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PDBsum entry 1ops
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Antifreeze protein PDB id
1ops

 

 

 

 

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Contents
Protein chain
64 a.a. *
Waters ×33
* Residue conservation analysis
PDB id:
1ops
Name: Antifreeze protein
Title: Ice-binding surface on a type iii antifreeze protein from ocean pout
Structure: Type iii antifreeze protein. Chain: a. Synonym: type iii afp
Source: Macrozoarces americanus. Ocean pout. Organism_taxid: 8199. Tissue: serum. Other_details: isoform hplc-3
Resolution:
2.00Å     R-factor:   0.204     R-free:   0.259
Authors: D.S.C.Yang,W.-C.Hon,S.Bubanko,Y.Xue,J.Seetharaman,C.L.Hew,F.Sicheri
Key ref: D.S.Yang et al. (1998). Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm. Biophys J, 74, 2142-2151. PubMed id: 9591641
Date:
17-Nov-97     Release date:   20-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P19608  (ANP1_ZOAAM) -  Ice-structuring protein SP2(HPLC 1) from Zoarces americanus
Seq:
Struc: 		64 a.a.
64 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Biophys J 74:2142-2151 (1998)
PubMed id: 9591641  
 
 
Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm.
D.S.Yang, W.C.Hon, S.Bubanko, Y.Xue, J.Seetharaman, C.L.Hew, F.Sicheri.
 
