1X1J

Crystal Structure of Xanthan Lyase (N194A) with a Substrate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Bacillus sp. GL1 Xanthan Lyase Complexed with a Substrate: Insights into the Enzyme Reaction Mechanism

Maruyama, Y.Hashimoto, W.Mikami, B.Murata, K.

(2005) J.Mol.Biol. 350: 974-986

  • DOI: 10.1016/j.jmb.2005.05.055
  • Primary Citation of Related Structures:  1X1H, 1X1I

  • PubMed Abstract: 
  • Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated ...

    Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated mannose (PyrMan) through a beta-elimination reaction. To clarify the enzyme reaction mechanism, i.e. its substrate recognition and catalytic reaction, we determined crystal structures of a mutant enzyme, N194A, in complexes with the product (PyrMan) and a substrate (pentasacharide) and in a ligand-free form at 1.8, 2.1, and 2.3A resolution. Based on the structures of the mutant in complexes with the product and substrate, we found that xanthan lyase recognized the PyrMan residue at subsite -1 and the GlcUA residue at +1 on the xanthan side-chain and underwent little interaction with the main chain of the polysaccharide. The structure of the mutant-substrate complex also showed that the hydroxyl group of Tyr255 was close to both the C-5 atom of the GlcUA residue and the oxygen atom of the glycosidic bond to be cleaved, suggesting that Tyr255 likely acts as a general base that extracts the proton from C-5 of the GlcUA residue and as a general acid that donates the proton to the glycosidic bond. A structural comparison of catalytic centers of PL-8 lyases indicated that the catalytic reaction mechanism is shared by all members of the family PL-8, while the substrate recognition mechanism differs.


    Organizational Affiliation

    Laboratory of Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
xanthan lyase
A
752Bacillus sp. (strain GL1)Gene Names: xly
EC: 4.2.2.12
Find proteins for Q9AQS0 (Bacillus sp. (strain GL1))
Go to UniProtKB:  Q9AQS0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
46D
Query on 46D

Download SDF File 
Download CCD File 
A
(4AR,6R,7S,8R,8AR)-8-((5R,6R)-3-CARBOXY-TETRAHYDRO-4,5,6-TRIHYDROXY-2H-PYRAN-2-YLOXY)-HEXAHYDRO-6,7-DIHYDROXY-2-METHYLPYRANO[3,2-D][1,3]DIOXINE-2-CARBOXYLIC ACID)
4,6-O-(1-CARBOXYETHYLIDENE)-BETA-D-MANNOSE-(1->4)-BETA-D-GLUCURONIC ACID
C15 H22 O14
GZJXZKGVHLWBOW-AISSFXTFSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.747α = 90.00
b = 90.026β = 91.06
c = 74.249γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance