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4df3

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Revision as of 16:11, 5 August 2016

Crystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A

Structural highlights

4df3 is a 2 chain structure with sequence from Aerpx. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	flpA, APE_2196 (AERPX)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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]

Publication Abstract from PubMed

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.

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^[1]

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

References

↑ de Silva U, Zhou Z, Brown BA 2nd. Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Aug;68(Pt 8):854-9. Epub, 2012 Jul 26. PMID:22869109 doi:http://dx.doi.org/10.1107/S1744309112026528

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4df3"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A==
 <StructureSection load='4df3' size='340' side='right' caption='[[4df3]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4df3]] is a 2 chain structure with sequence from [http://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 [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 [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>
 </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>
-<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 Aeropyrum pernix])</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='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://www.rcsb.org/pdb/explore.do?structureId=4df3 RCSB], [http://www.ebi.ac.uk/pdbsum/4df3 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=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>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4df3" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aeropyrum pernix]]
+[[Category: Aerpx]]
 [[Category: Silva, U de]]
 [[Category: Methyltransferase]]

4df3

From Proteopedia

Revision as of 16:11, 5 August 2016

Crystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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