2v3j: Difference between revisions

Latest revision as of 05:31, 17 October 2024

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.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	MSE, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NEP1_YEAST S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.^[1] ^[2] ^[3] ^[4] ^[5]

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^[6]

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:https://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:https://dx.doi.org/10.1128/EC.3.6.1619-1626.2004
↑ Meyer B, Wurm JP, Kotter P, Leisegang MS, Schilling V, Buchhaupt M, Held M, Bahr U, Karas M, Heckel A, Bohnsack MT, Wohnert J, Entian KD. The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA. Nucleic Acids Res. 2011 Mar;39(4):1526-37. doi: 10.1093/nar/gkq931. Epub 2010 Oct, 23. PMID:20972225 doi:https://dx.doi.org/10.1093/nar/gkq931
↑ 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:https://dx.doi.org/gkm1074

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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:https://dx.doi.org/10.1007/s00294-001-0269-4

[3] 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:https://dx.doi.org/10.1128/EC.3.6.1619-1626.2004

[4] Meyer B, Wurm JP, Kotter P, Leisegang MS, Schilling V, Buchhaupt M, Held M, Bahr U, Karas M, Heckel A, Bohnsack MT, Wohnert J, Entian KD. The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA. Nucleic Acids Res. 2011 Mar;39(4):1526-37. doi: 10.1093/nar/gkq931. Epub 2010 Oct, 23. PMID:20972225 doi:https://dx.doi.org/10.1093/nar/gkq931

[5] 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

[6] 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:https://dx.doi.org/gkm1074

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@@ Line 3: / Line 3: @@
 <StructureSection load='2v3j' size='340' side='right'caption='[[2v3j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v3j]] 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=2V3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V3J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v3j]] 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=2V3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V3J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 2&#8491;</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 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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v3k|2v3k]]</div></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=2v3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3j OCA], [https://pdbe.org/2v3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v3j RCSB], [https://www.ebi.ac.uk/pdbsum/2v3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v3j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>
+[https://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/2v3j_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Bohnsack, M T]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Graille, M]]
+[[Category: Bohnsack MT]]
-[[Category: Leulliot, N]]
+[[Category: Graille M]]
-[[Category: Tilbeurgh, H Van]]
+[[Category: Leulliot N]]
-[[Category: Tollervey, D]]
+[[Category: Tollervey D]]
-[[Category: Alpha/beta knot fold methyltransferase]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Emg1]]
-[[Category: Nuclear protein]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome biogenesis]]
-[[Category: Rrna processing]]

2v3j: Difference between revisions

Latest revision as of 05:31, 17 October 2024

The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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