  ABSTRACT  
 
Antifreeze proteins (AFPs) adsorb to surfaces of growing ice crystals, thereby arresting their growth. The prevailing hypothesis explains the nature of adsorption in terms of a match between the hydrophilic side chains on the AFP's ice-binding surface (IBS) and the water molecules on the ice surface. The number and spatial arrangement of hydrogen bonds thus formed have been proposed to account, respectively, for the binding affinity and specificity. The crystal structure of a type III AFP from ocean pout (isoform HPLC-3) has been determined to 2.0-A resolution. The structure reveals an internal dyad motif formed by two 19-residue, loop-shaped elements. Based on of the flatness observed on the type I alpha-helical AFP's IBS, an automated algorithm was developed to analyze the surface planarity of the globular type III AFP and was used to identify the IBS on this protein. The surface with the highest flatness score is formed by one loop of the dyad motif and is identical to the IBS deduced from earlier mutagenesis studies. Interestingly, 67% of this surface contains nonpolar solvent-accessible surface area. The success of our approach to identifying the IBS on an AFP, without considering the presence of polar side chains, indicates that flatness is the first approximation of an IBS. We further propose that the specificity of interactions between an IBS and a particular ice-crystallographic plane arises from surface complementarity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472814 E.I.Howard, M.P.Blakeley, M.Haertlein, I.P.Haertlein, A.Mitschler, S.J.Fisher, A.C.Siah, A.G.Salvay, A.Popov, C.M.Dieckmann, T.Petrova, and A.Podjarny (2011).
Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface.
  J Mol Recognit, 24, 724-732.
PDB code: 3qf6
21518869 K.A.Sharp (2011).
A peek at ice binding by antifreeze proteins.
  Proc Natl Acad Sci U S A, 108, 7281-7282.  
21115821 C.Deng, C.H.Cheng, H.Ye, X.He, and L.Chen (2010).
Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict.
  Proc Natl Acad Sci U S A, 107, 21593-21598.  
20024694 I.G.Gwak, W.S.Jung, H.J.Kim, S.H.Kang, and E.Jin (2010).
Antifreeze protein in Antarctic marine diatom, Chaetoceros neogracile.
  Mar Biotechnol (NY), 12, 630-639.  
  19342793 I.Petit-Haertlein, M.P.Blakeley, E.Howard, I.Hazemann, A.Mitschler, M.Haertlein, and A.Podjarny (2009).
Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 406-409.  
19187223 M.Takamichi, Y.Nishimiya, A.Miura, and S.Tsuda (2009).
Fully active QAE isoform confers thermal hysteresis activity on a defective SP isoform of type III antifreeze protein.
  FEBS J, 276, 1471-1479.  
18821129 Y.C.Tai, J.McGuire, O.Joshi, and D.Q.Wang (2009).
Solid surface chemical and physical effects on the adsorption of recombinant Factor VIII.
  Pharm Dev Technol, 14, 126-130.  
18796694 N.C.Benson, and V.Daggett (2008).
Dynameomics: large-scale assessment of native protein flexibility.
  Protein Sci, 17, 2038-2050.  
18339740 N.Pertaya, C.B.Marshall, Y.Celik, P.L.Davies, and I.Braslavsky (2008).
Direct visualization of spruce budworm antifreeze protein interacting with ice crystals: basal plane affinity confers hyperactivity.
  Biophys J, 95, 333-341.  
17158562 F.H.Lin, L.A.Graham, R.L.Campbell, and P.L.Davies (2007).
Structural modeling of snow flea antifreeze protein.
  Biophys J, 92, 1717-1723.  
17056724 N.B.Holland, Y.Nishimiya, S.Tsuda, and F.D.Sönnichsen (2007).
Activity of a two-domain antifreeze protein is not dependent on linker sequence.
  Biophys J, 92, 541-546.  
17325008 N.Pertaya, C.B.Marshall, C.L.DiPrinzio, L.Wilen, E.S.Thomson, J.S.Wettlaufer, P.L.Davies, and I.Braslavsky (2007).
Fluorescence microscopy evidence for quasi-permanent attachment of antifreeze proteins to ice surfaces.
  Biophys J, 92, 3663-3673.  
17189482 O.García-Arribas, R.Mateo, M.M.Tomczak, P.L.Davies, and M.G.Mateu (2007).
Thermodynamic stability of a cold-adapted protein, type III antifreeze protein, and energetic contribution of salt bridges.
  Protein Sci, 16, 227-238.  
16823370 A.C.Doxey, M.W.Yaish, M.Griffith, and B.J.McConkey (2006).
Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.
  Nat Biotechnol, 24, 852-855.  
16437556 S.P.Graether, C.M.Slupsky, and B.D.Sykes (2006).
Effect of a mutation on the structure and dynamics of an alpha-helical antifreeze protein in water and ice.
  Proteins, 63, 603-610.  
  16754975 Y.Nishimiya, H.Kondo, M.Yasui, H.Sugimoto, N.Noro, R.Sato, M.Suzuki, A.Miura, and S.Tsuda (2006).
Crystallization and preliminary X-ray crystallographic analysis of Ca2+-independent and Ca2+-dependent species of the type II antifreeze protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 538-541.  
15726609 C.Yang, and K.A.Sharp (2005).
Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition.
  Proteins, 59, 266-274.  
15654886 Y.Nishimiya, R.Sato, M.Takamichi, A.Miura, and S.Tsuda (2005).
Co-operative effect of the isoforms of type III antifreeze protein expressed in Notched-fin eelpout, Zoarces elongatus Kner.
  FEBS J, 272, 482-492.  
15291806 S.P.Graether, and B.D.Sykes (2004).
Cold survival in freeze-intolerant insects: the structure and function of beta-helical antifreeze proteins.
  Eur J Biochem, 271, 3285-3296.  
14586470 Q.Q.Hoang, F.Sicheri, A.J.Howard, and D.S.Yang (2003).
Bone recognition mechanism of porcine osteocalcin from crystal structure.
  Nature, 425, 977-980.
PDB code: 1q8h
12547803 T.P.Ko, H.Robinson, Y.G.Gao, C.H.Cheng, A.L.DeVries, and A.H.Wang (2003).
The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.
  Biophys J, 84, 1228-1237.
PDB code: 1ucs
12037324 E.K.Leinala, P.L.Davies, and Z.Jia (2002).
Elevated temperature and tyrosine iodination aid in the crystallization and structure determination of an antifreeze protein.
  Acta Crystallogr D Biol Crystallogr, 58, 1081-1083.  
12015145 E.K.Leinala, P.L.Davies, and Z.Jia (2002).
Crystal structure of beta-helical antifreeze protein points to a general ice binding model.
  Structure, 10, 619-627.
PDB code: 1l0s
12324437 Y.Cheng, Z.Yang, H.Tan, R.Liu, G.Chen, and Z.Jia (2002).
Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics.
  Biophys J, 83, 2202-2210.  
11852248 Z.Jia, and P.L.Davies (2002).
Antifreeze proteins: an unusual receptor-ligand interaction.
  Trends Biochem Sci, 27, 101-106.  
11181960 G.L.Fletcher, C.L.Hew, and P.L.Davies (2001).
Antifreeze proteins of teleost fishes.
  Annu Rev Physiol, 63, 359-390.  
11504613 J.Baardsnes, and P.L.Davies (2001).
Sialic acid synthase: the origin of fish type III antifreeze protein?
  Trends Biochem Sci, 26, 468-469.  
11240367 J.Barrett (2001).
Thermal hysteresis proteins.
  Int J Biochem Cell Biol, 33, 105-117.  
11222281 S.P.Graether, and Z.Jia (2001).
Modeling Pseudomonas syringae ice-nucleation protein as a beta-helical protein.
  Biophys J, 80, 1169-1173.  
10822254 J.D.Madura, K.Baran, and A.Wierzbicki (2000).
Molecular recognition and binding of thermal hysteresis proteins to ice.
  J Mol Recognit, 13, 101-113.  
10713525 Y.C.Liou, P.L.Davies, and Z.Jia (2000).
Crystallization and preliminary X-ray analysis of insect antifreeze protein from the beetle Tenebrio molitor.
  Acta Crystallogr D Biol Crystallogr, 56, 354-356.  
10465771 G.Chen, and Z.Jia (1999).
Ice-binding surface of fish type III antifreeze.
  Biophys J, 77, 1602-1608.  
10447672 Q.Lin, K.V.Ewart, Q.Yan, W.K.Wong, D.S.Yang, and C.L.Hew (1999).
Secretory expression and site-directed mutagenesis studies of the winter flounder skin-type antifreeze polypeptides.
  Eur J Biochem, 264, 49-54.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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