6KFN

Crystal structure of alginate lyase from Paenibacillus sp. str. FPU-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7.

Itoh, T.Nakagawa, E.Yoda, M.Nakaichi, A.Hibi, T.Kimoto, H.

(2019) Sci Rep 9: 14870-14870

  • DOI: 10.1038/s41598-019-51006-1
  • Primary Citation of Related Structures:  
    6KFN

  • PubMed Abstract: 
  • A novel alginate lyase, PsAly, with a molecular mass of 33 kDa and whose amino acid sequence shares no significant similarity to other known proteins, was biochemically and structurally characterised from Paenibacillus sp. str. FPU-7. The maximum PsAly activity was obtained at 65 °C, with an optimum pH of pH 7-7 ...

    A novel alginate lyase, PsAly, with a molecular mass of 33 kDa and whose amino acid sequence shares no significant similarity to other known proteins, was biochemically and structurally characterised from Paenibacillus sp. str. FPU-7. The maximum PsAly activity was obtained at 65 °C, with an optimum pH of pH 7-7.5. The activity was enhanced by divalent cations, such as Mg 2+ , Mn 2+ , or Co 2+ , and inhibited by a metal chelator, ethylenediaminetetraacetic acid. The reaction products indicated that PsAly is an endolytic enzyme with a preference for polymannuronate. Herein, we report a detailed crystal structure of PsAly at a resolution of 0.89 Å, which possesses a β-helix fold that creates a long cleft. The catalytic site was different from that of other polysaccharide lyases. Site-directed mutational analysis of conserved residues predicted Tyr184 and Lys221 as catalytic residues, abstracting from the C5 proton and providing a proton to the glycoside bond, respectively. One cation was found to bind to the bottom of the cleft and neutralise the carboxy group of the substrate, decreasing the pK a of the C5 proton to promote catalysis. Our study provides an insight into the structural basis for the catalysis of alginate lyases and β-helix polysaccharide lyases.


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka Kenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1142, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
alginate lyaseA307Paenibacillus sp. FPU-7Mutation(s): 0 
EC: 4.2.2.3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.635α = 90
b = 57.764β = 91.1
c = 39.714γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16K08114
Japan Society for the Promotion of ScienceJapan19K06340

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release