1UAI

Crystal Structure of the Alginate Lyase from Corynebacterium sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

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This is version 1.6 of the entry. See complete history


Literature

Crystal structure of the alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. at 1.2 A resolution

Osawa, T.Matsubara, Y.Muramatsu, T.Kimura, M.Kakuta, Y.

(2005) J Mol Biol 345: 1111-1118

  • DOI: https://doi.org/10.1016/j.jmb.2004.10.081
  • Primary Citation of Related Structures:  
    1UAI

  • PubMed Abstract: 

    The crystal structure of alginate (poly alpha-l-guluronate) lyase from Corynebacterium sp. (ALY-1) was determined at 1.2A resolution using the MAD method and bromide ions. The structure of ALY-1 is abundant in beta-strands and has a deep cleft, similar to the jellyroll beta-sandwich found in 1,3-1,4-beta-glucanase. The structure suggests that alginate molecules may penetrate into the cleft to interact with the catalytic site of ALY-1. The reported crystal structure of another type of alginate lyase, A1-III, differs from that of ALY-1 in that it consists almost entirely of alpha-helical structure. Nevertheless, the putative catalytic residues in both enzymes are positioned in space in nearly identical arrangements. This finding suggests that both alginate lyases may have evolved through convergent evolution.


  • Organizational Affiliation

    Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
polyguluronate lyase224Corynebacterium sp.Mutation(s): 0 
EC: 4.2.2.11
UniProt
Find proteins for Q9RB42 (Corynebacterium sp. ALY-1)
Explore Q9RB42 
Go to UniProtKB:  Q9RB42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RB42
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.925α = 90
b = 47.234β = 90.22
c = 50.307γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2004-07-27 
  • Deposition Author(s): Kakuta, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.6: 2024-11-13
    Changes: Structure summary