PDBsum entry: 2d5j

Hydrolase

PDB id: 2d5j

Contents

Protein chains

377 a.a. *

Waters ×835

* Residue conservation analysis

PDB id:

2d5j

Name:

Hydrolase

Title:

Unsaturated glucuronyl hydrolase triggers hydration of vinyl group but not of glycosidic bond

Structure:

Unsaturated glucuronyl hydrolase. Chain: a, b. Engineered: yes

Source:

Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.186 R-free: 0.220

Authors:

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

Key ref:

T.Itoh et al. (2006). Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism. J Biol Chem, 281, 29807-29816. PubMed id: 16893885 DOI: 10.1074/jbc.M604975200

Date:

02-Nov-05 Release date: 15-Aug-06

Protein chains

Q9RC92  (UGL_BACGL) -  Unsaturated glucuronyl hydrolase

Seq: 377 a.a.

Struc: 377 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.179

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (3 terms)

DOI no: 10.1074/jbc.M604975200

J Biol Chem 281:29807-29816 (2006)

PubMed id: 16893885

Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism.

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

ABSTRACT

Unsaturated glucuronyl hydrolase (UGL), which is a member of glycoside hydrolase family GH-88, is a bacterial enzyme that degrades mammalian glycosaminoglycans and bacterial biofilms. The enzyme, which acts on unsaturated oligosaccharides with an alpha-glycoside bond produced by microbial polysaccharide lyases responsible for bacterial invasion of host cells, was believed to release 4-deoxy-l-threo-5-hexosulose-uronate (unsaturated glucuronic acid, or DeltaGlcA) and saccharide with a new nonreducing terminus by hydrolyzing the glycosidic bond. We detail the crystal structures of wild-type inactive mutant UGL of Bacillus sp. GL1 and its complex with a substrate (unsaturated chondroitin disaccharide), identify active site residues, and postulate a reaction mechanism catalyzed by UGL that triggers the hydration of the vinyl ether group in DeltaGlcA, based on the structural analysis of the enzyme-substrate complex and biochemical analysis. The proposed catalytic mechanism of UGL is a novel case among known glycosidases. Under the proposed mechanism, Asp-149 acts as a general acid and base catalyst to protonate the DeltaGlcA C4 atom and to deprotonate the water molecule. The deprotonated water molecule attacks the DeltaGlcA C5 atom to yield unstable hemiketal; this is followed by spontaneous conversion to an aldehyde (4-deoxy-l-threo-5-hexosulose-uronate) and saccharide through hemiacetal formation and cleavage of the glycosidic bond. UGL is the first clarified alpha(6)/alpha(6)-barrel enzyme using aspartic acid as the general acid/base catalyst.

Selected figure(s)

Figure 1.
FIGURE 1. Structures of unsaturated oligosaccharides. a, unsaturated chondroitin disaccharide ( GlcA-GalNAc); b, unsaturated hyaluronate disaccharide ( GlcA-GlcNAc); c, unsaturated xanthan trisaccharide ( GlcA-Man-Glc); and d, unsaturated gellan tetrasaccharide ( GlcA-Glc-Rha-Glc). Arrows indicate the cleavage site of UGL. The dashed-line arrow indicates UGL hydrolysis. The product is 4-deoxy-L-threo-5-hexosulose-uronate.

Figure 5.
FIGURE 5. Proposed catalytic reaction mechanism of UGL. The catalytic reaction proceeds through the water addition reaction of the vinyl ether group, as described in the text. Important residues surrounding the substrate are shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 29807-29816) copyright 2006.

Figures were selected by an automated process.