PDBsum entry: 3gd9

Hydrolase

PDB id: 3gd9

Contents

Protein chain

362 a.a. *

Ligands

GLC-BGC-BGC-BGC

Waters ×652

* Residue conservation analysis

PDB id:

3gd9

Name:

Hydrolase

Title:

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

Structure:

Laminaripentaose-producing beta-1,3-guluase (lphase). Chain: a. Engineered: yes

Source:

Streptomyces matensis. Organism_taxid: 67325. Strain: dic-108. Gene: lphase. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.172 R-free: 0.217

Authors:

H.M.Wu,M.T.Hsu,S.W.Liu,C.C.Lai,Y.K.Li,W.C.Wang

Key ref:

H.M.Wu et al. (2009). Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase. J Biol Chem, 284, 26708-26715. PubMed id: 19640850 DOI: 10.1074/jbc.M109.010983

Date:

23-Feb-09 Release date: 28-Jul-09

Protein chain

Q9Z4I2  (Q9Z4I2_9ACTO) -  Laminaripentaose-producing beta-1,3-guluase (LPHase)

Seq: 401 a.a.

Struc: 362 a.a.

DOI no: 10.1074/jbc.M109.010983

J Biol Chem 284:26708-26715 (2009)

PubMed id: 19640850

Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase.

H.M.Wu, S.W.Liu, M.T.Hsu, C.L.Hung, C.C.Lai, W.C.Cheng, H.J.Wang, Y.K.Li, W.C.Wang.

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.