PDBsum entry 2d8l

Hydrolase

PDB id: 2d8l

Contents

Protein chain

363 a.a.

Ligands

NGA-GCD

Waters ×625

References listed in PDB file

Key reference

Title

A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide.

Authors

T.Itoh, A.Ochiai, B.Mikami, W.Hashimoto, K.Murata.

Ref.

J Mol Biol, 2006, 360, 573-585. [DOI no: 10.1016/j.jmb.2006.04.047]

PubMed id

16781735

Abstract

YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.

Figure 2.
Figure 2. (a) Structural comparison of the overall structures of UGL (pink) and hypothetical protein YteR (blue). Superimposed results are shown schematically in C^α traces. (b) Structural comparison of the active pocket of UGL and YteR. Main- chains of UGL are in pink and those of YteR in blue. Side-chains of UGL are in red and those of YteR in cyan. Coordinates of UGL (1VD5) and YteR (1NC5) were obtained from the RCSB Protein Data Bank. The structure was prepared by ribbon stereo diagrams using MOLSCRIPT^39 and Raster3D^40 [http://www.pdbbeta.rcsb.org].

Figure 5.
Figure 5. pH profiles of YteR (□) and YesR (•).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 573-585) copyright 2006.