1JAB

TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T18S

PDB DOI: 10.2210/pdb1JAB/pdb

Classification: ANTIFREEZE PROTEIN
Organism(s): Zoarces americanus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1999-01-24 Released: 1999-04-29
Deposition Author(s): Graether, S.P., Deluca, C.I., Baardsnes, J., Hill, G.A., Davies, P.L., Jia, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.217
R-Value Work: 0.197

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

PubMed: 10207002 Search on PubMed
DOI: 10.1074/jbc.274.17.11842
Primary Citation of Related Structures:
1B7I, 1B7J, 1B7K, 1EKL, 1JAB, 1MSJ, 2AME, 2JIA, 2MSJ, 2SPG, 3AME, 4AME, 6AME, 7AME, 8AME, 8MSI, 9AME, 9MSI

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 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:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ANTIFREEZE PROTEIN TYPE III)	A	66	Zoarces americanus	Mutation(s): 3
UniProt
Find proteins for P19614 (Zoarces americanus) Explore P19614 Go to UniProtKB: P19614
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19614
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Reference Sequence