2pko

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{{Seed}}
 
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[[Image:2pko.png|left|200px]]
 
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==Crystal structure of yeast Urm1 at 1.8 A resolution==
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The line below this paragraph, containing "STRUCTURE_2pko", creates the "Structure Box" on the page.
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<StructureSection load='2pko' size='340' side='right'caption='[[2pko]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2pko]] 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKO 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]] 1.8&#8491;</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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [https://pdbe.org/2pko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [https://www.ebi.ac.uk/pdbsum/2pko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko ProSAT]</span></td></tr>
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{{STRUCTURE_2pko| PDB=2pko | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>
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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/pk/2pko_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=2pko ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Because of mechanistic parallels in the activation of ubiquitin and the biosynthesis of several sulfur-containing cofactors, we have characterized the human Urm1 and Saccharomyces cerevisiae Uba4 proteins, which are very similar in sequence to MOCS2A and MOCS3, respectively, two proteins essential for the biosynthesis of the molybdenum cofactor (Moco) in humans. Phylogenetic analyses of MOCS3 homologues showed that Uba4 is the MOCS3 homologue in yeast and thus the only remaining protein of the Moco biosynthetic pathway in this organism. Because of the high levels of sequence identity of human MOCS3 and yeast Uba4, we purified Uba4 and characterized the catalytic activity of the protein in detail. We demonstrate that the C-terminal domain of Uba4, like MOCS3, has rhodanese activity and is able to transfer the sulfur from thiosulfate to cyanide in vitro. In addition, we were able to copurify stable heterotetrameric complexes of Uba4 with both human Urm1 and MOCS2A. The N-terminal domain of Uba4 catalyzes the activation of either MOCS2A or Urm1 by formation of an acyl-adenylate bond. After adenylation, persulfurated Uba4 was able to form a thiocarboxylate group at the C-terminal glycine of either Urm1 or MOCS2A. The formation of a thioester intermediate between Uba4 and Urm1 or MOCS2A was not observed. The functional similarities between Uba4 and MOCS3 further demonstrate the evolutionary link between ATP-dependent protein conjugation and ATP-dependent cofactor sulfuration.
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===Crystal structure of yeast Urm1 at 1.8 A resolution===
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The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins.,Schmitz J, Chowdhury MM, Hanzelmann P, Nimtz M, Lee EY, Schindelin H, Leimkuhler S Biochemistry. 2008 Jun 17;47(24):6479-89. Epub 2008 May 21. PMID:18491921<ref>PMID:18491921</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18491921}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2pko" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18491921 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18491921}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2PKO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PKO OCA].
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==Reference==
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The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins., Schmitz J, Chowdhury MM, Hanzelmann P, Nimtz M, Lee EY, Schindelin H, Leimkuhler S, Biochemistry. 2008 Jun 17;47(24):6479-89. Epub 2008 May 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18491921 18491921]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Lake MW]]
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[[Category: Lake, M W.]]
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[[Category: Lee EY]]
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[[Category: Lee, E Y.]]
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[[Category: Schindelin H]]
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[[Category: Schindelin, H.]]
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[[Category: Beta grasp fold ubiquitin-like protein]]
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[[Category: Protein binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 21:23:36 2008''
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Current revision

Crystal structure of yeast Urm1 at 1.8 A resolution

PDB ID 2pko

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