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2rfm

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(New page: 200px<br /><applet load="2rfm" size="350" color="white" frame="true" align="right" spinBox="true" caption="2rfm, resolution 1.650&Aring;" /> '''Structure of a Ther...)
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[[Image:2rfm.jpg|left|200px]]<br /><applet load="2rfm" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2rfm, resolution 1.650&Aring;" />
 
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'''Structure of a Thermophilic Ankyrin Repeat Protein'''<br />
 
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==Overview==
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==Structure of a Thermophilic Ankyrin Repeat Protein==
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Repeat proteins are widespread in nature, with many of them functioning as binding molecules in protein-protein recognition. Their simple structural architecture is used in biotechnology for generating proteins with high affinities to target proteins. Recent folding studies of ankyrin repeat (AR) proteins revealed a new mechanism of protein folding. The formation of an intermediate state is rate limiting in the folding reaction, suggesting a scaffold function of this transient state for intrinsically less stable ARs. To investigate a possible common mechanism of AR folding, we studied the structure and folding of a new thermophilic AR protein (tANK) identified in the archaeon Thermoplasma volcanium. The x-ray structure of the evolutionary much older tANK revealed high homology to the human CDK inhibitor p19(INK4d), whose sequence was used for homology search. As for p19(INK4d), equilibrium and kinetic folding analyses classify tANK to the family of sequential three-state folding proteins, with an unusual fast equilibrium between native and intermediate state. Under equilibrium conditions, the intermediate can be populated to &gt;90%, allowing characterization on a residue-by-residue level using NMR spectroscopy. These data clearly show that the three C-terminal ARs are natively folded in the intermediate state, whereas native cross-peaks for the rest of the molecule are missing. Therefore, the formation of a stable folding unit consisting of three ARs is the necessary rate-limiting step before AR 1 and 2 can assemble to form the native state.
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<StructureSection load='2rfm' size='340' side='right'caption='[[2rfm]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2rfm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_volcanium Thermoplasma volcanium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RFM FirstGlance]. <br>
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2RFM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoplasma_volcanium Thermoplasma volcanium] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=144:'>144</scene>, <scene name='pdbligand=BU2:'>BU2</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+A+190'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+B+190'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+191'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+B+192'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+A+191'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+A+193'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+B+193'>AC7</scene>, <scene name='pdbsite=AC8:Cl+Binding+Site+For+Residue+B+194'>AC8</scene>, <scene name='pdbsite=AC9:Cl+Binding+Site+For+Residue+B+195'>AC9</scene>, <scene name='pdbsite=BC1:144+Binding+Site+For+Residue+A+194'>BC1</scene>, <scene name='pdbsite=BC2:Bu2+Binding+Site+For+Residue+B+197'>BC2</scene>, <scene name='pdbsite=BC3:Bu2+Binding+Site+For+Residue+B+198'>BC3</scene>, <scene name='pdbsite=BC4:Bu2+Binding+Site+For+Residue+A+195'>BC4</scene>, <scene name='pdbsite=BC5:Bu2+Binding+Site+For+Residue+A+196'>BC5</scene>, <scene name='pdbsite=BC6:Gol+Binding+Site+For+Residue+B+199'>BC6</scene>, <scene name='pdbsite=BC7:Gol+Binding+Site+For+Residue+B+200'>BC7</scene>, <scene name='pdbsite=BC8:Gol+Binding+Site+For+Residue+A+197'>BC8</scene>, <scene name='pdbsite=BC9:Gol+Binding+Site+For+Residue+B+201'>BC9</scene>, <scene name='pdbsite=CC1:Gol+Binding+Site+For+Residue+A+198'>CC1</scene> and <scene name='pdbsite=CC2:Gol+Binding+Site+For+Residue+A+199'>CC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RFM OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=BU2:1,3-BUTANEDIOL'>BU2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rfm OCA], [https://pdbe.org/2rfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rfm RCSB], [https://www.ebi.ac.uk/pdbsum/2rfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rfm ProSAT]</span></td></tr>
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Structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein., Low C, Weininger U, Neumann P, Klepsch M, Lilie H, Stubbs MT, Balbach J, Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3779-84. Epub 2008 Feb 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18305166 18305166]
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</table>
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[[Category: Single protein]]
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== Function ==
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[https://www.uniprot.org/uniprot/Y1425_THEVO Y1425_THEVO]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rf/2rfm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rfm ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Thermoplasma volcanium]]
[[Category: Thermoplasma volcanium]]
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[[Category: Balbach, J.]]
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[[Category: Balbach J]]
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[[Category: Loew, C.]]
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[[Category: Loew C]]
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[[Category: Neumann, P.]]
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[[Category: Neumann P]]
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[[Category: Stubbs, M T.]]
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[[Category: Stubbs MT]]
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[[Category: Weininger, U.]]
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[[Category: Weininger U]]
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[[Category: 144]]
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[[Category: BU2]]
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[[Category: CL]]
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[[Category: GOL]]
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[[Category: SO4]]
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[[Category: ank repeat]]
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[[Category: ankyrin repeat]]
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[[Category: protein binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:35:23 2008''
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Current revision

Structure of a Thermophilic Ankyrin Repeat Protein

PDB ID 2rfm

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