PDBsum entry: 2cl2

Hydrolase

PDB id: 2cl2

Contents

Protein chain

298 a.a. *

Ligands

NAG-NAG-BMA-MAN-MAN-MAN-MAN

Waters ×540

* Residue conservation analysis

PDB id:

2cl2

Name:

Hydrolase

Title:

Endo-1,3(4)-beta-glucanase from phanerochaete chrysosporium, solved using native sulfur sad, exhibiting intact heptasaccharide glycosylation

Structure:

Putative laminarinase. Chain: a. Synonym: glycosyde hydrolase. Engineered: yes

Source:

Phanerochaete chrysosporium. White-rot fungus. Organism_taxid: 5306. Strain: k-3. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.35Å R-factor: 0.145 R-free: 0.167

Authors:

J.Vasur,R.Kawai,K.Igarashi,M.Sandgren,M.Samejima, J.Stahlberg

Key ref:

J.Vasur et al. (2006). X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium. Acta Crystallogr D Biol Crystallogr, 62, 1422-1429. PubMed id: 17057348 DOI: 10.1107/S0907444906036407

Date:

25-Apr-06 Release date: 25-Oct-06

Protein chain

Q874E3  (Q874E3_PHACH) -  Putative laminarinase

Seq: 318 a.a.

Struc: 298 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: hydrolase activity, hydrolyzing O-glycosyl compounds (1 term)

DOI no: 10.1107/S0907444906036407

Acta Crystallogr D Biol Crystallogr 62:1422-1429 (2006)

PubMed id: 17057348

X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.

J.Vasur, R.Kawai, A.M.Larsson, K.Igarashi, M.Sandgren, M.Samejima, J.Ståhlberg.

ABSTRACT

Laminarinase Lam16A from Phanerochaete chrysosporium was recombinantly expressed in Pichia pastoris, crystallized and the structure was solved at 1.34 A resolution using native sulfur SAD X-ray crystallography. It is the first structure of a non-specific 1,3(4)-beta-D-glucanase from glycoside hydrolase family 16 (GH16). P. chrysosporium is a wood-degrading basidiomycete fungus and Lam16A is the predominant extracellular protein expressed when laminarin is used as the sole carbon source. The protein folds into a curved beta-sandwich homologous to those of other known GH16 enzyme structures (especially kappa-carrageenase from Pseudoalteromonas carrageenovora and beta-agarase from Zobelia galactanivorans). A notable likeness is also evident with the related glycoside hydrolase family 7 (GH7) enzymes. A mammalian lectin, p58/ERGIC, as well as polysaccharide lyase (PL7) enzymes also showed significant similarity to Lam16A. The enzyme has two potential N-glycosylation sites. One such site, at Asn43, displayed a branched heptasaccharide sufficiently stabilized to be interpreted from the X-ray diffraction data. The other N-glycosylation motif was found close to the catalytic centre and is evidently not glycosylated.

Selected figure(s)

Figure 2.
Figure 2 The N-glycosylation on Lam16A. Seven sugar residues of the attached N-glycan at Asn43 could be unambiguously positioned in the electron-density map (2F[o] - F[c], contoured at = 1.0 Å around the carbohydrate model). The chitobiose moiety and the -1,6-arm of the -mannose residue are well ordered and make several interactions with protein residues, while there is no clear density for the 3-hydroxyl of the -mannose or any attached -1,3 arm at this position. In the schematic representation, GlcNAc is represented by squares and Man by circles containing crosses, respectively. Putative hydrogen bonds are shown as dashed lines.

Figure 4.
Figure 4 Space-filling model of Lam16A. The proposed catalytic residues (magenta) are located in the middle of a substrate-binding cleft that forms a straight and rather narrow canyon. There are three tryptophan residues in the cleft (green): Trp110 at proposed subsite -2, Trp103 at -1 and Trp257 at +1. The attached N-glycan is shown with pink C atoms.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1422-1429) copyright 2006.

Figures were selected by an automated process.