Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose

Experimental Data Snapshot

  • Resolution: 1.32 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases

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

(2009) J Biol Chem 284: 10181-10189

  • DOI: https://doi.org/10.1074/jbc.M807799200
  • Primary Citation of Related Structures:  
    2ZUX, 2ZUY

  • PubMed Abstract: 

    A saprophytic Bacillus subtilis secretes two types of rhamnogalacturonan (RG) lyases, endotype YesW and exotype YesX, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 YesW and YesX with a significant sequence identity (67.8%) cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Here we show the structural determinants for substrate recognition and the mode of action in polysaccharide lyase family 11 lyases. The crystal structures of YesW in complex with rhamnose and ligand-free YesX were determined at 1.32 and 1.65 A resolution, respectively. The YesW amino acid residues such as Asn(152), Asp(172), Asn(532), Gly(533), Thr(534), and Tyr(595) in the active cleft bind to rhamnose molecules through hydrogen bonds and van der Waals contacts. Other rhamnose molecules are accommodated at the noncatalytic domain far from the active cleft, revealing that the domain possibly functions as a novel carbohydrate-binding module. A structural comparison between YesW and YesX indicates that a specific loop in YesX for recognizing the terminal saccharide molecule sterically inhibits penetration of the polymer over the active cleft. The loop-deficient YesX mutant exhibits YesW-like endotype activity, demonstrating that molecular conversion regarding the mode of action is achieved by the addition/removal of the loop for recognizing the terminal saccharide. This is the first report on a structural insight into RG-I recognition and molecular conversion of exotype to endotype in polysaccharide lyases.

  • Organizational Affiliation

    Laboratory of Basic and Applied Molecular Biotechnology.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YesW protein
A, B
591Bacillus subtilisMutation(s): 0 
Gene Names: yesWBSU07050
EC: 4.2.2
Find proteins for O31526 (Bacillus subtilis (strain 168))
Explore O31526 
Go to UniProtKB:  O31526
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31526
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RAM

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
M [auth A]
N [auth A]
BA [auth B],
CA [auth B],
DA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
C6 H12 O5
Query on MPD

Download Ideal Coordinates CCD File 
EA [auth B],
Q [auth A]
C6 H14 O2
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.32 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.282α = 90
b = 105.858β = 94.82
c = 100.967γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary