1C8A

NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR analysis of type III antifreeze protein intramolecular dimer. Structural basis for enhanced activity.

Miura, K.Ohgiya, S.Hoshino, T.Nemoto, N.Suetake, T.Miura, A.Spyracopoulos, L.Kondo, H.Tsuda, S.

(2001) J.Biol.Chem. 276: 1304-1310

  • DOI: 10.1074/jbc.M007902200
  • Primary Citation of Related Structures:  1C89

  • PubMed Abstract: 
  • The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translationa ...

    The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translational topology of two homologous type III AFP globular domains, each containing one flat, ice binding plane. The ice binding plane of the N domain is located approximately 3.5 A "behind" that of the C domain. The two ice binding planes are located laterally with an angle of 32 +/- 12 degrees between the planes. These results suggest that the C domain plane of RD3 binds first to the ice [1010] prism plane in the <0001> direction, which induces successive ice binding of the N domain in the <0101> direction. This manner of ice binding caused by the unique structural topology of RD3 is thought to be crucial for the significant enhancement of antifreeze activity, especially at low AFP concentrations.


    Related Citations: 
    • 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
    • Antifreeze Peptide Heterogeneity in an Antarctic Eel Pout Includes an Unusually Large Major Variant Comprised of Two 7 kDa Type III Afps Linked in Tandem
      Wang, X.,Devries, A.L.,Cheng, C.H.
      (1995) Biochim.Biophys.Acta 1247: 163
    • Refined Solution Structure of Type III Antifreeze Protein: Hydrophobic Groups May be Involved in the Energetics of the Protein-Ice Interaction
      Sonnichsen, F.D.,Deluca, C.I.,Davies, P.L.,Sykes, B.D.
      (1996) Structure 4: 1325
    • Determination of the Solution Structure of the N-Domain Plus Linker of Antarctic Eel Pout Antifreeze Protein Rd3
      Miura, K.,Ohgiya, S.,Hoshino, T.,Nemoto, N.,Odaira, M.,Nitta, K.,Tsuda, S.
      (1999) J.Biochem.(Tokyo) 126: 387


    Organizational Affiliation

    Bioscience and Chemistry Division, Hokkaido National Industrial Research Institute, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ANTIFREEZE PROTEIN TYPE III)
A
134Lycodichthys dearborniN/A
Find proteins for P35753 (Lycodichthys dearborni)
Go to UniProtKB:  P35753
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-05-04 
  • Released Date: 2001-02-28 
  • Deposition Author(s): Miura, K., Tsuda, S.

Revision History 

  • Version 1.0: 2001-02-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance