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2pko

From Proteopedia

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Crystal structure of yeast Urm1 at 1.8 A resolution

Structural highlights

2pko 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 1.8Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[8]

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

References

↑ Furukawa K, Mizushima N, Noda T, Ohsumi Y. A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes. J Biol Chem. 2000 Mar 17;275(11):7462-5. PMID:10713047
↑ Goehring AS, Rivers DM, Sprague GF Jr. Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p. Eukaryot Cell. 2003 Oct;2(5):930-6. PMID:14555475
↑ Goehring AS, Rivers DM, Sprague GF Jr. Urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast. Mol Biol Cell. 2003 Nov;14(11):4329-41. Epub 2003 Jul 25. PMID:14551258 doi:http://dx.doi.org/10.1091/mbc.E03-02-0079
↑ Nakai Y, Nakai M, Hayashi H. Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems. J Biol Chem. 2008 Oct 10;283(41):27469-76. Epub 2008 Jul 29. PMID:18664566 doi:http://dx.doi.org/M804043200
↑ Huang B, Lu J, Bystrom AS. A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA. 2008 Oct;14(10):2183-94. doi: 10.1261/rna.1184108. Epub 2008 Aug 28. PMID:18755837 doi:10.1261/rna.1184108
↑ Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M. Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature. 2009 Mar 12;458(7235):228-32. doi: 10.1038/nature07643. Epub 2009 Jan 14. PMID:19145231 doi:http://dx.doi.org/10.1038/nature07643
↑ Noma A, Sakaguchi Y, Suzuki T. Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions. Nucleic Acids Res. 2009 Mar;37(4):1335-52. doi: 10.1093/nar/gkn1023. Epub 2009, Jan 16. PMID:19151091 doi:http://dx.doi.org/10.1093/nar/gkn1023
↑ Schmitz J, Chowdhury MM, Hanzelmann P, Nimtz M, Lee EY, Schindelin H, Leimkuhler S. The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins. Biochemistry. 2008 Jun 17;47(24):6479-89. Epub 2008 May 21. PMID:18491921 doi:10.1021/bi800477u

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pko"

Categories: Large Structures | Saccharomyces cerevisiae | Lake MW | Lee EY | Schindelin H

@@ Line 3: / Line 3: @@
 <StructureSection load='2pko' size='340' side='right'caption='[[2pko]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pko]] 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
+<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>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">URM1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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]] 1.8&#8491;</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=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>
 </table>
 == Function ==
-[[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>
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Lake, M W]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Lee, E Y]]
+[[Category: Lake MW]]
-[[Category: Schindelin, H]]
+[[Category: Lee EY]]
-[[Category: Beta grasp fold ubiquitin-like protein]]
+[[Category: Schindelin H]]
-[[Category: Protein binding]]

2pko

From Proteopedia

Current revision

Crystal structure of yeast Urm1 at 1.8 A resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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