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4i3d

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Revision as of 08:38, 9 November 2022

Crystal structure of fluorescent protein UnaG N57A mutant

Structural highlights

4i3d is a 4 chain structure with sequence from Anguilla japonica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UNAG_ANGJA Beta-barrel protein that binds unconjugated bilirubin with high affinity. Excitation of the bilirubin-bound protein gives rise to green fluorescence, both under normoxia and hypoxia. The apoprotein is not fluorescent. Does not emit fluorescence in the presence of ditauro-bilirubin, urobilin or biliverdin.^[1]

Publication Abstract from PubMed

The fluorescent protein toolbox has revolutionized experimental biology. Despite this advance, no fluorescent proteins have been identified from vertebrates, nor has chromogenic ligand-inducible activation or clinical utility been demonstrated. Here, we report the cloning and characterization of UnaG, a fluorescent protein from Japanese eel. UnaG belongs to the fatty-acid-binding protein (FABP) family, and expression in eel is restricted to small-diameter muscle fibers. On heterologous expression in cell lines or mouse brain, UnaG produces oxygen-independent green fluorescence. Remarkably, UnaG fluorescence is triggered by an endogenous ligand, bilirubin, a membrane-permeable heme metabolite and clinical health biomarker. The holoUnaG structure at 1.2 A revealed a biplanar coordination of bilirubin by reversible pi-conjugation, and we used this high-affinity and high-specificity interaction to establish a fluorescence-based human bilirubin assay with promising clinical utility. UnaG will be the prototype for a versatile class of ligand-activated fluorescent proteins, with applications in research, medicine, and bioengineering.

A bilirubin-inducible fluorescent protein from eel muscle.,Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A Cell. 2013 Jun 20;153(7):1602-11. doi: 10.1016/j.cell.2013.05.038. Epub 2013 Jun , 13. PMID:23768684^[2]

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

References

↑ Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. A bilirubin-inducible fluorescent protein from eel muscle. Cell. 2013 Jun 20;153(7):1602-11. doi: 10.1016/j.cell.2013.05.038. Epub 2013 Jun , 13. PMID:23768684 doi:10.1016/j.cell.2013.05.038
↑ Kumagai A, Ando R, Miyatake H, Greimel P, Kobayashi T, Hirabayashi Y, Shimogori T, Miyawaki A. A bilirubin-inducible fluorescent protein from eel muscle. Cell. 2013 Jun 20;153(7):1602-11. doi: 10.1016/j.cell.2013.05.038. Epub 2013 Jun , 13. PMID:23768684 doi:10.1016/j.cell.2013.05.038

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4i3d"

@@ Line 3: / Line 3: @@
 <StructureSection load='4i3d' size='340' side='right'caption='[[4i3d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i3d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Angja Angja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I3D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i3d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Anguilla_japonica Anguilla japonica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I3D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLR:3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic+acid'>BLR</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLR:3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic+acid'>BLR</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4i3b|4i3b]], [[4i3c|4i3c]]</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=4i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3d OCA], [https://pdbe.org/4i3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i3d RCSB], [https://www.ebi.ac.uk/pdbsum/4i3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3d 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=4i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i3d OCA], [http://pdbe.org/4i3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i3d RCSB], [http://www.ebi.ac.uk/pdbsum/4i3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i3d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UNAG_ANGJA UNAG_ANGJA]] Beta-barrel protein that binds unconjugated bilirubin with high affinity. Excitation of the bilirubin-bound protein gives rise to green fluorescence, both under normoxia and hypoxia. The apoprotein is not fluorescent. Does not emit fluorescence in the presence of ditauro-bilirubin, urobilin or biliverdin.<ref>PMID:23768684</ref>
+[https://www.uniprot.org/uniprot/UNAG_ANGJA UNAG_ANGJA] Beta-barrel protein that binds unconjugated bilirubin with high affinity. Excitation of the bilirubin-bound protein gives rise to green fluorescence, both under normoxia and hypoxia. The apoprotein is not fluorescent. Does not emit fluorescence in the presence of ditauro-bilirubin, urobilin or biliverdin.<ref>PMID:23768684</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Angja]]
+[[Category: Anguilla japonica]]
 [[Category: Large Structures]]
-[[Category: Ando, R]]
+[[Category: Ando R]]
-[[Category: Kumagai, A]]
+[[Category: Kumagai A]]
-[[Category: Miyatake, H]]
+[[Category: Miyatake H]]
-[[Category: Miyawaki, A]]
+[[Category: Miyawaki A]]
-[[Category: Beta barrel]]
-[[Category: Bilirubin binding protein]]
-[[Category: Cytosol]]
-[[Category: Fluorescent protein]]
-[[Category: Lipocalin]]

4i3d

From Proteopedia

Revision as of 08:38, 9 November 2022

Crystal structure of fluorescent protein UnaG N57A mutant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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