2PYH

Azotobacter vinelandii Mannuronan C-5 epimerase AlgE4 A-module complexed with mannuronan trisaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.

Rozeboom, H.J.Bjerkan, T.M.Kalk, K.H.Ertesvag, H.Holtan, S.Aachmann, F.L.Valla, S.Dijkstra, B.W.

(2008) J.Biol.Chem. 283: 23819-23828

  • DOI: 10.1074/jbc.M804119200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alginate is a family of linear copolymers of (1-->4)-linked beta-d-mannuronic acid and its C-5 epimer alpha-l-guluronic acid. The polymer is first produced as polymannuronic acid and the guluronic acid residues are then introduced at the polymer leve ...

    Alginate is a family of linear copolymers of (1-->4)-linked beta-d-mannuronic acid and its C-5 epimer alpha-l-guluronic acid. The polymer is first produced as polymannuronic acid and the guluronic acid residues are then introduced at the polymer level by mannuronan C-5-epimerases. The structure of the catalytic A-module of the Azotobacter vinelandii mannuronan C-5-epimerase AlgE4 has been determined by x-ray crystallography at 2.1-A resolution. AlgE4A folds into a right-handed parallel beta-helix structure originally found in pectate lyase C and subsequently in several polysaccharide lyases and hydrolases. The beta-helix is composed of four parallel beta-sheets, comprising 12 complete turns, and has an amphipathic alpha-helix near the N terminus. The catalytic site is positioned in a positively charged cleft formed by loops extending from the surface encompassing Asp(152), an amino acid previously shown to be important for the reaction. Site-directed mutagenesis further implicates Tyr(149), His(154), and Asp(178) as being essential for activity. Tyr(149) probably acts as the proton acceptor, whereas His(154) is the proton donor in the epimerization reaction.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, GBB, University of Groningen, Nijenborgh 4, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(beta-D-mannuronate) C5 epimerase 4
A, B
377Azotobacter vinelandiiMutation(s): 0 
Gene Names: algE4
EC: 5.1.3.37
Find proteins for Q44493 (Azotobacter vinelandii)
Go to UniProtKB:  Q44493
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAV
Query on MAV

Download SDF File 
Download CCD File 
D
alpha-D-mannopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-BYHBOUFCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 169.551α = 90.00
b = 121.790β = 90.00
c = 45.068γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSphasing
CNSrefinement
PROTEUM PLUSdata collection
XPREPdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance