3rdn

From Proteopedia

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Current revision

NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, MINIMIZED AVERAGE STRUCTURE

Structural highlights

3rdn is a 1 chain structure with sequence from Lycodichthys dearborni. 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

ANP3_LYCDA 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 (By similarity).

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

Antifreeze proteins (AFPs) have the unique ability to adsorb to ice and inhibit its growth. Many organisms ranging from fish to bacteria use AFPs to retard freezing or lessen the damage incurred upon freezing and thawing. The ice-binding mechanism of the long linear alpha-helical type I AFPs has been attributed to their regularly spaced polar residues matching the ice lattice along a pyramidal plane. In contrast, it is not known how globular antifreeze proteins such as type III AFP that lack repeating ice-binding residues bind to ice. Here we report the 1.25 A crystal structure of recombinant type III AFP (QAE isoform) from eel pout (Macrozoarces americanus), which reveals a remarkably flat amphipathic ice-binding site where five hydrogen-bonding atoms match two ranks of oxygens on the [1010] ice prism plane in the <0001> direction, giving high ice-binding affinity and specificity. This binding site, substantiated by the structures and properties of several ice-binding site mutants, suggests that the AFP occupies a niche in the ice surface in which it covers the basal plane while binding to the prism face.

Structural basis for the binding of a globular antifreeze protein to ice.,Jia Z, DeLuca CI, Chao H, Davies PL Nature. 1996 Nov 21;384(6606):285-8. PMID:8918883^[1]

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

References

↑ Jia Z, DeLuca CI, Chao H, Davies PL. Structural basis for the binding of a globular antifreeze protein to ice. Nature. 1996 Nov 21;384(6606):285-8. PMID:8918883 doi:10.1038/384285a0

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/3rdn"

@@ Line 1: / Line 1: @@
 ==NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, MINIMIZED AVERAGE STRUCTURE==
-<StructureSection load='3rdn' size='340' side='right' caption='[[3rdn]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='3rdn' size='340' side='right'caption='[[3rdn]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rdn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Antarctic_eel_pout Antarctic eel pout]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rdn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lycodichthys_dearborni Lycodichthys dearborni]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDN FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdn OCA], [http://pdbe.org/3rdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rdn RCSB], [http://www.ebi.ac.uk/pdbsum/3rdn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rdn ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdn OCA], [https://pdbe.org/3rdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rdn RCSB], [https://www.ebi.ac.uk/pdbsum/3rdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rdn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ANP3_RHIDE ANP3_RHIDE]] 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 (By similarity).
+[https://www.uniprot.org/uniprot/ANP3_LYCDA ANP3_LYCDA] 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 (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/3rdn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/3rdn_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 ==See Also==
-*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Antarctic eel pout]]
+[[Category: Large Structures]]
-[[Category: Hikichi, K]]
+[[Category: Lycodichthys dearborni]]
-[[Category: Hoshino, T]]
+[[Category: Hikichi K]]
-[[Category: Miura, K]]
+[[Category: Hoshino T]]
-[[Category: Nemoto, N]]
+[[Category: Miura K]]
-[[Category: Ohgiya, S]]
+[[Category: Nemoto N]]
-[[Category: Tsuda, S]]
+[[Category: Ohgiya S]]
-[[Category: Antifreeze]]
+[[Category: Tsuda S]]
-[[Category: Antifreeze protein]]
-[[Category: Ice binding protein]]
-[[Category: Thermal hysteresis protein]]

3rdn

From Proteopedia

Current revision

NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, 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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