1UAI

Crystal Structure of the Alginate Lyase from Corynebacterium sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.jmb.2004.10.081

  • 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, simil ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
polyguluronate lyase
A
224Corynebacterium sp. ALY-1Mutation(s): 0 
Gene Names: alyPG
EC: 4.2.2.11
Find proteins for Q9RB42 (Corynebacterium sp. ALY-1)
Go to UniProtKB:  Q9RB42
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.925α = 90.00
b = 47.234β = 90.22
c = 50.307γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-03-11 
  • Released Date: 2004-07-27 
  • Deposition Author(s): Kakuta, Y.

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-04-16
    Type: Other
  • Version 1.4: 2017-10-04
    Type: Refinement description