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| | <StructureSection load='4df3' size='340' side='right'caption='[[4df3]], [[Resolution|resolution]] 1.73Å' scene=''> | | <StructureSection load='4df3' size='340' side='right'caption='[[4df3]], [[Resolution|resolution]] 1.73Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4df3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DF3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DF3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4df3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DF3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DF3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 1.73Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">flpA, APE_2196 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></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=4df3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4df3 OCA], [http://pdbe.org/4df3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4df3 RCSB], [http://www.ebi.ac.uk/pdbsum/4df3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4df3 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=4df3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4df3 OCA], [https://pdbe.org/4df3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4df3 RCSB], [https://www.ebi.ac.uk/pdbsum/4df3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4df3 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/FLPA_AERPE FLPA_AERPE]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] | + | [https://www.uniprot.org/uniprot/FLPA_AERPE FLPA_AERPE] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Fibrillarin is the key methyltransferase associated with the C/D class of small nuclear ribonucleoproteins (snRNPs) and participates in the preliminary step of pre-ribosomal rRNA processing. This molecule is found in the fibrillar regions of the eukaryotic nucleolus and is involved in methylation of the 2'-O atom of ribose in rRNA. Human fibrillarin contains an N-terminal GAR domain, a central RNA-binding domain comprising an RNP-2-like superfamily consensus sequence and a catalytic C-terminal helical domain. Here, Aeropyrum pernix fibrillarin is described, which is homologous to the C-terminal domain of human fibrillarin. The protein was crystallized with an S-adenosyl-L-methionine (SAM) ligand bound in the active site. The molecular structure of this complex was solved using X-ray crystallography at a resolution of 1.7 A using molecular replacement with fibrillarin structural homologs. The structure shows the atomic details of SAM and its active-site interactions; there are a number of conserved residues that interact directly with the cofactor. Notably, the adenine ring of SAM is stabilized by pi-pi interactions with the conserved residue Phe110 and by electrostatic interactions with the Asp134, Ala135 and Gln157 residues. The pi-pi interaction appears to play a critical role in stabilizing the association of SAM with fibrillarin. Furthermore, comparison of A. pernix fibrillarin with homologous structures revealed different orientations of Phe110 and changes in alpha-helix 6 of fibrillarin and suggests key differences in its interactions with the adenine ring of SAM in the active site and with the C/D RNA. These differences may play a key role in orienting the SAM ligand for catalysis as well as in the assembly of other ribonucleoproteins and in the interactions with C/D RNA.
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| - | Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 A resolution.,de Silva U, Zhou Z, Brown BA 2nd Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Aug;68(Pt 8):854-9. Epub, 2012 Jul 26. PMID:22869109<ref>PMID:22869109</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4df3" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aerpx]] | + | [[Category: Aeropyrum pernix]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Silva, U de]] | + | [[Category: De Silva U]] |
| - | [[Category: Methyltransferase]]
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| - | [[Category: Nadp rossmann superfamily]]
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| - | [[Category: Nucleolus]]
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| - | [[Category: Transferase]]
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