1KTW

IOTA-CARRAGEENASE COMPLEXED TO IOTA-CARRAGEENAN FRAGMENTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1016/j.jmb.2003.09.056
  • Primary Citation of Related Structures:  
    1KTW

  • 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 hydrolases, fold into a right-handed beta-helix ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IOTA-CARRAGEENASEA, B464Alteromonas macleodiiMutation(s): 0 
Gene Names: cgiA
EC: 3.2.1.157
UniProt
Find proteins for Q9F5I8 (Alteromonas macleodii)
Explore Q9F5I8 
Go to UniProtKB:  Q9F5I8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G58187OK
GlyCosmos:  G58187OK
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranoseD4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G24165XP
GlyCosmos:  G24165XP
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , M [auth B] , N [auth B] , O [auth B] , 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A], T [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], R [auth B], S [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.73α = 90
b = 122.31β = 90.99
c = 91.941γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary