Complex structure of alginate lyase AlyV with M8

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 

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Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements.

Zhang, K.Li, Z.Zhu, Q.Cao, H.He, X.Zhang, X.H.Liu, W.Lyu, Q.

(2022) Commun Biol 5: 782-782

  • DOI: https://doi.org/10.1038/s42003-022-03721-1
  • Primary Citation of Related Structures:  
    7W12, 7W13, 7W16, 7W18

  • PubMed Abstract: 

    Alginate lyases can be used to produce well-defined alginate oligosaccharides (AOSs) because of their specificities for AOS products. A large number of alginate lyases have been recorded in the CAZy database; however, the majority are annotated-only alginate lyases that include little information on their products, thus limiting their applications. Here, we establish a simple and experiment-saving approach to predict product distributions for PL7 alginate lyases through extensive structural biology, bioinformatics and biochemical studies. Structural study on several PL7 alginate lyases reveals that two loops around the substrate binding cleft determine product distribution. Furthermore, a database containing the loop information of all annotated-only single-domain PL7 alginate lyases is constructed, enabling systematic exploration of the association between loop and product distribution. Based on these results, a simplified loop/product distribution relationship is proposed, giving us information on product distribution directly from the amino acid sequence.

  • Organizational Affiliation

    MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alginate lyase303Vibrio pelagiusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
Glycosylation Resources
GlyTouCan:  G06440CO
GlyCosmos:  G06440CO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.405α = 90
b = 80.405β = 90
c = 113.775γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release