2SPG

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Quantitative and qualitative analysis of type III antifreeze protein structure and function.

Graether, S.P.DeLuca, C.I.Baardsnes, J.Hill, G.A.Davies, P.L.Jia, Z.

(1999) J Biol Chem 274: 11842-11847

  • DOI: 10.1074/jbc.274.17.11842
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, the mechan ...

    Some cold water marine fishes avoid cellular damage because of freezing by expressing antifreeze proteins (AFPs) that bind to ice and inhibit its growth; one such protein is the globular type III AFP from eel pout. Despite several studies, the mechanism of ice binding remains unclear because of the difficulty in modeling the AFP-ice interaction. To further explore the mechanism, we have determined the x-ray crystallographic structure of 10 type III AFP mutants and combined that information with 7 previously determined structures to mainly analyze specific AFP-ice interactions such as hydrogen bonds. Quantitative assessment of binding was performed using a neural network with properties of the structure as input and predicted antifreeze activity as output. Using the cross-validation method, a correlation coefficient of 0.60 was obtained between measured and predicted activity, indicating successful learning and good predictive power. A large loss in the predictive power of the neural network occurred after properties related to the hydrophobic surface were left out, suggesting that van der Waal's interactions make a significant contribution to ice binding. By combining the analysis of the neural network with antifreeze activity and x-ray crystallographic structures of the mutants, we extend the existing ice-binding model to a two-step process: 1) probing of the surface for the correct ice-binding plane by hydrogen-bonding side chains and 2) attractive van der Waal's interactions between the other residues of the ice-binding surface and the ice, which increases the strength of the protein-ice interaction.


    Related Citations: 
    • The effects of steric mutations on the structure of type III antifreeze protein and its interaction with ice.
      DeLuca, C.I., Davies, P.L., Ye, Q., Jia, Z.
      (1998) J Mol Biol 275: 515
    • Structural basis for the binding of a globular antifreeze protein to ice.
      Jia, Z., DeLuca, C.I., Chao, H., Davies, P.L.
      (1996) Nature 384: 285
    • Crystallization and preliminary X-ray crystallographic studies on Type III antifreeze protein.
      Jia, Z., DeLuca, C.I., Davies, P.L.
      (1995) Protein Sci 4: 1236
    • Use of proline mutants to help solve the NMR solution structure of type III antifreeze protein.
      Chao, H., Davies, P.L., Sykes, B.D., Sonnichsen, F.D.
      (1993) Protein Sci 2: 1411
    • Multiple genes provide the basis for antifreeze protein diversity and dosage in the ocean pout, Macrozoarces americanus.
      Hew, C.L., Wang, N.C., Joshi, S., Fletcher, G.L., Scott, G.K., Hayes, P.H., Buettner, B., Davies, P.L.
      (1988) J Biol Chem 263: 12049

    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6 Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ANTIFREEZE PROTEIN TYPE III)A66Zoarces americanusMutation(s): 3 
Find proteins for P19614 (Zoarces americanus)
Explore P19614 
Go to UniProtKB:  P19614
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.276α = 90
b = 39.873β = 90
c = 44.67γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-27
    Changes: Database references