4NEI

Alg17c PL17 Family Alginate Lyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a PL17 Family Alginate Lyase Demonstrates Functional Similarities among Exotype Depolymerases.

Park, D.Jagtap, S.Nair, S.K.

(2014) J.Biol.Chem. 289: 8645-8655

  • DOI: 10.1074/jbc.M113.531111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Brown macroalgae represent an ideal source for complex polysaccharides that can be utilized as precursors for cellulosic biofuels. The lack of recalcitrant lignin components in macroalgae polysaccharide reserves provides a facile route for depolymeri ...

    Brown macroalgae represent an ideal source for complex polysaccharides that can be utilized as precursors for cellulosic biofuels. The lack of recalcitrant lignin components in macroalgae polysaccharide reserves provides a facile route for depolymerization of constituent polysaccharides into simple monosaccharides. The most abundant sugars in macroalgae are alginate, mannitol, and glucan, and although several classes of enzymes that can catabolize the latter two have been characterized, studies of alginate-depolymerizing enzymes have lagged. Here, we present several crystal structures of Alg17c from marine bacterium Saccharophagus degradans along with structure-function characterization of active site residues that are suggested to be involved in the exolytic mechanism of alginate depolymerization. This represents the first structural and biochemical characterization of a family 17 polysaccharide lyase enzyme. Despite the lack of appreciable sequence conservation, the structure and β-elimination mechanism for glycolytic bond cleavage by Alg17c are similar to those observed for family 15 polysaccharide lyases and other lyases. This work illuminates the evolutionary relationships among enzymes within this unexplored class of polysaccharide lyases and reinforces the notion of a structure-based hierarchy in the classification of these enzymes.


    Organizational Affiliation

    From the Departments of Biochemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alginate lyase
A, B
736Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)Mutation(s): 0 
Gene Names: alg17C (alg17A)
EC: 4.2.2.26
Find proteins for Q21FJ0 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024))
Go to UniProtKB:  Q21FJ0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.530α = 90.00
b = 126.351β = 111.51
c = 87.631γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SHARPphasing
HKL-2000data reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-29 
  • Released Date: 2014-01-29 
  • Deposition Author(s): Park, D.S., Nair, S.K.

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references