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PDBsum entry 1wfb

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Antifreeze polypeptide PDB id
1wfb
Jmol
Contents
Protein chains
38 a.a.
Waters ×390
PDB id:
1wfb
Name: Antifreeze polypeptide
Title: Winter flounder antifreeze protein isoform hplc6 at-180 degrees c
Structure: Antifreeze protein isoform hplc6. Chain: a, b. Engineered: yes
Source: Pseudopleuronectes americanus. Winter flounder. Organism_taxid: 8265
Resolution:
1.50Å     R-factor:   0.177     R-free:   0.196
Authors: D.S.C.Yang,F.Sicheri
Key ref: F.Sicheri and D.S.Yang (1995). Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature, 375, 427-431. PubMed id: 7760940 DOI: 10.1038/375427a0
Date:
03-Apr-95     Release date:   03-Jun-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04002  (ANPA_PSEAM) -  Ice-structuring protein A
Seq:
Struc:
82 a.a.
38 a.a.*
Key:    PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     homoiothermy   2 terms 
  Biochemical function     ice binding     1 term  

 

 
DOI no: 10.1038/375427a0 Nature 375:427-431 (1995)
PubMed id: 7760940  
 
 
Ice-binding structure and mechanism of an antifreeze protein from winter flounder.
F.Sicheri, D.S.Yang.
 
  ABSTRACT  
 
Antifreeze proteins provide fish with protection against the freezing effect of polar environments by binding to ice surfaces and inhibiting growth of ice crystals. We present the X-ray crystal structure at 1.5 A resolution of a lone alpha-helical antifreeze protein from winter flounder, which provides a detailed look at its ice-binding features. These consist of four repeated ice-binding motifs, the side chains of which are inherently rigid or restrained by pair-wise side-chain interactions to form a flat binding surface. Elaborate amino- and carboxy-terminal cap structures are also present, which explain the protein's rich alpha-helical content in solution. We propose an ice-binding model that accounts for the binding specificity of the antifreeze protein along the <0112> axes of the (2021) ice planes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482800 C.P.Garnham, R.L.Campbell, and P.L.Davies (2011).
Anchored clathrate waters bind antifreeze proteins to ice.
  Proc Natl Acad Sci U S A, 108, 7363-7367.
PDB code: 3p4g
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
21518869 K.A.Sharp (2011).
A peek at ice binding by antifreeze proteins.
  Proc Natl Acad Sci U S A, 108, 7281-7282.  
20846837 O.Younes-Metzler, R.N.Ben, and J.B.Giorgi (2011).
The adsorption of antifreeze glycoprotein fraction 8 on dry and wet mica.
  Colloids Surf B Biointerfaces, 82, 134-140.  
  21470833 Y.Mao, M.Jeong, T.Wang, and Y.Ba (2011).
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
  Solid State Nucl Magn Reson, 39, 7.  
20139981 S.Bhushan, M.Gartmann, M.Halic, J.P.Armache, A.Jarasch, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
  Nat Struct Mol Biol, 17, 313-317.  
20936690 S.N.Patel, and S.P.Graether (2010).
Increased flexibility decreases antifreeze protein activity.
  Protein Sci, 19, 2356-2365.  
20453925 S.N.Patel, and S.P.Graether (2010).
Structures and ice-binding faces of the alanine-rich type I antifreeze proteins.
  Biochem Cell Biol, 88, 223-229.  
20215465 Y.Celik, L.A.Graham, Y.F.Mok, M.Bar, P.L.Davies, and I.Braslavsky (2010).
Superheating of ice crystals in antifreeze protein solutions.
  Proc Natl Acad Sci U S A, 107, 5423-5428.  
19383454 D.L.Masica, and J.J.Gray (2009).
Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.
  Biophys J, 96, 3082-3091.  
20021652 F.Cruz, J.Roux, and M.Robinson-Rechavi (2009).
The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes.
