View source for 6aii


==Catalytic domain of PdAgaC==
<StructureSection load='6aii' size='340' side='right'caption='[[6aii]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6aii]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Persicobacter Persicobacter]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AII FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.63&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=6aii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aii OCA], [https://pdbe.org/6aii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aii RCSB], [https://www.ebi.ac.uk/pdbsum/6aii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aii ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a beta-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 beta-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest Vmax value at 2.9 x 10(3) U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical beta-jelly roll fold with two additional insertions, and a well-conserved but wider substrate-binding cleft with some minor changes. Among the unique differences, two unconserved residues, Asn226 and Arg286, may potentially contribute additional hydrogen bonds to subsites -1 and +2, respectively, while a third, His185 from one of the additional insertions, may further contribute another bond to subsite +2. These additional hydrogen bonds may probably have enhanced PdAgaC's affinity for short agaro-oligosaccharides such as neoagarotetraose (NA4), rendering it capable of binding NA4 strongly enough for rapid degradation into NA2.

Crystal structure of a neoagarobiose-producing GH16 family beta-agarase from Persicobacter sp. CCB-QB2.,Teh AH, Fazli NH, Furusawa G Appl Microbiol Biotechnol. 2020 Jan;104(2):633-641. doi:, 10.1007/s00253-019-10237-y. Epub 2019 Nov 29. PMID:31784792<ref>PMID:31784792</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Persicobacter]]
[[Category: Fazli NH]]
[[Category: Teh AH]]