6AII
Catalytic domain of PdAgaC
Summary for 6AII
| Entry DOI | 10.2210/pdb6aii/pdb |
| Descriptor | Beta-agarase, CALCIUM ION (3 entities in total) |
| Functional Keywords | agarase, lyase |
| Biological source | Persicobacter |
| Total number of polymer chains | 1 |
| Total formula weight | 38479.31 |
| Authors | Teh, A.H.,Fazli, N.H. (deposition date: 2018-08-23, release date: 2019-08-28, Last modification date: 2023-11-22) |
| Primary citation | Teh, A.H.,Fazli, N.H.,Furusawa, G. Crystal structure of a neoagarobiose-producing GH16 family beta-agarase from Persicobacter sp. CCB-QB2. Appl.Microbiol.Biotechnol., 104:633-641, 2020 Cited by PubMed Abstract: PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a β-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 β-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest V value at 2.9 × 10 U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical β-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. PubMed: 31784792DOI: 10.1007/s00253-019-10237-y PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.63 Å) |
Structure validation
Download full validation report