  BMC Genomics, 10, 619.  
19376768 I.Grunwald, K.Rischka, S.M.Kast, T.Scheibel, and H.Bargel (2009).
Mimicking biopolymers on a molecular scale: nano(bio)technology based on engineered proteins.
  Philos Transact A Math Phys Eng Sci, 367, 1727-1747.  
19746966 S.Wang, N.Amornwittawat, V.Juwita, Y.Kao, J.G.Duman, T.A.Pascal, W.A.Goddard, and X.Wen (2009).
Arginine, a key residue for the enhancing ability of an antifreeze protein of the beetle Dendroides canadensis.
  Biochemistry, 48, 9696-9703.  
19309754 T.Kacar, M.T.Zin, C.So, B.Wilson, H.Ma, N.Gul-Karaguler, A.K.Jen, M.Sarikaya, and C.Tamerler (2009).
Directed self-immobilization of alkaline phosphatase on micro-patterned substrates via genetically fused metal-binding peptide.
  Biotechnol Bioeng, 103, 696-705.  
18172904 G.Goobes, R.Goobes, W.J.Shaw, J.M.Gibson, J.R.Long, V.Raghunathan, O.Schueler-Furman, J.M.Popham, D.Baker, C.T.Campbell, P.S.Stayton, and G.P.Drobny (2008).
The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite.
  Magn Reson Chem, 45, S32-S47.  
18234809 H.Xu, S.Perumal, X.Zhao, N.Du, X.Y.Liu, Z.Jia, and J.R.Lu (2008).
Interfacial adsorption of antifreeze proteins: a neutron reflection study.
  Biophys J, 94, 4405-4413.  
18560157 M.Sugahara, Y.Asada, Y.Morikawa, Y.Kageyama, and N.Kunishima (2008).
Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites.
  Acta Crystallogr D Biol Crystallogr, 64, 686-695.
PDB codes: 1wmm 2dpn 2hd9 2zbn
18620083 N.Amornwittawat, S.Wang, J.G.Duman, and X.Wen (2008).
Polycarboxylates enhance beetle antifreeze protein activity.
  Biochim Biophys Acta, 1784, 1942-1948.  
18322856 S.Venketesh, and C.Dayananda (2008).
Properties, potentials, and prospects of antifreeze proteins.
  Crit Rev Biotechnol, 28, 57-82.  
18192371 W.J.Shaw, K.Ferris, B.Tarasevich, and J.L.Larson (2008).
The structure and orientation of the C-terminus of LRAP.
  Biophys J, 94, 3247-3257.  
17526572 A.Wierzbicki, P.Dalal, T.E.Cheatham, J.E.Knickelbein, A.D.Haymet, and J.D.Madura (2007).
Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins.
  Biophys J, 93, 1442-1451.  
17868093 H.Kun, and Y.Mastai (2007).
Activity of short segments of Type I antifreeze protein.
  Biopolymers, 88, 807-814.  
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.  
17558025 Z.Ma, J.Huang, J.Sun, G.Wang, C.Li, L.Xie, and R.Zhang (2007).
A novel extrapallial fluid protein controls the morphology of nacre lamellae in the pearl oyster, Pinctada fucata.
  J Biol Chem, 282, 23253-23263.  
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.  
17140379 S.Sivakumar, O.L.Franco, B.Thayumanavan, A.M.Murad, A.Manickam, M.Mohan, and M.Mridula (2006).
Cloning and structural analysis of an Indian little millet (Panicum sumatrense) zein-like storage protein: implications for molecular assembly.
  Biochemistry (Mosc), 71, 1183-1191.  
16648161 Y.Mao, and Y.Ba (2006).
Insight into the binding of antifreeze proteins to ice surfaces via 13C spin lattice relaxation solid-state NMR.
  Biophys J, 91, 1059-1068.  
  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.  
