3oer: Difference between revisions

Latest revision as of 09:37, 6 September 2023

Crystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt

Structural highlights

3oer is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Ligands:	CO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FRDA_YEAST Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. Plays a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+). Can store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization. May be involved in regulation of the mitochondrial electron transport chain.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Frataxin is a mitochondrial protein with a central role in iron homeostasis. Defects in frataxin function lead to Friedreich's ataxia, a progressive neurodegenerative disease with childhood onset. The function of frataxin has been shown to be closely associated with its ability to form oligomeric species; however, the factors controlling oligomerization and the types of oligomers present in solution are a matter of debate. Using small-angle X-ray scattering, we found that Co(2+), glycerol, and a single amino acid substitution at the N-terminus, Y73A, facilitate oligomerization of yeast frataxin, resulting in a dynamic equilibrium between monomers, dimers, trimers, hexamers, and higher-order oligomers. Using X-ray crystallography, we found that Co(2+) binds inside the channel at the 3-fold axis of the trimer, which suggests that the metal has an oligomer-stabilizing role. The results reveal the types of oligomers present in solution and support our earlier suggestions that the trimer is the main building block of yeast frataxin oligomers. They also indicate that different mechanisms may control oligomer stability and oligomerization in vivo.

Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering.,Soderberg CA, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S J Mol Biol. 2011 Dec 16;414(5):783-97. Epub 2011 Oct 25. PMID:22051511^[7]

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

References

↑ Babcock M, de Silva D, Oaks R, Davis-Kaplan S, Jiralerspong S, Montermini L, Pandolfo M, Kaplan J. Regulation of mitochondrial iron accumulation by Yfh1p, a putative homolog of frataxin. Science. 1997 Jun 13;276(5319):1709-12. PMID:9180083
↑ Radisky DC, Babcock MC, Kaplan J. The yeast frataxin homologue mediates mitochondrial iron efflux. Evidence for a mitochondrial iron cycle. J Biol Chem. 1999 Feb 19;274(8):4497-9. PMID:9988680
↑ Gonzalez-Cabo P, Vazquez-Manrique RP, Garcia-Gimeno MA, Sanz P, Palau F. Frataxin interacts functionally with mitochondrial electron transport chain proteins. Hum Mol Genet. 2005 Aug 1;14(15):2091-8. Epub 2005 Jun 16. PMID:15961414 doi:10.1093/hmg/ddi214
↑ Gakh O, Park S, Liu G, Macomber L, Imlay JA, Ferreira GC, Isaya G. Mitochondrial iron detoxification is a primary function of frataxin that limits oxidative damage and preserves cell longevity. Hum Mol Genet. 2006 Feb 1;15(3):467-79. Epub 2005 Dec 21. PMID:16371422 doi:10.1093/hmg/ddi461
↑ Leidgens S, De Smet S, Foury F. Frataxin interacts with Isu1 through a conserved tryptophan in its beta-sheet. Hum Mol Genet. 2010 Jan 15;19(2):276-86. Epub 2009 Nov 2. PMID:19884169 doi:ddp495
↑ Karlberg T, Schagerlof U, Gakh O, Park S, Ryde U, Lindahl M, Leath K, Garman E, Isaya G, Al-Karadaghi S. The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron. Structure. 2006 Oct;14(10):1535-46. PMID:17027502 doi:10.1016/j.str.2006.08.010
↑ Soderberg CA, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S. Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering. J Mol Biol. 2011 Dec 16;414(5):783-97. Epub 2011 Oct 25. PMID:22051511 doi:10.1016/j.jmb.2011.10.034

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Babcock M, de Silva D, Oaks R, Davis-Kaplan S, Jiralerspong S, Montermini L, Pandolfo M, Kaplan J. Regulation of mitochondrial iron accumulation by Yfh1p, a putative homolog of frataxin. Science. 1997 Jun 13;276(5319):1709-12. PMID:9180083

