PDBsum entry: 1vd5

Hydrolase

PDB id: 1vd5

Contents

Protein chain

377 a.a. *

Ligands

GLY ×4

DTT ×2

MPD

Waters ×478

* Residue conservation analysis

PDB id:

1vd5

Name:

Hydrolase

Title:

Crystal structure of unsaturated glucuronyl hydrolase, respo the degradation of glycosaminoglycan, from bacillus sp. Gl1 resolution

Structure:

Unsaturated glucuronyl hydrolase. Chain: a. Engineered: yes

Source:

Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.168 R-free: 0.189

Authors:

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

Key ref:

T.Itoh et al. (2004). Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution. J Biol Chem, 279, 31804-31812. PubMed id: 15148314 DOI: 10.1074/jbc.M403288200

Date:

18-Mar-04 Release date: 13-Jul-04

Protein chain

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.M403288200

J Biol Chem 279:31804-31812 (2004)

PubMed id: 15148314

Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.

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

ABSTRACT

Unsaturated glucuronyl hydrolase (UGL) is a novel glycosaminoglycan hydrolase that releases unsaturated d-glucuronic acid from oligosaccharides produced by polysaccharide lyases. The x-ray crystallographic structure of UGL from Bacillus sp. GL1 was first determined by multiple isomorphous replacement (mir) and refined at 1.8 A resolution with a final R-factor of 16.8% for 25 to 1.8 A resolution data. The refined UGL structure consists of 377 amino acid residues and 478 water molecules, four glycine molecules, two dithiothreitol (DTT) molecules, and one 2-methyl-2,4-pentanediol (MPD) molecule. UGL includes an alpha(6)/alpha(6)-barrel, whose structure is found in the six-hairpin enzyme superfamily of an alpha/alpha-toroidal fold. One side of the UGL alpha(6)/alpha(6)-barrel structure consists of long loops containing three short beta-sheets and contributes to the formation of a deep pocket. One glycine molecule and two DTT molecules surrounded by highly conserved amino acid residues in UGLs were found in the pocket, suggesting that catalytic and substrate-binding sites are located in this pocket. The overall UGL structure, with the exception of some loops, very much resembled that of the Bacillus subtilis hypothetical protein Yter, whose function is unknown and which exhibits little amino acid sequence identity with UGL. In the active pocket, residues possibly involved in substrate recognition and catalysis by UGL are conserved in UGLs and Yter. The most likely candidate catalytic residues for glycosyl hydrolysis are Asp(88) and Asp(149). This was supported by site-directed mutagenesis studies in Asp(88) and Asp(149).

Selected figure(s)

Figure 4.
FIG. 4. Structural comparison of overall structures of UGL (pink) and hypothetical protein Yter (blue). Superimposed results are shown schematically in C^ traces. Coordinates of Yter (1NC5 [PDB] ) were taken from the RCSB Protein Data Bank (28). The figure was drawn using the GRASP (32) program.

Figure 7.
FIG. 7. Structural comparison of the active site arrangement of UGL and hypothetical protein Yter. Main chains are pink for UGL and blue for Yter. Side chains are red for UGL and cyan for Yter. The figure was prepared using MOLSCRIPT (30) and RASTER3D (31).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31804-31812) copyright 2004.

Figures were selected by an automated process.