5GMT

Crystal structure of the marine PL-14 alginate lyase from Aplysia kurodai


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.

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

(2017) J. Biol. Chem. 292: 2182-2190

  • DOI: 10.1074/jbc.M116.749929

  • PubMed Abstract: 
  • Alginate is an abundant algal polysaccharide, composed of β-d-mannuronate and its C5 epimer α-l-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4. ...

    Alginate is an abundant algal polysaccharide, composed of β-d-mannuronate and its C5 epimer α-l-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4.2.2.3) from Aplysia kurodai , AkAly30, is a eukaryotic member of the polysaccharide lyase 14 (PL-14) family and degrades alginate by cleaving the glycosidic bond through a β-elimination reaction. Here, we present the structural basis for the substrate specificity, with a preference for polymannuronate, of AkAly30. The crystal structure of AkAly30 at a 1.77 Å resolution and the putative substrate-binding model show that the enzyme adopts a β-jelly roll fold at the core of the structure and that Lys-99, Tyr-140, and Tyr-142 form catalytic residues in the active site. Their arrangements allow the carboxyl group of mannuronate residues at subsite +1 to form ionic bonds with Lys-99. The coupled tyrosine forms a hydrogen bond network with the glycosidic bond, and the hydroxy group of Tyr-140 is located near the C5 atom of the mannuronate residue. These interactions could promote the β-elimination of the mannuronate residue at subsite +1. More interestingly, Gly-118 and the disulfide bond formed by Cys-115 and Cys-124 control the conformation of an active-site loop, which makes the space suitable for substrate entry into subsite -1. The cleavage efficiency of AkAly30 is enhanced relative to that of mutants lacking either Gly-118 or the Cys-115-Cys-124 disulfide bond. The putative binding model and mutagenesis studies provide a novel substrate recognition mode explaining the polymannuronate specificity of PL-14 alginate lyases.


    Organizational Affiliation

    From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan, amtanok@mail.ecc.u-tokyo.ac.jp.,the College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China.,the Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan, and.,the Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, 2-8-30 Kounodai, Ichikawa-shi, Chiba 272-0827, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alginate lyase
A, B
279Aplysia kurodaiMutation(s): 0 
Gene Names: AkAly30
Find proteins for E7FLQ2 (Aplysia kurodai)
Go to UniProtKB:  E7FLQ2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.450α = 82.57
b = 44.990β = 88.79
c = 73.020γ = 63.70
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science, and TechnologyJapan--

Revision History 

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references