15716269 C.B.Marshall, A.Chakrabartty, and P.L.Davies (2005).
Hyperactive antifreeze protein from winter flounder is a very long rod-like dimer of alpha-helices.
  J Biol Chem, 280, 17920-17929.  
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.  
16218962 R.P.Evans, and G.L.Fletcher (2005).
Type I antifreeze proteins expressed in snailfish skin are identical to their plasma counterparts.
  FEBS J, 272, 5327-5336.  
15723360 S.Mayewski (2005).
A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing.
  Proteins, 59, 152-169.  
16128813 S.Y.Gauthier, C.B.Marshall, G.L.Fletcher, and P.L.Davies (2005).
Hyperactive antifreeze protein in flounder species. The sole freeze protectant in American plaice.
  FEBS J, 272, 4439-4449.  
15152087 A.Jorov, B.S.Zhorov, and D.S.Yang (2004).
Theoretical study of interaction of winter flounder antifreeze protein with ice.
  Protein Sci, 13, 1524-1537.  
15356865 D.H.Nguyen, M.E.Colvin, Y.Yeh, R.E.Feeney, and W.H.Fink (2004).
Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state.
  Biopolymers, 75, 109-117.  
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.  
12824479 M.E.Daley, and B.D.Sykes (2003).
The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein.
  Protein Sci, 12, 1323-1331.  
12524307 S.P.Graether, C.M.Slupsky, and B.D.Sykes (2003).
Freezing of a fish antifreeze protein results in amyloid fibril formation.
  Biophys J, 84, 552-557.  
12525484 W.K.Low, Q.Lin, and C.L.Hew (2003).
The role of N and C termini in the antifreeze activity of winter flounder (Pleuronectes americanus) antifreeze proteins.
  J Biol Chem, 278, 10334-10343.  
12105229 E.K.Leinala, P.L.Davies, D.Doucet, M.G.Tyshenko, V.K.Walker, and Z.Jia (2002).
A beta-helical antifreeze protein isoform with increased activity. Structural and functional insights.
  J Biol Chem, 277, 33349-33352.
PDB code: 1m8n
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
11856360 E.Liepinsh, G.Otting, M.M.Harding, L.G.Ward, J.P.Mackay, and A.D.Haymet (2002).
Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein.
  Eur J Biochem, 269, 1259-1266.
PDB codes: 1j5b 1k16
11940576 K.Fairley, B.J.Westman, L.H.Pham, A.D.Haymet, M.M.Harding, and J.P.Mackay (2002).
Type I shorthorn sculpin antifreeze protein: recombinant synthesis, solution conformation, and ice growth inhibition studies.
  J Biol Chem, 277, 24073-24080.  
11906602 M.J.Kuiper, J.V.Fecondo, and M.G.Wong (2002).
Rational design of alpha-helical antifreeze peptides.
  J Pept Res, 59, 1-8.  
12171647 M.Smallwood, and D.J.Bowles (2002).
Plants in a cold climate.
  Philos Trans R Soc Lond B Biol Sci, 357, 831-847.  
12171656 P.L.Davies, J.Baardsnes, M.J.Kuiper, and V.K.Walker (2002).
Structure and function of antifreeze proteins.
  Philos Trans R Soc Lond B Biol Sci, 357, 927-935.  
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.  
11181960 G.L.Fletcher, C.L.Hew, and P.L.Davies (2001).
Antifreeze proteins of teleost fishes.
  Annu Rev Physiol, 63, 359-390.  
11714925 J.Baardsnes, M.Jelokhani-Niaraki, L.H.Kondejewski, M.J.Kuiper, C.M.Kay, R.S.Hodges, and P.L.Davies (2001).
Antifreeze protein from shorthorn sculpin: identification of the ice-binding surface.
  Protein Sci, 10, 2566-2576.  
11240367 J.Barrett (2001).
Thermal hysteresis proteins.
  Int J Biochem Cell Biol, 33, 105-117.  
