CBM32 of AlyQ

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 

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Structural basis for binding uronic acids by family 32 carbohydrate-binding modules.

Teh, A.H.Sim, P.F.Hisano, T.

(2020) Biochem Biophys Res Commun 533: 257-261

  • DOI: https://doi.org/10.1016/j.bbrc.2020.09.064
  • Primary Citation of Related Structures:  
    7D29, 7D2A

  • PubMed Abstract: 

    The alginate lyase AlyQ from Persicobacter sp. CCB-QB2 is a three-domained enzyme with a carbohydrate-binding module (CBM) from family 32. The CBM32 domain, AlyQ B , binds enzymatically cleaved but not intact alginate. Co-crystallisation of AlyQ B with the cleaved alginate reveals that it binds to the 4,5-unsaturated mannuronic acid of the non-reducing end. The binding pocket contains a conserved R248 that interacts with the sugar's carboxyl group, as well as an invariant W303 that stacks against the unsaturated pyranose ring. Targeting specifically the non-reducing end is more efficient than the reducing end since the latter consists of a mixture of mannuronic acid and guluronic acid. AlyQ B also seems unable to bind these two saturated sugars as they contain OH groups that will clash with the pocket. Docking analysis of YeCBM32, which binds oligogalacturonic acid, shows that the stacking of the pyranose ring is shifted in order to accommodate the sugar's axial C1-OH, and its R69 is accordingly elevated to bind the sugar's carboxyl group. Unlike AlyQ B , YeCBM32's binding pocket is able to accommodate both saturated and unsaturated galacturonic acid.

  • Organizational Affiliation

    Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900, Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800, Penang, Malaysia. Electronic address: aikhong@usm.my.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AlyQ149Persicobacter sp. CCB-QB2Mutation(s): 0 
Find proteins for A0A3B6UEP6 (Persicobacter sp. CCB-QB2)
Explore A0A3B6UEP6 
Go to UniProtKB:  A0A3B6UEP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B6UEP6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.447α = 90
b = 55.67β = 90
c = 58.496γ = 90
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentMalaysia--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description