3B9D

Crystal structure of Vibrio harveyi chitinase A complexed with pentasaccharide

Summary for 3B9D

• Entry DOI: 10.2210/pdb3b9d/pdb
• Related: 3B8S 3B9A 3B9E
• Descriptor: Chitinase A, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: tim-barrel, pentasaccharide complex, glycosidase, hydrolase
• Biological source: Vibrio harveyi
• Total number of polymer chains: 1
• Total formula weight: 64674.64

Authors

Songsiriritthigul, C.,Aguda, A.H.,Robinson, R.C.,Suginta, W. (deposition date: 2007-11-05, release date: 2008-04-01, Last modification date: 2024-11-13)

Primary citation

Songsiriritthigul, C.,Pantoom, S.,Aguda, A.H.,Robinson, R.C.,Suginta, W.
Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism
J.Struct.Biol., 162:491-499, 2008

PubMed Abstract: This research describes four X-ray structures of Vibrio harveyi chitinase A and its catalytically inactive mutant (E315M) in the presence and absence of substrates. The overall structure of chitinase A is that of a typical family-18 glycosyl hydrolase comprising three distinct domains: (i) the amino-terminal chitin-binding domain; (ii) the main catalytic (alpha/beta)(8) TIM-barrel domain; and (iii) the small (alpha+beta) insertion domain. The catalytic cleft of chitinase A has a long, deep groove, which contains six chitooligosaccharide ring-binding subsites (-4)(-3)(-2)(-1)(+1)(+2). The binding cleft of the ligand-free E315M is partially blocked by the C-terminal (His)(6)-tag. Structures of E315M-chitooligosaccharide complexes display a linear conformation of pentaNAG, but a bent conformation of hexaNAG. Analysis of the final 2F(o)-F(c) omit map of E315M-NAG6 reveals the existence of the linear conformation of the hexaNAG at a lower occupancy with respect to the bent conformation. These crystallographic data provide evidence that the interacting sugars undergo conformational changes prior to hydrolysis by the wild-type enzyme.

PubMed: 18467126
DOI: 10.1016/j.jsb.2008.03.008

Experimental method

X-RAY DIFFRACTION (1.72 Å)