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1pae

From Proteopedia

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(New page: 200px<br /><applet load="1pae" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pae, resolution 2.70&Aring;" /> '''nucleoside diphospha...)
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[[Image:1pae.gif|left|200px]]<br /><applet load="1pae" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pae, resolution 2.70&Aring;" />
 
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'''nucleoside diphosphate kinase'''<br />
 
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==Overview==
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==nucleoside diphosphate kinase==
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A protocol for the quantitative incorporation of both selenomethionine and, selenocysteine into recombinant proteins overexpressed in Escherichia coli, is described. This methodology is based on the use of a suitable cysteine, auxotrophic strain and a minimal medium supplemented with selenium-labeled, methionine and cysteine. The proteins chosen for these studies are the, cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase., Analysis of the purified proteins by electrospray mass spectrometry and, X-ray crystallography revealed that both cysteine and methionine residues, were isomorphously replaced by selenocysteine and selenomethionine., Moreover, selenocysteines allowed the formation of unstrained and stable, diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This, novel selenium double-labeling method is proposed as a general approach to, increase the efficiency of the MAD technique used for phase determination, in protein crystallography.
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<StructureSection load='1pae' size='340' side='right'caption='[[1pae]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pae]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PAE FirstGlance]. <br>
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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]] 2.7&#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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr>
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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=1pae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pae OCA], [https://pdbe.org/1pae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pae RCSB], [https://www.ebi.ac.uk/pdbsum/1pae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pae ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
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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/pa/1pae_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=1pae ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PAE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum] with SE as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PAE OCA].
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing., Strub MP, Hoh F, Sanchez JF, Strub JM, Bock A, Aumelas A, Dumas C, Structure. 2003 Nov;11(11):1359-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14604526 14604526]
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[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Aumelas A]]
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[[Category: Aumelas, A.]]
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[[Category: Bock A]]
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[[Category: Bock, A.]]
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[[Category: Dumas C]]
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[[Category: Dumas, C.]]
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[[Category: Hoh F]]
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[[Category: Hoh, F.]]
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[[Category: Sanchez J-F]]
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[[Category: Sanchez, J.F.]]
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[[Category: Strub JM]]
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[[Category: Strub, J.M.]]
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[[Category: Strub M-P]]
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[[Category: Strub, M.P.]]
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[[Category: SE]]
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[[Category: selenocysteine selenomethionine]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:38:05 2007''
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Current revision

nucleoside diphosphate kinase

PDB ID 1pae

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