PDBsum entry 2zgn

Hydrolase

PDB id: 2zgn

Contents

Protein chains

158 a.a. *

Ligands

GAL

Waters ×90

* Residue conservation analysis

PDB id:

2zgn

Name:

Hydrolase

Title:

Crystal structure of recombinant agrocybe aegerita lectin, raal, complex with galactose

Structure:

Anti-tumor lectin. Chain: a, b. Synonym: aal. Engineered: yes

Source:

Agrocybe aegerita. Black poplar mushroom. Organism_taxid: 5400. Gene: aal. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.223 R-free: 0.279

Authors:

N.Yang,D.F.Li,D.C.Wang

Key ref:

N.Yang et al. (2009). Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita. J Mol Biol, 387, 694-705. PubMed id: 19361423 DOI: 10.1016/j.jmb.2009.02.002

Date:

23-Jan-08 Release date: 20-Jan-09

Protein chains

Q6WY08  (ATLE_CYCAE) -  Anti-tumor lectin (Fragment) from Cyclocybe aegerita

Seq: 158 a.a.

Struc: 158 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.21.- - ?????

DOI no: 10.1016/j.jmb.2009.02.002

J Mol Biol 387:694-705 (2009)

PubMed id: 19361423

Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita.

N.Yang, D.F.Li, L.Feng, Y.Xiang, W.Liu, H.Sun, D.C.Wang.

ABSTRACT

Lectin AAL (Agrocybe aegerita lectin) from the edible mushroom A. aegerita is an antitumor protein that exerts its tumor-suppressing function via apoptosis-inducing activity in cancer cells. The crystal structures of ligand-free AAL and its complex with lactose have been determined. The AAL structure shows a dimeric organization, and each protomer adopts a prototype galectin fold. To identify the structural determinants for antitumor effects arising from the apoptosis-inducing activity of AAL, 11 mutants were prepared and subjected to comprehensive investigations covering oligomerization detection, carbohydrate binding test, apoptosis-inducing activity assay, and X-ray crystallographic analysis. The results show that dimerization of AAL is a prerequisite for its tumor cell apoptosis-inducing activity, and both galactose and glucose are basic moieties of functional carbohydrate ligands for lectin bioactivity. Furthermore, we have identified a hydrophobic pocket that is essential for the protein's apoptosis-inducing activity but independent of its carbohydrate binding and dimer formation. This hydrophobic pocket comprises a hydrophobic cluster including residues Leu33, Leu35, Phe93, and Ile144, and is involved in AAL's function mechanism as an integrated structural motif. Single mutants such as F93G or I144G do not disrupt carbohydrate binding and homodimerization capabilities, but abolish the bioactivity of the protein. These findings reveal the structural basis for the antitumor property of AAL, which may lead to de novo designs of antitumor drugs based on AAL as a prototype model.

Selected figure(s)

Figure 2.
Fig. 2. The carbohydrate recognition site of AAL. (a) The dimer structure of the rAAL–lactose complex. The lactose and sulfate ions bound to the CRD concave of AAL are shown in a ball-and-stick model. (b) The electrostatic potential map on the rAAL surface showing a positively charged cavity bound with lactose. (c) The carbohydrate recognition site bound with lactose. Residues of AAL and lactose involved in recognition are shown. The F[o ]− F[c] omit electron density map is calculated without the ligand and contoured at 3.0σ. (d) The interactions between lactose and AAL. A total of 10 hydrogen bonds are involved in contacts between six residues and lactose. Residues Asn43, His59, Asn72, and Trp80 are involved in galactose moiety reorganization, whereas residue Arg85 is involved in glucose moiety, and Arg63 and Glu83 contact both galactose and glucose moieties. In these figures, lactose, sulfate ion, and residues involved in recognition are represented as a ball-and-stick model.

Figure 5.
Fig. 5. The structure of a unique hydrophobic pocket found in the F–S cavity of AAL. (a) Structural alignment of AAL (main chains in green and side chains in magenta) and galectin-1 (blue; PDB code 1LSA). It shows a structurally homologous cavity between the F and S β-sheet layers in which a functionally important hydrophobic pocket is identified in galectin-1. (b) The hydrophobic pocket resided in the F–S cavity of AAL, which consists of two hydrophobic residue clusters, LLFI (Leu33, Leu35, Phe93, and Ile144; in magenta) and FLV (F28, Leu47, and Val102; in cyan). (c) The unique LLFI cluster adopted an integrated structural organization.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 387, 694-705) copyright 2009.

Figures were selected by an automated process.