Crystal structure of exotype alginate lyase Atu3025 H531A complexed with alginate trisaccharide

Experimental Data Snapshot

  • Resolution: 2.99 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens

Ochiai, A.Yamasaki, M.Mikami, B.Hashimoto, W.Murata, K.

(2010) J Biol Chem 285: 24519-24528

  • DOI: https://doi.org/10.1074/jbc.M110.125450
  • Primary Citation of Related Structures:  
    3A0O, 3AFL

  • PubMed Abstract: 

    Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a beta-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-l-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/DeltaGGG) were determined at 2.10- and 2.99-A resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an alpha/alpha-barrel + anti-parallel beta-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/DeltaGGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His(311) and Tyr(365) as the catalytic base and acid, respectively. Two structural determinants, i.e. a short alpha-helix in the central alpha/alpha-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme.

  • Organizational Affiliation

    Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligo alginate lyase776Agrobacterium fabrum str. C58Mutation(s): 1 
Gene Names: AGR_L_3558Atu3025
EC: 4.2.2
Find proteins for A9CEJ9 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CEJ9 
Go to UniProtKB:  A9CEJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CEJ9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid
Glycosylation Resources
GlyTouCan:  G31814BT
GlyCosmos:  G31814BT
Experimental Data & Validation

Experimental Data

  • Resolution: 2.99 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.845α = 90
b = 99.643β = 90
c = 109.168γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary