/6eom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eom RCSB], [https://www.ebi.ac.uk/pdbsum/6eom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eom 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/H1XW48_9BACT H1XW48_9BACT]
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Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.
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The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity.,Sabljic I, Tomin M, Matovina M, Sucec I, Tomasic Paic A, Tomic A, Abramic M, Tomic S PLoS One. 2018 Feb 8;13(2):e0192488. doi: 10.1371/journal.pone.0192488., eCollection 2018. PMID:29420664<ref>PMID:29420664</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 6eom" 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: Sabljic, I]]
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[[Category: Caldithrix abyssi DSM 13497]]
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[[Category: Caldithrix abyssi]]
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[[Category: Large Structures]]
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[[Category: Dipeptidyl peptidase iii]]
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[[Category: Sabljic I]]
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[[Category: Dpp iii]]
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[[Category: Hydrolase]]
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[[Category: Metallopeptidase]]
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[[Category: Zinc-hydrolase]]
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Current revision

Structure of DPP III from Caldithrix abyssi

PDB ID 6eom

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