2WDA

The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex with Chondroitin sulphate

2WDA の概要

• エントリーDOI: 10.2210/pdb2wda/pdb
• 関連するPDBエントリー: 2WCO 2X03
• 分子名称: PUTATIVE SECRETED LYASE, 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose, FORMIC ACID, ... (7 entities in total)
• 機能のキーワード: lyase, hyaluronate lyase, chondroitin lyase, family 8
• 由来する生物種: STREPTOMYCES VIOLACEORUBER
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 84967.41

構造登録者

Elmabrouk, Z.H.,Taylor, E.J.,Vincent, F.,Smith, N.L.,Turkenburg, J.P.,Davies, G.J.,Black, G.W. (登録日: 2009-03-23, 公開日: 2010-04-21, 最終更新日: 2023-12-13)

主引用文献

Elmabrouk, Z.H.,Vincent, F.,Zhang, M.,Smith, N.L.,Turkenburg, J.P.,Charnock, S.J.,Black, G.W.,Taylor, E.J.
Crystal Structures of a Family 8 Polysaccharide Lyase Reveal Open and Highly Occluded Substrate-Binding Cleft Conformations.
Proteins, 79:965-, 2011

PubMed Abstract: Bacterial enzymatic degradation of glycosaminoglycans such as hyaluronan and chondroitin is facilitated by polysaccharide lyases. Family 8 polysaccharide lyase (PL8) enzymes contain at least two domains: one predominantly composed of α-helices, the α-domain, and another predominantly composed of β-sheets, the β-domain. Simulation flexibility analyses indicate that processive exolytic cleavage of hyaluronan, by PL8 hyaluronate lyases, is likely to involve an interdomain shift, resulting in the opening/closing of the substrate-binding cleft between the α- and β-domains, facilitating substrate translocation. Here, the Streptomyces coelicolor A3(2) PL8 enzyme was recombinantly expressed in and purified from Escherichia coli and biochemically characterized as a hyaluronate lyase. By using X-ray crystallography its structure was solved in complex with hyaluronan and chondroitin disaccharides. These findings show key catalytic interactions made by the different substrates, and on comparison with all other PL8 structures reveals that the substrate-binding cleft of the S. coelicolor enzyme is highly occluded. A third structure of the enzyme, harboring a mutation of the catalytic tyrosine, created via site-directed mutagenesis, interestingly revealed an interdomain shift that resulted in the opening of the substrate-binding cleft. These results add further support to the proposed processive mechanism of action of PL8 hyaluronate lyases and may indicate that the mechanism of action is likely to be universally used by PL8 hyaluronate lyases.

PubMed: 21287626
DOI: 10.1002/PROT.22938

実験手法

X-RAY DIFFRACTION (2.3 Å)