3VN3

Fungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

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Literature

Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation

Kondo, H., Hanada, Y., Sugimoto, H., Hoshino, T., Garnham, C.P., Davies, P.L., Tsuda, S.

(2012) Proc Natl Acad Sci U S A 109: 9360-9365

  • DOI: 10.1073/pnas.1121607109
  • Primary Citation of Related Structures:  
    3VN3

  • PubMed Abstract: 

    • Antifreeze proteins (AFPs) are found in organisms ranging from fish to bacteria, where they serve different functions to facilitate survival of their host. AFPs that protect freeze-intolerant fish and insects from internal ice growth bind to ice using a regular array of well-conserved residues/motifs ...

    Antifreeze proteins (AFPs) are found in organisms ranging from fish to bacteria, where they serve different functions to facilitate survival of their host. AFPs that protect freeze-intolerant fish and insects from internal ice growth bind to ice using a regular array of well-conserved residues/motifs. Less is known about the role of AFPs in freeze-tolerant species, which might be to beneficially alter the structure of ice in or around the host. Here we report the 0.95-Å high-resolution crystal structure of a 223-residue secreted AFP from the snow mold fungus Typhula ishikariensis. Its main structural element is an irregular β-helix with six loops of 18 or more residues that lies alongside an α-helix. β-Helices have independently evolved as AFPs on several occasions and seem ideally structured to bind to several planes of ice, including the basal plane. A novelty of the β-helical fold is the nonsequential arrangement of loops that places the N- and C termini inside the solenoid of β-helical coils. The ice-binding site (IBS), which could not be predicted from sequence or structure, was located by site-directed mutagenesis to the flattest surface of the protein. It is remarkable for its lack of regularity and its poor conservation in homologs from psychrophilic diatoms and bacteria and other fungi.

    Organizational Affiliation: 

    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antifreeze proteinA, B223Typhula ishikariensisMutation(s): 0 
Gene Names: K3-B1
UniProt
Find proteins for Q76CE6 (Typhula ishikariensis)
Explore Q76CE6 
Go to UniProtKB:  Q76CE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76CE6
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IYR
Query on IYR		A, B L-PEPTIDE LINKINGC9 H10 I N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.89α = 81.53
b = 41.63β = 83.13
c = 70.25γ = 62.43
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references