3T7Z

Structure of Methanocaldococcus jannaschii Nop N-terminal domain

Summary for 3T7Z

• Entry DOI: 10.2210/pdb3t7z/pdb
• Descriptor: Nucleolar protein Nop 56/58, ACETATE ION, SODIUM ION, ... (5 entities in total)
• Functional Keywords: alpha beta fold, rnp assembly and methylation, l7ae, box c/d rna, protein binding
• Biological source: Methanocaldococcus jannaschii
• Total number of polymer chains: 1
• Total formula weight: 14331.23

Authors

Biswas, S.,Maxwell, S. (deposition date: 2011-07-31, release date: 2012-04-11, Last modification date: 2024-02-28)

Primary citation

Gagnon, K.T.,Biswas, S.,Zhang, X.,Brown, B.A.,Wollenzien, P.,Mattos, C.,Maxwell, E.S.
Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity.
J.Biol.Chem., 287:19418-19428, 2012

PubMed Abstract: Box C/D RNA-protein complexes (RNPs) guide the 2'-O-methylation of nucleotides in both archaeal and eukaryotic ribosomal RNAs. The archaeal box C/D and C'/D' RNP subcomplexes are each assembled with three sRNP core proteins. The archaeal Nop56/58 core protein mediates crucial protein-protein interactions required for both sRNP assembly and the methyltransferase reaction by bridging the L7Ae and fibrillarin core proteins. The interaction of Methanocaldococcus jannaschii (Mj) Nop56/58 with the methyltransferase fibrillarin has been investigated using site-directed mutagenesis of specific amino acids in the N-terminal domain of Nop56/58 that interacts with fibrillarin. Extensive mutagenesis revealed an unusually strong Nop56/58-fibrillarin interaction. Only deletion of the NTD itself prevented dimerization with fibrillarin. The extreme stability of the Nop56/58-fibrillarin heterodimer was confirmed in both chemical and thermal denaturation analyses. However, mutations that did not affect Nop56/58 binding to fibrillarin or sRNP assembly nevertheless disrupted sRNP-guided nucleotide modification, revealing a role for Nop56/58 in methyltransferase activity. This conclusion was supported with the cross-linking of Nop56/58 to the target RNA substrate. The Mj Nop56/58 NTD was further characterized by solving its three-dimensional crystal structure to a resolution of 1.7 Å. Despite low primary sequence conservation among the archaeal Nop56/58 homologs, the overall structure of the archaeal NTD domain is very well conserved. In conclusion, the archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.

PubMed: 22496443
DOI: 10.1074/jbc.M111.323253

Experimental method

X-RAY DIFFRACTION (1.7 Å)