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6m8n

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Current revision (14:41, 13 March 2024) (edit) (undo)
 
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==Endo-fucoidan hydrolase P5AFcnA from glycoside hydrolase family 107==
==Endo-fucoidan hydrolase P5AFcnA from glycoside hydrolase family 107==
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<StructureSection load='6m8n' size='340' side='right' caption='[[6m8n]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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<StructureSection load='6m8n' size='340' side='right'caption='[[6m8n]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6m8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Psychromonas Psychromonas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M8N FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6m8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychromonas Psychromonas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M8N 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 1.55&#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=6m8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8n OCA], [http://pdbe.org/6m8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m8n RCSB], [http://www.ebi.ac.uk/pdbsum/6m8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8n 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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=6m8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m8n OCA], [https://pdbe.org/6m8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m8n RCSB], [https://www.ebi.ac.uk/pdbsum/6m8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m8n 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/A0A452CSY7_9GAMM A0A452CSY7_9GAMM]
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Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry, and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes, MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas. Using carbohydrate-polyacrylamide gel electrophoresis, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 alpha-L-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine sidechain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.
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Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to alpha-L-fucosidases from GH29.,Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins ML, Springate CM, Burke JE, Withers SG, Boraston AB J Biol Chem. 2018 Oct 3. pii: RA118.005134. doi: 10.1074/jbc.RA118.005134. PMID:30282808<ref>PMID:30282808</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 6m8n" 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: Large Structures]]
[[Category: Psychromonas]]
[[Category: Psychromonas]]
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[[Category: Abe, K]]
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[[Category: Abe K]]
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[[Category: Boraston, A B]]
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[[Category: Boraston AB]]
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[[Category: Salama-Alber, O]]
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[[Category: Salama-Alber O]]
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[[Category: Vickers, C J]]
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[[Category: Vickers CJ]]
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[[Category: Fucan]]
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[[Category: Fucoidan]]
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[[Category: Glycoside hydrolase]]
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[[Category: Hydrolase]]
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[[Category: Retaining mechanism]]
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Current revision

Endo-fucoidan hydrolase P5AFcnA from glycoside hydrolase family 107

PDB ID 6m8n

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