1UR9

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

Summary for 1UR9

• Entry DOI: 10.2210/pdb1ur9/pdb
• Related: 1E15 1E6N 1E6P 1E6R 1E6Z 1GOI 1GPF 1OGB 1UR8
• Descriptor: CHITINASE B, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone, GLYCEROL, ... (6 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: 119113.94

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: 2024-10-16)

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

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: 14597613
DOI: 10.1074/JBC.M310057200

Experimental method

X-RAY DIFFRACTION (1.8 Å)