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.

2v3j

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 14:48, 25 December 2014

THE YEAST RIBOSOME SYNTHESIS FACTOR EMG1 ALPHA BETA KNOT FOLD METHYLTRANSFERASE

Structural highlights

2v3j 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.
Ligands:
NonStd Res:
Related:	2v3k
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[EMG1_YEAST] Has an essential role in 40S ribosomal subunit biogenesis and 18S rRNA processing. Probably catalyzes the N1-methylation of pseudouridine at position 1189 (Psi1189) in 18S rRNA. Thus, is most likely the methyltransferase involved in the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in position 1189 in 18S rRNA. Is also involved in ribosome assembly.^[1] ^[2] ^[3] ^[4]

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

Emg1 was previously shown to be required for maturation of the 18S rRNA and biogenesis of the 40S ribosomal subunit. Here we report the determination of the crystal structure of Emg1 at 2 A resolution in complex with the methyl donor, S-adenosyl-methionine (SAM). This structure identifies Emg1 as a novel member of the alpha/beta knot fold methyltransferase (SPOUT) superfamily. In addition to the conserved SPOUT core, Emg1 has two unique domains that form an extended surface, which we predict to be involved in binding of RNA substrates. A point mutation within a basic patch on this surface almost completely abolished RNA binding in vitro. Three point mutations designed to disrupt the interaction of Emg1 with SAM each caused>100-fold reduction in SAM binding in vitro. Expression of only Emg1 with these mutations could support growth and apparently normal ribosome biogenesis in strains genetically depleted of Emg1. We conclude that the catalytic activity of Emg1 is not essential and that the presence of the protein is both necessary and sufficient for ribosome biogenesis.

The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases.,Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H Nucleic Acids Res. 2008 Feb;36(2):629-39. Epub 2007 Dec 6. PMID:18063569^[5]

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

References

↑ Liu PC, Thiele DJ. Novel stress-responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis. Mol Biol Cell. 2001 Nov;12(11):3644-57. PMID:11694595
↑ Eschrich D, Buchhaupt M, Kotter P, Entian KD. Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis. Curr Genet. 2002 Feb;40(5):326-38. Epub 2002 Feb 6. PMID:11935223 doi:http://dx.doi.org/10.1007/s00294-001-0269-4
↑ Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ. The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell. 2004 Dec;3(6):1619-26. PMID:15590835 doi:http://dx.doi.org/10.1128/EC.3.6.1619-1626.2004
↑ Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA. Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res. 2010 Nov 17. PMID:21087996 doi:10.1093/nar/gkq1131
↑ Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H. The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Nucleic Acids Res. 2008 Feb;36(2):629-39. Epub 2007 Dec 6. PMID:18063569 doi:http://dx.doi.org/gkm1074

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/2v3j"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2v3j]] is a 1 chain structure with 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=2V3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V3J FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v3k|2v3k]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v3k|2v3k]]</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v3j RCSB], [http://www.ebi.ac.uk/pdbsum/2v3j 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=2v3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v3j RCSB], [http://www.ebi.ac.uk/pdbsum/2v3j PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/EMG1_YEAST EMG1_YEAST]] Has an essential role in 40S ribosomal subunit biogenesis and 18S rRNA processing. Probably catalyzes the N1-methylation of pseudouridine at position 1189 (Psi1189) in 18S rRNA. Thus, is most likely the methyltransferase involved in the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in position 1189 in 18S rRNA. Is also involved in ribosome assembly.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:21087996</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 </StructureSection>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Bohnsack, M T.]]
+[[Category: Bohnsack, M T]]
-[[Category: Graille, M.]]
+[[Category: Graille, M]]
-[[Category: Leulliot, N.]]
+[[Category: Leulliot, N]]
-[[Category: Tilbeurgh, H Van.]]
+[[Category: Tilbeurgh, H Van]]
-[[Category: Tollervey, D.]]
+[[Category: Tollervey, D]]
 [[Category: Alpha/beta knot fold methyltransferase]]
 [[Category: Emg1]]

2v3j

From Proteopedia

Revision as of 14:48, 25 December 2014

THE YEAST RIBOSOME SYNTHESIS FACTOR EMG1 ALPHA BETA KNOT FOLD METHYLTRANSFERASE

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