2FV1

UGL_D88N/dGlcA-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1

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

(2006) Biochem.Biophys.Res.Commun. 344: 253-262

  • DOI: 10.1016/j.bbrc.2006.03.141
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial unsaturated glucuronyl hydrolases (UGLs) together with polysaccharide lyases are responsible for the complete depolymerization of mammalian extracellular matrix glycosaminoglycans. UGL acts on various oligosaccharides containing unsaturated ...

    Bacterial unsaturated glucuronyl hydrolases (UGLs) together with polysaccharide lyases are responsible for the complete depolymerization of mammalian extracellular matrix glycosaminoglycans. UGL acts on various oligosaccharides containing unsaturated glucuronic acid (DeltaGlcA) at the nonreducing terminus and releases DeltaGlcA through hydrolysis. In this study, we demonstrate the substrate recognition mechanism of the UGL of Bacillus sp. GL1 by determining the X-ray crystallographic structure of its substrate-enzyme complexes. The tetrasaccharide-enzyme complex demonstrated that at least four subsites are present in the active pocket. Although several amino acid residues are crucial for substrate binding, the enzyme strongly recognizes DeltaGlcA at subsite -1 through the formation of hydrogen bonds and stacking interactions, and prefers N-acetyl-d-galactosamine and glucose rather than N-acetyl-d-glucosamine as a residue accommodated in subsite +1, due to the steric hindrance.


    Organizational Affiliation

    Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Unsaturated glucuronyl hydrolase
A, B
377Bacillus sp. (strain GL1)Mutation(s): 1 
Gene Names: ugl
EC: 3.2.1.179
Find proteins for Q9RC92 (Bacillus sp. (strain GL1))
Go to UniProtKB:  Q9RC92
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAD
Query on GAD

Download SDF File 
Download CCD File 
A, B
2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC ACID
C6 H8 O5
GQECVRZDTXJRPX-IMJSIDKUSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.735α = 90.00
b = 94.890β = 90.00
c = 95.410γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance