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| | <StructureSection load='3bbh' size='340' side='right'caption='[[3bbh]], [[Resolution|resolution]] 2.25Å' scene=''> | | <StructureSection load='3bbh' size='340' side='right'caption='[[3bbh]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bbh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3bbh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bbd|3bbd]], [[3bbe|3bbe]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Nep1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3bbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbh OCA], [https://pdbe.org/3bbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbh RCSB], [https://www.ebi.ac.uk/pdbsum/3bbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbh ProSAT]</span></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=3bbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbh OCA], [https://pdbe.org/3bbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbh RCSB], [https://www.ebi.ac.uk/pdbsum/3bbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbh ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>
| + | [https://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Ribosome biogenesis protein|Ribosome biogenesis protein]] | + | *[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43067]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Entian, K D]] | + | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Hart, P J]] | + | [[Category: Entian K-D]] |
| - | [[Category: Kotter, P]] | + | [[Category: Hart PJ]] |
| - | [[Category: Leal, B Z]] | + | [[Category: Kotter P]] |
| - | [[Category: Meyer, B]] | + | [[Category: Leal BZ]] |
| - | [[Category: Taylor, A B]] | + | [[Category: Meyer B]] |
| - | [[Category: Wohnert, J]] | + | [[Category: Taylor AB]] |
| - | [[Category: Methyltransferase]]
| + | [[Category: Wohnert J]] |
| - | [[Category: Ribosome biogenesis]]
| + | |
| - | [[Category: Rrna processing]]
| + | |
| - | [[Category: S-adenosyl-methionine]]
| + | |
| - | [[Category: Sinefungin]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
NEP1_METJA Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.[1]
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
Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 A resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.,Taylor AB, Meyer B, Leal BZ, Kotter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wohnert J Nucleic Acids Res. 2008 Mar;36(5):1542-54. Epub 2008 Jan 21. PMID:18208838[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kotter P, Engels JW, Heckel A, Karas M, Entian KD, Wohnert J. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res. 2010 Jan 4. PMID:20047967 doi:http://dx.doi.org/gkp1189
- ↑ Taylor AB, Meyer B, Leal BZ, Kotter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wohnert J. The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res. 2008 Mar;36(5):1542-54. Epub 2008 Jan 21. PMID:18208838 doi:10.1093/nar/gkm1172
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