3o7b: Difference between revisions

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<StructureSection load='3o7b' size='340' side='right'caption='[[3o7b]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='3o7b' size='340' side='right'caption='[[3o7b]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3o7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O7B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3o7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O7B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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]] 1.45&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AF_0734 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></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=3o7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o7b OCA], [https://pdbe.org/3o7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o7b RCSB], [https://www.ebi.ac.uk/pdbsum/3o7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o7b 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=3o7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o7b OCA], [https://pdbe.org/3o7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o7b RCSB], [https://www.ebi.ac.uk/pdbsum/3o7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o7b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NEP1_ARCFU NEP1_ARCFU]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of the pseudouridine corresponding to position 914 in M.jannaschii 16S rRNA (By similarity).  
[https://www.uniprot.org/uniprot/NEP1_ARCFU NEP1_ARCFU] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of the pseudouridine corresponding to position 914 in M.jannaschii 16S rRNA (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen-Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.
 
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.,Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA Nucleic Acids Res. 2010 Nov 17. PMID:21087996<ref>PMID:21087996</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3o7b" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfl]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: LaRonde-LeBlanc, N]]
[[Category: LaRonde-LeBlanc N]]
[[Category: Thomas, S R]]
[[Category: Thomas SR]]
[[Category: Methyltransferase]]
[[Category: Ribosome biogenesis]]
[[Category: Rrna processing]]
[[Category: Spout]]
[[Category: Transferase]]

Revision as of 13:03, 14 February 2024

Crystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteineCrystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteine

Structural highlights

3o7b is a 1 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.45Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NEP1_ARCFU Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of the pseudouridine corresponding to position 914 in M.jannaschii 16S rRNA (By similarity).

3o7b, resolution 1.45Å

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