This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2ax5

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:22, 10 September 2015

Solution Structure of Urm1 from Saccharomyces Cerevisiae

Structural highlights

2ax5 is a 1 chain structure with sequence from Atcc 18824. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	YIL008W (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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

Protein modifiers are involved in diverse biological processes and regulate the activity or function of target proteins by covalently conjugating to them. Although ubiquitin and a number of ubiquitin-like protein modifiers (Ubls) in eukaryotes have been identified, no protein modifier has been found in prokaryotes; thus, their evolutionary origin remains a puzzle. To infer the evolutionary relationships between the protein modifiers and sulfur carrier proteins, we solved the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae. Both structural comparison and phylogenetic analysis of the ubiquitin superfamily, with emphasis on the Urm1 family, indicate that Urm1 is the unique "molecular fossil" that has the most conserved structural and sequence features of the common ancestor of the entire superfamily. The similarities of 3D structure and hydrophobic and electrostatic surface features between Urm1 and MoaD (molybdopterin synthase small subunit) suggest that they may interact with partners in a similar manner, and similarities between Urm1-Uba4 and MoaD-MoeB establish an evolutionary link between ATP-dependent protein conjugation in eukaryotes and ATP-dependent cofactor sulfuration.

Solution structure of Urm1 and its implications for the origin of protein modifiers.,Xu J, Zhang J, Wang L, Zhou J, Huang H, Wu J, Zhong Y, Shi Y Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11625-30. Epub 2006 Jul 24. PMID:16864801^[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
↑ Xu J, Zhang J, Wang L, Zhou J, Huang H, Wu J, Zhong Y, Shi Y. Solution structure of Urm1 and its implications for the origin of protein modifiers. Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11625-30. Epub 2006 Jul 24. PMID:16864801

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/2ax5"

@@ Line 2: / Line 2: @@
 <StructureSection load='2ax5' size='340' side='right' caption='[[2ax5]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ax5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AX5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AX5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ax5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AX5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AX5 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YIL008W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YIL008W ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ax5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ax5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ax5 RCSB], [http://www.ebi.ac.uk/pdbsum/2ax5 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ax5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ax5 OCA], [http://pdbe.org/2ax5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ax5 RCSB], [http://www.ebi.ac.uk/pdbsum/2ax5 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2ax5" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Atcc 18824]]
 [[Category: Huang, H]]
 [[Category: Shi, Y]]

2ax5

From Proteopedia

Revision as of 19:22, 10 September 2015

Solution Structure of Urm1 from Saccharomyces Cerevisiae

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox