3uyv

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a glycosylated ice-binding protein (LeIBP) from Arctic yeast

Structural highlights

3uyv is a 1 chain structure with sequence from Leucosporidium sp. AY30. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.43Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IBP_LEUSY Confers freeze tolerance. Binds to the surface of ice crystals and inhibits their growth. Has low thermal hysteresis (TH) activity, which is the ability to lower the freezing point of an aqueous solution below its melting point (PubMed:20067781, PubMed:22303017, PubMed:22426061, PubMed:22622645, PubMed:23203635, PubMed:24699650). The TH activity of this protein is approximately 0.2 degrees Celsius at 50 uM and 0.3 degrees Celsius at 400 uM (PubMed:24699650).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of approximately 25 kDa, which can lower the freezing point below the melting point once it binds to ice. LeIBP is a member of a large class of ice-binding proteins, the structures of which are unknown. Here, we report the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57 A and 2.43 A resolution, respectively. Structural analysis of the LeIBPs revealed a dimeric right-handed beta-helix fold, which is composed of three parts: a large coiled structural domain, a long helix region (residues 96-115 form a long alpha-helix that packs along one face of the beta-helix) and a C-terminal hydrophobic loop region (243-PFVPAPEVV-251). Unexpectedly, the C-terminal hydrophobic loop region has an extended conformation pointing away from the body of the coiled structural domain and forms intertwined dimer interactions. In addition, structural analysis of glycosylated LeIBP with sugar moieties attached to Asn185 provides a basis for interpreting previous biochemical analyses as well as the increased stability and secretion of glycosylated LeIBP. We also determined that the aligned Thr/Ser/Ala residues are critical for ice binding within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a common beta-helical fold similar to that of canonical hyperactive antifreeze proteins, the ice-binding site is more complex and does not have a simple ice-binding motif. In conclusion, we could identify the ice-binding site of LeIBP and discuss differences in the ice-binding modes compared to other known AFPs and IBPs.

Structural basis for the antifreeze activity of an ice-binding protein from an Arctic yeast.,Lee JH, Park AK, Do H, Park KS, Moh SH, Chi YM, Kim HJ J Biol Chem. 2012 Feb 2. PMID:22303017^[7]

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

References

↑ Lee JK, Park KS, Park S, Park H, Song YH, Kang SH, Kim HJ. An extracellular ice-binding glycoprotein from an Arctic psychrophilic yeast. Cryobiology. 2010 Apr;60(2):222-8. PMID:20067781 doi:10.1016/j.cryobiol.2010.01.002
↑ Lee JH, Park AK, Do H, Park KS, Moh SH, Chi YM, Kim HJ. Structural basis for the antifreeze activity of an ice-binding protein from an Arctic yeast. J Biol Chem. 2012 Feb 2. PMID:22303017 doi:10.1074/jbc.M111.331835
↑ Park KS, Do H, Lee JH, Park SI, Kim Ej, Kim SJ, Kang SH, Kim HJ. Characterization of the ice-binding protein from Arctic yeast Leucosporidium sp. AY30. Cryobiology. 2012 Jun;64(3):286-96. PMID:22426061 doi:10.1016/j.cryobiol.2012.02.014
↑ Lee SG, Koh HY, Lee JH, Kang SH, Kim HJ. Cryopreservative effects of the recombinant ice-binding protein from the arctic yeast Leucosporidium sp. on red blood cells. Appl Biochem Biotechnol. 2012 Jun;167(4):824-34. PMID:22622645 doi:10.1007/s12010-012-9739-z
↑ Lee JH, Lee SG, Do H, Park JC, Kim E, Choe YH, Han SJ, Kim HJ. Optimization of the pilot-scale production of an ice-binding protein by fed-batch culture of Pichia pastoris. Appl Microbiol Biotechnol. 2013 Apr;97(8):3383-93. PMID:23203635 doi:10.1007/s00253-012-4594-y
↑ Do H, Kim SJ, Kim HJ, Lee JH. Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1. Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1061-73. doi:, 10.1107/S1399004714000996. Epub 2014 Mar 19. PMID:24699650 doi:http://dx.doi.org/10.1107/S1399004714000996
↑ Lee JH, Park AK, Do H, Park KS, Moh SH, Chi YM, Kim HJ. Structural basis for the antifreeze activity of an ice-binding protein from an Arctic yeast. J Biol Chem. 2012 Feb 2. PMID:22303017 doi:10.1074/jbc.M111.331835

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3uyv"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a glycosylated ice-binding protein (LeIBP) from Arctic yeast==
-<StructureSection load='3uyv' size='340' side='right' caption='[[3uyv]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
+<StructureSection load='3uyv' size='340' side='right'caption='[[3uyv]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3uyv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leucosporidium Leucosporidium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UYV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3uyv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leucosporidium_sp._AY30 Leucosporidium sp. AY30]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UYV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3uyu|3uyu]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5277 Leucosporidium])</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=3uyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uyv OCA], [https://pdbe.org/3uyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uyv RCSB], [https://www.ebi.ac.uk/pdbsum/3uyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uyv ProSAT]</span></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=3uyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uyv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uyv RCSB], [http://www.ebi.ac.uk/pdbsum/3uyv PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/IBP_LEUSY IBP_LEUSY] Confers freeze tolerance. Binds to the surface of ice crystals and inhibits their growth. Has low thermal hysteresis (TH) activity, which is the ability to lower the freezing point of an aqueous solution below its melting point (PubMed:20067781, PubMed:22303017, PubMed:22426061, PubMed:22622645, PubMed:23203635, PubMed:24699650). The TH activity of this protein is approximately 0.2 degrees Celsius at 50 uM and 0.3 degrees Celsius at 400 uM (PubMed:24699650).<ref>PMID:20067781</ref> <ref>PMID:22303017</ref> <ref>PMID:22426061</ref> <ref>PMID:22622645</ref> <ref>PMID:23203635</ref> <ref>PMID:24699650</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3uyv" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Leucosporidium]]
+[[Category: Large Structures]]
-[[Category: Chi, Y M]]
+[[Category: Leucosporidium sp. AY30]]
-[[Category: Do, H]]
+[[Category: Chi YM]]
-[[Category: Kim, H J]]
+[[Category: Do H]]
-[[Category: Lee, J H]]
+[[Category: Kim HJ]]
-[[Category: Moh, S H]]
+[[Category: Lee JH]]
-[[Category: Park, A K]]
+[[Category: Moh SH]]
-[[Category: Park, K S]]
+[[Category: Park AK]]
-[[Category: Antifreeze protein]]
+[[Category: Park KS]]
-[[Category: Ice binding protein]]
-[[Category: Right-handed beta-helix fold]]

3uyv

From Proteopedia

Current revision

Crystal structure of a glycosylated ice-binding protein (LeIBP) from Arctic yeast

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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