4df3

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

spinqualitylabelsall models 4df3, resolution 1.73Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D 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: SAM 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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