1UR8
Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone
Summary for 1UR8
Entry DOI | 10.2210/pdb1ur8/pdb |
Related | 1E15 1E6N 1E6P 1E6R 1E6Z 1GOI 1GPF 1OGB |
Descriptor | CHITINASE B, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone, GLYCEROL, ... (5 entities in total) |
Functional Keywords | hydrolase, chitinase, inhibition, lactone, chitin degradation, glycosidase |
Biological source | SERRATIA MARCESCENS |
Total number of polymer chains | 2 |
Total formula weight | 113382.08 |
Authors | Vaaje-Kolstad, G.,Vasella, A.,Peter, M.G.,Netter, C.,Houston, D.R.,Westereng, B.,Synstad, B.,Eijsink, V.G.H.,Van Aalten, D.M.F. (deposition date: 2003-10-27, release date: 2004-04-27, Last modification date: 2023-12-13) |
Primary citation | Vaaje-Kolstad, G.,Vasella, A.,Peter, M.G.,Netter, C.,Houston, D.R.,Westereng, B.,Synstad, B.,Eijsink, V.G.H.,Van Aalten, D.M.F. Interactions of a Family 18 Chitinase with the Designed Inhibitor Hm508 and its Degradation Product, Chitobiono-Delta-Lactone. J.Biol.Chem., 279:3612-, 2004 Cited by PubMed Abstract: We describe enzymological and structural analyses of the interaction between the family 18 chitinase ChiB from Serratia marcescens and the designed inhibitor N,N'-diacetylchitobionoxime-N-phenylcarbamate (HM508). HM508 acts as a competitive inhibitor of this enzyme with a K(i) in the 50 microM range. Active site mutants of ChiB show K(i) values ranging from 1 to 200 microM, providing insight into some of the interactions that determine inhibitor affinity. Interestingly, the wild type enzyme slowly degrades HM508, but the inhibitor is essentially stable in the presence of the moderately active D142N mutant of ChiB. The crystal structure of the D142N-HM508 complex revealed that the two sugar moieties bind to the -2 and -1 subsites, whereas the phenyl group interacts with aromatic side chains that line the +1 and +2 subsites. Enzymatic degradation of HM508, as well as a Trp --> Ala mutation in the +2 subsite of ChiB, led to reduced affinity for the inhibitor, showing that interactions between the phenyl group and the enzyme contribute to binding. Interestingly, a complex of enzymatically degraded HM508 with the wild type enzyme showed a chitobiono-delta-lactone bound in the -2 and -1 subsites, despite the fact that the equilibrium between the lactone and the hydroxy acid forms in solution lies far toward the latter. This shows that the active site preferentially binds the (4)E conformation of the -1 sugar, which resembles the proposed transition state of the reaction. PubMed: 14597613DOI: 10.1074/JBC.M310057200 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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