1V5D

The crystal structure of the active form chitosanase from Bacillus sp. K17 at pH6.4

Summary for 1V5D

• Entry DOI: 10.2210/pdb1v5d/pdb
• Related: 1V5C
• Descriptor: chitosanase, PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) (3 entities in total)
• Functional Keywords: chitosan degradation, hydrolase, glycosil hydrolase, family 8
• Biological source: Bacillus sp.
• Total number of polymer chains: 2
• Total formula weight: 87519.76

Authors

Adachi, W.,Shimizu, S.,Sunami, T.,Fukazawa, T.,Suzuki, M.,Yatsunami, R.,Nakamura, S.,Takenaka, A. (deposition date: 2003-11-22, release date: 2004-12-07, Last modification date: 2023-12-27)

Primary citation

Adachi, W.,Sakihama, Y.,Shimizu, S.,Sunami, T.,Fukazawa, T.,Suzuki, M.,Yatsunami, R.,Nakamura, S.,Takenaka, A.
Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17
J.MOL.BIOL., 343:785-795, 2004

PubMed Abstract: Crystal structures of chitosanase from Bacillus sp. K17 (ChoK) have been determined at 1.5 A resolution in the active form and at 2.0 A resolution in the inactive form. This enzyme belongs to the family GH-8, out of 93 glycoside hydrolase families, and exhibits the substrate specificity of subclass II chitosanase. The catalytic site is constructed on the scaffold of a double-alpha(6)/alpha(6)-barrel, which is formed by six repeating helix-loop-helix motifs. This structure is quite different from those of the GH-46 chitosanases and of GH-5. Structural comparison with CelA (a cellulase belonging to the same family GH-8) suggests that the proton donor Glu122 is conserved, but the proton acceptor is the inserted Glu309 residue, and that the corresponding Asp278 residue in CelA is inactivated in ChoK. The four acidic residues, Asp179, Glu309, Asp183 and Glu107, can be involved in substrate recognition through interactions with the amino groups of the glucosamine residues bound in the -3, -2, -1 and +1 sites, respectively. The hydrophobic Trp235, Trp166, Phe413 and Tyr318 residues are highly conserved for binding of the hexose rings at the -3, -2, +1 and +2 sites, respectively. These structural features indicate that enzymes in GH-8 can be further divided into three subfamilies. Different types of chitosanases are discussed in terms of convergent evolution from different structural ancestors.

PubMed: 15465062
DOI: 10.1016/j.jmb.2004.08.028

Experimental method

X-RAY DIFFRACTION (1.5 Å)