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| | ==Crystal structure of an ice-binding protein (FfIBP) from the Antarctic bacterium, Flavobacterium frigoris PS1== | | ==Crystal structure of an ice-binding protein (FfIBP) from the Antarctic bacterium, Flavobacterium frigoris PS1== |
| - | <StructureSection load='4nu2' size='340' side='right' caption='[[4nu2]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='4nu2' size='340' side='right'caption='[[4nu2]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4nu2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_frigoris_ps1 Flavobacterium frigoris ps1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NU2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4nu2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_frigoris_PS1 Flavobacterium frigoris PS1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NU2 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nu3|4nu3]], [[4nuh|4nuh]]</td></tr> | + | </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=4nu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nu2 OCA], [https://pdbe.org/4nu2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nu2 RCSB], [https://www.ebi.ac.uk/pdbsum/4nu2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nu2 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HJ01_03463 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1086011 Flavobacterium frigoris PS1])</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=4nu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nu2 OCA], [http://pdbe.org/4nu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nu2 RCSB], [http://www.ebi.ac.uk/pdbsum/4nu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nu2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/IBP_FLAFP IBP_FLAFP] Has antifreeze activity for survival in a subzero environment. Binds to the surface of ice crystals and inhibits their growth. Has high thermal hysteresis (TH) activity, which is the ability to lower the freezing point of an aqueous solution below its melting point, and thus the freezing of the cell fluid can be prevented protecting the organism from ice damage (PubMed:22750870, PubMed:24699650, PubMed:27737617). The TH activity of this protein is 2.2 degrees Celsius at 5 uM and 2.5 degrees Celsius at 50 uM (PubMed:24699650).<ref>PMID:22750870</ref> <ref>PMID:24699650</ref> <ref>PMID:27737617</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Antifreeze protein|Antifreeze protein]] | + | *[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium frigoris ps1]] | + | [[Category: Flavobacterium frigoris PS1]] |
| - | [[Category: Do, H]] | + | [[Category: Large Structures]] |
| - | [[Category: Kim, H J]] | + | [[Category: Do H]] |
| - | [[Category: Kim, S J]] | + | [[Category: Kim HJ]] |
| - | [[Category: Lee, J H]] | + | [[Category: Kim SJ]] |
| - | [[Category: Lee, S G]] | + | [[Category: Lee JH]] |
| - | [[Category: Park, H]] | + | [[Category: Lee SG]] |
| - | [[Category: Antifreeze activity]] | + | [[Category: Park H]] |
| - | [[Category: Antifreeze protein]]
| + | |
| - | [[Category: Beta-helical]]
| + | |
| - | [[Category: Ice crystal]]
| + | |
| Structural highlights
Function
IBP_FLAFP Has antifreeze activity for survival in a subzero environment. Binds to the surface of ice crystals and inhibits their growth. Has high thermal hysteresis (TH) activity, which is the ability to lower the freezing point of an aqueous solution below its melting point, and thus the freezing of the cell fluid can be prevented protecting the organism from ice damage (PubMed:22750870, PubMed:24699650, PubMed:27737617). The TH activity of this protein is 2.2 degrees Celsius at 5 uM and 2.5 degrees Celsius at 50 uM (PubMed:24699650).[1] [2] [3]
Publication Abstract from PubMed
Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. FfIBP is an ice-binding protein encoded by the Antarctic bacterium Flavobacterium frigoris PS1. The X-ray crystal structure of FfIBP was determined to 2.1 A resolution to gain insight into its ice-binding mechanism. The refined structure of FfIBP shows an intramolecular disulfide bond, and analytical ultracentrifugation and analytical size-exclusion chromatography show that it behaves as a monomer in solution. Sequence alignments and structural comparisons of IBPs allowed two groups of IBPs to be defined, depending on sequence differences between the alpha2 and alpha4 loop regions and the presence of the disulfide bond. Although FfIBP closely resembles Leucosporidium (recently re-classified as Glaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH) activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding residues as well as a greater surface area in the ice-binding site. Notably, the ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is proposed that the difference in TH activity between FfIBP and LeIBP may arise from the amino-acid composition of the ice-binding site, which correlates with differences in affinity and surface complementarity to the ice crystal. In conclusion, this study provides a molecular basis for understanding the antifreeze mechanism of FfIBP and provides new insights into the reasons for the higher TH activity of FfIBP compared with LeIBP.
Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1.,Do H, Kim SJ, Kim HJ, Lee JH Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1061-73. doi:, 10.1107/S1399004714000996. Epub 2014 Mar 19. PMID:24699650[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Do H, Lee JH, Lee SG, Kim HJ. Crystallization and preliminary X-ray crystallographic analysis of an ice-binding protein (FfIBP) from Flavobacterium frigoris PS1. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Jul 1;68(Pt 7):806-9. doi: , 10.1107/S1744309112020465. Epub 2012 Jun 28. PMID:22750870 doi:http://dx.doi.org/10.1107/S1744309112020465
- ↑ 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
- ↑ Kim EJ, Lee JH, Lee SG, Han SJ. Improving thermal hysteresis activity of antifreeze protein from recombinant Pichia pastoris by removal of N-glycosylation. Prep Biochem Biotechnol. 2017 Mar 16;47(3):299-304. doi: , 10.1080/10826068.2016.1244682. Epub 2016 Oct 13. PMID:27737617 doi:http://dx.doi.org/10.1080/10826068.2016.1244682
- ↑ 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
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