11181959 J.G.Duman (2001).
Antifreeze and ice nucleator proteins in terrestrial arthropods.
  Annu Rev Physiol, 63, 327-357.  
11721016 M.J.Kuiper, P.L.Davies, and V.K.Walker (2001).
A theoretical model of a plant antifreeze protein from Lolium perenne.
  Biophys J, 81, 3560-3565.
PDB code: 1i3b
11509380 S.P.Graether, C.M.Slupsky, P.L.Davies, and B.D.Sykes (2001).
Structure of type I antifreeze protein and mutants in supercooled water.
  Biophys J, 81, 1677-1683.  
10984522 F.Avbelj, P.Luo, and R.L.Baldwin (2000).
Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities.
  Proc Natl Acad Sci U S A, 97, 10786-10791.  
11106437 M.Miao, S.L.Chan, G.L.Fletcher, and C.L.Hew (2000).
The rat ortholog of the presumptive flounder antifreeze enhancer-binding protein is a helicase domain-containing protein.
  Eur J Biochem, 267, 7237-7246.  
  10892812 M.V.Katti, R.Sami-Subbu, P.K.Ranjekar, and V.S.Gupta (2000).
Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications.
  Protein Sci, 9, 1203-1209.  
10625646 V.Gerbaud, D.Pignol, E.Loret, J.A.Bertrand, Y.Berland, J.C.Fontecilla-Camps, J.P.Canselier, N.Gabas, and J.M.Verdier (2000).
Mechanism of calcite crystal growth inhibition by the N-terminal undecapeptide of lithostathine.
  J Biol Chem, 275, 1057-1064.
PDB code: 1qdd
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.  
10491111 M.M.Harding, L.G.Ward, and A.D.Haymet (1999).
Type I 'antifreeze' proteins. Structure-activity studies and mechanisms of ice growth inhibition.
  Eur J Biochem, 264, 653-665.  
10024024 N.Kessler, D.Perl-Treves, L.Addadi, and M.Eisenstein (1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
  Proteins, 34, 383-394.  
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.  
9512046 C.I.DeLuca, R.Comley, and P.L.Davies (1998).
Antifreeze proteins bind independently to ice.
  Biophys J, 74, 1502-1508.  
9591641 D.S.Yang, W.C.Hon, S.Bubanko, Y.Xue, J.Seetharaman, C.L.Hew, and F.Sicheri (1998).
Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm.
  Biophys J, 74, 2142-2151.
PDB code: 1ops
9770443 J.R.Long, J.L.Dindot, H.Zebroski, S.Kiihne, R.H.Clark, A.A.Campbell, P.S.Stayton, and G.P.Drobny (1998).
A peptide that inhibits hydroxyapatite growth is in an extended conformation on the crystal surface.
  Proc Natl Acad Sci U S A, 95, 12083-12087.  
9521729 K.V.Ewart, Z.Li, D.S.Yang, G.L.Fletcher, and C.L.Hew (1998).
The ice-binding site of Atlantic herring antifreeze protein corresponds to the carbohydrate-binding site of C-type lectins.
  Biochemistry, 37, 4080-4085.  
9519299 K.W.Plaxco, D.S.Riddle, V.Grantcharova, and D.Baker (1998).
Simplified proteins: minimalist solutions to the 'protein folding problem'.
  Curr Opin Struct Biol, 8, 80-85.  
9922140 M.C.Loewen, W.Gronwald, F.D.Sönnichsen, B.D.Sykes, and P.L.Davies (1998).
The ice-binding site of sea raven antifreeze protein is distinct from the carbohydrate-binding site of the homologous C-type lectin.
  Biochemistry, 37, 17745-17753.  
9565593 M.E.Houston, H.Chao, R.S.Hodges, B.D.Sykes, C.M.Kay, F.D.Sönnichsen, M.C.Loewen, and P.L.Davies (1998).
Binding of an oligopeptide to a specific plane of ice.
