7W18

Complex structure of alginate lyase PyAly with M5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


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Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alginate lyase241Neopyropia yezoensisMutation(s): 2 
Gene Names: PyAly
UniProt
Find proteins for D2KX85 (Neopyropia yezoensis)
Explore D2KX85 
Go to UniProtKB:  D2KX85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2KX85
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid
B
5N/A
Glycosylation Resources
GlyTouCan:  G61688UV
GlyCosmos:  G61688UV
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.272α = 90
b = 62.272β = 90
c = 113.271γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2024-05-29
    Changes: Data collection