1KTW

IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structural Bases of the Processive Degradation of iota-Carrageenan, a Main Cell Wall Polysaccharide of Red Algae.

Michel, G.Helbert, W.Kahn, R.Dideberg, O.Kloareg, B.

(2003) J.Mol.Biol. 334: 421-433


  • PubMed Abstract: 
  • iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydr ...

    iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers.


    Related Citations: 
    • The Iota-Carrageenase of Alteromonas Fortis. A Beta-Helix Fold-Containing Enzyme for the Degradation of a Highly Polyanionic Polysaccharide
      Michel, G.,Chantalat, L.,Fanchon, E.,Henrissat, B.,Kloareg, B.,Dideberg, O.
      (2001) J.Biol.Chem. 276: 40202


    Organizational Affiliation

    Végétaux Marins et Biomolécules, UMR 7139 (CNRS/UPMC/Laboratories Goëmar), Station Biologique de Roscoff, Place Georges Teissier, BP 74, 29682 Roscoff Cedex, Brittany, France.kloareg@sb-rosecoff.ff




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IOTA-CARRAGEENASE
A, B
464Alteromonas fortisMutation(s): 0 
Gene Names: cgiA
EC: 3.2.1.157
Find proteins for Q9F5I8 (Alteromonas fortis)
Go to UniProtKB:  Q9F5I8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4S
Query on G4S

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Download CCD File 
A
4-O-sulfo-beta-D-galactopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-DGPNFKTASA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A
3,6-ANHYDRO-D-GALACTOSE-2-SULFATE
C6 H10 O8 S
BBGPRYFPTZDJIZ-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.730α = 90.00
b = 122.310β = 90.99
c = 91.941γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance