5Y33

Crystal structure of alginate lyase from Flavobacterium sp. UMI-01 reveals polymannuronate specificity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Literature

Structural basis for controlling the enzymatic properties of polymannuronate preferred alginate lyase FlAlyA from the PL-7 family.

Qin, H.M., Miyakawa, T., Inoue, A., Nishiyama, R., Nakamura, A., Asano, A., Ojima, T., Tanokura, M.

(2018) Chem Commun (Camb) 54: 555-558

  • DOI: https://doi.org/10.1039/c7cc06523j
  • Primary Citation of Related Structures:  
    5Y33

  • PubMed Abstract: 

    FlAlyA is an endolytic enzyme with a preference for polymannuronate. The crystal structure and mutagenesis studies elucidated that the structural variations at outer uronate-binding subsites +2, +3 and -2 control the enzymatic properties of PL-7 family enzymes. Lys158 mutations changed the pH dependency and enhanced the production of mono- and disaccharides.

    • Organizational Affiliation: 

    Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan. amtanok@mail.ecc.u-tokyo.ac.jp.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alginate lyase260Flavobacterium sp. UMI-01Mutation(s): 0 
UniProt
Find proteins for A0A068PC91 (Flavobacterium sp. UMI-01)
Explore A0A068PC91 
Go to UniProtKB:  A0A068PC91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068PC91
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.75α = 90
b = 71.75β = 90
c = 50.88γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXdata reduction
PHENIXdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references