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1kdf

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NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, MINIMIZED AVERAGE STRUCTURE

Structural highlights

1kdf is a 1 chain structure with sequence from Zoarces americanus. The December 2009 RCSB PDB Molecule of the Month feature on Antifreeze Proteins by David Goodsell is 10.2210/rcsb_pdb/mom_2009_12. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ANP12_ZOAAM Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BACKGROUND: Antifreeze proteins are found in certain fish inhabiting polar sea water. These proteins depress the freezing points of blood and body fluids below that of the surrounding sea water by binding to and inhibiting the growth of seed ice crystals. The proteins are believed to bind irreversibly to growing ice crystals in such a way as to change the curvature of the ice-water interface, leading to freezing point depression, but the mechanism of high-affinity ice binding is not yet fully understood. RESULTS: The solution structure of the type III antifreeze protein was determined by multidimensional NMR spectroscopy. Twenty-two structures converged and display a root mean square difference from the mean of 0.26 A for backbone atoms and 0.62 A for all non-hydrogen atoms. The protein exhibits a compact fold with a relatively large hydrophobic core, several short and irregular beta sheets and one helical turn. The ice-binding site, which encompasses parts of the C-terminal sheet and a loop, is planar and relatively nonpolar. The site is further characterized by the low solvent accessibilities and the specific spatial arrangement of the polar side-chain atoms of the putative ice-binding residues Gln9, Asn14, Thr15, Thr18 and Gln44. CONCLUSIONS: In agreement with the adsorption-inhibition mechanism of action, interatomic distances between active polar protein residues match the spacing of water molecules in the prism planes ( inverted question mark10&1macr;0 inverted question mark) of the hexagonal ice crystal. The particular side-chain conformations, however, limit the number and strength of possible proten-ice hydrogen bonds. This suggests that other entropic and enthalpic contributions, such as those arising from hydrophobic groups, could play a role in the high-affinity protein-ice adsorption.

Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction.,Sonnichsen FD, DeLuca CI, Davies PL, Sykes BD Structure. 1996 Nov 15;4(11):1325-37. PMID:8939756^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sonnichsen FD, DeLuca CI, Davies PL, Sykes BD. Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction. Structure. 1996 Nov 15;4(11):1325-37. PMID:8939756

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kdf"

@@ Line 1: / Line 1: @@
 ==NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, MINIMIZED AVERAGE STRUCTURE==
-<StructureSection load='1kdf' size='340' side='right'caption='[[1kdf]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1kdf' size='340' side='right'caption='[[1kdf]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1kdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Blennius_americanus Blennius americanus]. The December 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antifreeze Proteins''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_12 10.2210/rcsb_pdb/mom_2009_12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoarces_americanus Zoarces americanus]. The December 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antifreeze Proteins''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_12 10.2210/rcsb_pdb/mom_2009_12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDF FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kde|1kde]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">K38 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8199 Blennius americanus])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdf OCA], [https://pdbe.org/1kdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdf RCSB], [https://www.ebi.ac.uk/pdbsum/1kdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ANP12_ZOAAM ANP12_ZOAAM] Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 </StructureSection>
 [[Category: Antifreeze Proteins]]
-[[Category: Blennius americanus]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Davies, P L]]
+[[Category: Zoarces americanus]]
-[[Category: Deluca, C I]]
+[[Category: Davies PL]]
-[[Category: Sonnichsen, F D]]
+[[Category: Deluca CI]]
-[[Category: Sykes, B D]]
+[[Category: Sonnichsen FD]]
-[[Category: Antifreeze protein]]
+[[Category: Sykes BD]]
-[[Category: Glycoprotein]]
-[[Category: Ice binding protein]]
-[[Category: Thermal hysteresis protein]]

1kdf

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Current revision

NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, MINIMIZED AVERAGE STRUCTURE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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