6aii
Catalytic domain of PdAgaC
Structural highlights
Publication Abstract from PubMedPdAgaC 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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