  J Biol Chem, 273, 11714-11718.  
9572849 N.Li, B.A.Chibber, F.J.Castellino, and J.G.Duman (1998).
Mapping of disulfide bridges in antifreeze proteins from overwintering larvae of the beetle Dendroides canadensis.
  Biochemistry, 37, 6343-6350.  
9537986 W.Gronwald, M.C.Loewen, B.Lix, A.J.Daugulis, F.D.Sönnichsen, P.L.Davies, and B.D.Sykes (1998).
The solution structure of type II antifreeze protein reveals a new member of the lectin family.
  Biochemistry, 37, 4712-4721.
PDB code: 2afp
9722537 W.K.Low, M.Miao, K.V.Ewart, D.S.Yang, G.L.Fletcher, and C.L.Hew (1998).
Skin-type antifreeze protein from the shorthorn sculpin, Myoxocephalus scorpius. Expression and characterization of a Mr 9, 700 recombinant protein.
  J Biol Chem, 273, 23098-23103.  
9857006 W.Zhang, and R.A.Laursen (1998).
Structure-function relationships in a type I antifreeze polypeptide. The role of threonine methyl and hydroxyl groups in antifreeze activity.
  J Biol Chem, 273, 34806-34812.  
9414201 A.Cheng, and K.M.Merz (1997).
Ice-binding mechanism of winter flounder antifreeze proteins.
  Biophys J, 73, 2851-2873.  
9306395 C.Hew (1997).
Insect antifreezes come in from the cold.
  Nat Biotechnol, 15, 844.  
9306405 M.G.Tyshenko, D.Doucet, P.L.Davies, and V.K.Walker (1997).
The antifreeze potential of the spruce budworm thermal hysteresis protein.
  Nat Biotechnol, 15, 887-890.  
9434903 P.L.Davies, and B.D.Sykes (1997).
Antifreeze proteins.
  Curr Opin Struct Biol, 7, 828-834.  
8804585 A.Wierzbicki, M.S.Taylor, C.A.Knight, J.D.Madura, J.P.Harrington, and C.S.Sikes (1996).
Analysis of shorthorn sculpin antifreeze protein stereospecific binding to (2-1 0) faces of ice.
  Biophys J, 71, 8.  
8913575 C.I.DeLuca, H.Chao, F.D.Sönnichsen, B.D.Sykes, and P.L.Davies (1996).
Effect of type III antifreeze protein dilution and mutation on the growth inhibition of ice.
  Biophys J, 71, 2346-2355.  
8939756 F.D.Sönnichsen, C.I.DeLuca, P.L.Davies, and B.D.Sykes (1996).
Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction.
  Structure, 4, 1325-1337.
PDB codes: 1kde 1kdf
  8762146 H.Chao, R.S.Hodges, C.M.Kay, S.Y.Gauthier, and P.L.Davies (1996).
A natural variant of type I antifreeze protein with four ice-binding repeats is a particularly potent antifreeze.
  Protein Sci, 5, 1150-1156.  
  8654365 J.A.Bertrand, D.Pignol, J.P.Bernard, J.M.Verdier, J.C.Dagorn, and J.C.Fontecilla-Camps (1996).
Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation.
  EMBO J, 15, 2678-2684.
PDB code: 1lit
8988006 W.Gronwald, H.Chao, D.V.Reddy, P.L.Davies, B.D.Sykes, and F.D.Sönnichsen (1996).
NMR characterization of side chain flexibility and backbone structure in the type I antifreeze protein at near freezing temperatures.
  Biochemistry, 35, 16698-16704.  
8626748 Z.Gong, K.V.Ewart, Z.Hu, G.L.Fletcher, and C.L.Hew (1996).
Skin antifreeze protein genes of the winter flounder, Pleuronectes americanus, encode distinct and active polypeptides without the secretory signal and prosequences.
  J Biol Chem, 271, 4106-4112.  
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.