[2] Radisky DC, Babcock MC, Kaplan J. The yeast frataxin homologue mediates mitochondrial iron efflux. Evidence for a mitochondrial iron cycle. J Biol Chem. 1999 Feb 19;274(8):4497-9. PMID:9988680

[3] Gonzalez-Cabo P, Vazquez-Manrique RP, Garcia-Gimeno MA, Sanz P, Palau F. Frataxin interacts functionally with mitochondrial electron transport chain proteins. Hum Mol Genet. 2005 Aug 1;14(15):2091-8. Epub 2005 Jun 16. PMID:15961414 doi:10.1093/hmg/ddi214

[4] Gakh O, Park S, Liu G, Macomber L, Imlay JA, Ferreira GC, Isaya G. Mitochondrial iron detoxification is a primary function of frataxin that limits oxidative damage and preserves cell longevity. Hum Mol Genet. 2006 Feb 1;15(3):467-79. Epub 2005 Dec 21. PMID:16371422 doi:10.1093/hmg/ddi461

[5] Leidgens S, De Smet S, Foury F. Frataxin interacts with Isu1 through a conserved tryptophan in its beta-sheet. Hum Mol Genet. 2010 Jan 15;19(2):276-86. Epub 2009 Nov 2. PMID:19884169 doi:ddp495

[6] Karlberg T, Schagerlof U, Gakh O, Park S, Ryde U, Lindahl M, Leath K, Garman E, Isaya G, Al-Karadaghi S. The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron. Structure. 2006 Oct;14(10):1535-46. PMID:17027502 doi:10.1016/j.str.2006.08.010

[7] Soderberg CA, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S. Oligomerization Propensity and Flexibility of Yeast Frataxin Studied by X-ray Crystallography and Small-Angle X-ray Scattering. J Mol Biol. 2011 Dec 16;414(5):783-97. Epub 2011 Oct 25. PMID:22051511 doi:10.1016/j.jmb.2011.10.034

[1]

[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='3oer' size='340' side='right'caption='[[3oer]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3oer]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OER FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3oer]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OER FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 3.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fql|2fql]], [[3oeq|3oeq]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YFH1, YDL120W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3oer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oer OCA], [https://pdbe.org/3oer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oer RCSB], [https://www.ebi.ac.uk/pdbsum/3oer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oer ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/FRDA_YEAST FRDA_YEAST]] Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. Plays a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+). Can store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization. May be involved in regulation of the mitochondrial electron transport chain.<ref>PMID:9180083</ref> <ref>PMID:9988680</ref> <ref>PMID:15961414</ref> <ref>PMID:16371422</ref> <ref>PMID:19884169</ref> <ref>PMID:17027502</ref>
+[https://www.uniprot.org/uniprot/FRDA_YEAST FRDA_YEAST] Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. Plays a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+). Can store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization. May be involved in regulation of the mitochondrial electron transport chain.<ref>PMID:9180083</ref> <ref>PMID:9988680</ref> <ref>PMID:15961414</ref> <ref>PMID:16371422</ref> <ref>PMID:19884169</ref> <ref>PMID:17027502</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Al-Karadaghi, S]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Gakh, O]]
+[[Category: Al-Karadaghi S]]
-[[Category: Isaya, G]]
+[[Category: Gakh O]]
-[[Category: Rajan, S]]
+[[Category: Isaya G]]
-[[Category: Soderberg, C A.G]]
+[[Category: Rajan S]]
-[[Category: Ta, C]]
+[[Category: Soderberg CAG]]
-[[Category: Alpha/beta sandwich]]
+[[Category: Ta C]]
-[[Category: Iron-storage]]
-[[Category: Metallochaperone]]
-[[Category: Transport protein]]

3oer: Difference between revisions

Latest revision as of 09:37, 6 September 2023

Crystal structure of trimeric frataxin from the yeast saccharomyces cerevisiae, complexed with cobalt

Structural highlights

Function

Publication Abstract from PubMed

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References

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