3GD9

Crystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose

Summary for 3GD9

• Entry DOI: 10.2210/pdb3gd9/pdb
• Related: 3GD0
• Descriptor: Laminaripentaose-producing beta-1,3-guluase (LPHase), beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose (3 entities in total)
• Functional Keywords: glycoside hydrolases, laminaripentaose-producing beta-1, 3-glucnase (lphase), multi-wavelength anomalous dispersion (mad), hydrolase
• Biological source: Streptomyces matensis
• Total number of polymer chains: 1
• Total formula weight: 40259.49

Authors

Wu, H.M.,Hsu, M.T.,Liu, S.W.,Lai, C.C.,Li, Y.K.,Wang, W.C. (deposition date: 2009-02-23, release date: 2009-07-28, Last modification date: 2023-11-01)

Primary citation

Wu, H.M.,Liu, S.W.,Hsu, M.T.,Hung, C.L.,Lai, C.C.,Cheng, W.C.,Wang, H.J.,Li, Y.K.,Wang, W.C.
Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase.
J.Biol.Chem., 284:26708-26715, 2009

PubMed Abstract: Laminaripentaose-producing beta-1,3-glucanase (LPHase), a member of glycoside hydrolase family 64, cleaves a long-chain polysaccharide beta-1,3-glucan into specific pentasaccharide oligomers. The crystal structure of LPHase from Streptomyces matensis DIC-108 was solved to 1.62 A resolution using multiple-wavelength anomalous dispersion methods. The LPHase structure reveals a novel crescent-like fold; it consists of a barrel domain and a mixed (alpha/beta) domain, forming a wide-open groove between the two domains. The liganded crystal structure was also solved to 1.80 A, showing limited conformational changes. Within the wide groove, a laminaritetraose molecule is found to sit in an electronegatively charged central region and is proximal to several conserved residues including two carboxylates (Glu(154) and Asp(170)) and four other sugar-binding residues (Thr(156), Asn(158), Trp(163), and Thr(167)). Molecular modeling using a laminarihexaose as a substrate suggests roles for Glu(154) and Asp(170) as acid and base catalysts, respectively, whereas the side chains of Thr(156), Asn(158), and Trp(163) demarcate subsite +5. Site-directed mutagenesis of Glu(154) and Asp(170) confirms that both carboxylates are essential for catalysis. Together, our results suggest that LPHase uses a direct displacement mechanism involving Glu(154) and Asp(170) to cleave a beta-1,3-glucan into specific alpha-pentasaccharide oligomers.

PubMed: 19640850
DOI: 10.1074/jbc.M109.010983

Experimental method

X-RAY DIFFRACTION (1.8 Å)