Crystal structure of unsaturated glucuronyl hydrolase from Streptcoccus agalactiae

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan

Maruyama, Y.Nakamichi, Y.Itoh, T.Mikami, B.Hashimoto, W.Murata, K.

(2009) J Biol Chem 284: 18059-18069

  • DOI: https://doi.org/10.1074/jbc.M109.005660
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Unsaturated glucuronyl hydrolase (UGL) categorized into the glycoside hydrolase family 88 catalyzes the hydrolytic release of an unsaturated glucuronic acid from glycosaminoglycan disaccharides, which are produced from mammalian extracellular matrices through the beta-elimination reaction of polysaccharide lyases. Here, we show enzyme characteristics of pathogenic streptococcal UGLs and structural determinants for the enzyme substrate specificity. The putative genes for UGL and phosphotransferase system for amino sugar, a component of glycosaminoglycans, are assembled into a cluster in the genome of pyogenic and hemolytic streptococci such as Streptococcus agalactiae, Streptococcus pneumoniae, and Streptococcus pyogenes, which produce extracellular hyaluronate lyase as a virulent factor. The UGLs of these three streptococci were overexpressed in Escherichia coli cells, purified, and characterized. Streptococcal UGLs degraded unsaturated hyaluronate and chondroitin disaccharides most efficiently at approximately pH 5.5 and 37 degrees C. Distinct from Bacillus sp. GL1 UGL, streptococcal UGLs preferred sulfated substrates. DNA microarray and Western blotting indicated that the enzyme was constitutively expressed in S. agalactiae cells, although the expression level increased in the presence of glycosaminoglycan. The crystal structure of S. agalactiae UGL (SagUGL) was determined at 1.75 A resolution by x-ray crystallography. SagUGL adopts alpha(6)/alpha(6)-barrel structure as a basic scaffold similar to Bacillus UGL, but the arrangement of amino acid residues in the active site differs between the two. SagUGL Arg-236 was found to be one of the residues involved in its activity for the sulfated substrate through structural comparison and site-directed mutagenesis. This is the first report on the structure and function of streptococcal UGLs.

  • Organizational Affiliation

    Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Unsaturated glucuronyl hydrolase397Streptococcus agalactiaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.08α = 90
b = 116.08β = 90
c = 78.125γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-04-14 
  • Deposition Author(s): Maruyama, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2013-11-27
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description