Structure and function of archaeal box C/D sRNP core proteins

Aittaleb, Mohamed; Rashid, Rumana; Chen, Qiong; Palmer, John R.; Daniels, Charles J.

doi:10.1038/nsb905

Cited by 114 publications

(199 citation statements)

References 34 publications

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“…The second evidence came from the crystal structure of an archaeal fibrillarin homolog from Methanococcus jannaschii (MJ), which revealed the conservation of the AdoMet-binding fold that is common to all known MTase structures (10). We recently determined a co-crystal structure of fibrillarin complexed with Nop5p from Archaeoglobus fulgidus (AF), which contained a bound AdoMet at the predicted binding site in fibrillarin (11). This result establishes further the role of fibrillarin as the methyltransferase.…”

mentioning

confidence: 80%

“…To elucidate the structural conformation around the cofactor binding site in the absence of a bound cofactor, we have now refined the coordinates of fibrillarinNop5p complex against the data set collected at the selenine K-edge. This data set has the best statistics among the three data sets (11). Refinement was carried out using crystallography NMR software (CNS) (16) by including all 10 selenine atoms and keeping the Bijvoet pairs separated.…”

Section: Methodsmentioning

confidence: 99%

“…Protein Purification-The wild-type Nop5p-fibrillarin protein complex and fibrillarin alone were purified as described previously by Aittaleb et al (11). All the mutations were performed within co-expressing fibrillarin and Nop5p genes using the QuikChange mutagenesis kit from Stratagene.…”

Section: Methodsmentioning

confidence: 99%

“…There are currently three known fibrillarin crystal structures, all from Archaea, MJ (10), AF (11), and Puroccocus furiosus (PF) (14). Among these three structures, only that in complex with AF Nop5p had the cofactor bound at the predicted AdoMet-binding site.…”

mentioning

confidence: 99%

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Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

Aittaleb¹,

Visone²,

Fenley

2004

Journal of Biological Chemistry

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In Archaea, fibrillarin and Nop5p form the core complex of box C/D small ribonucleoprotein particles, which are responsible for site-specific 2 -hydroxyl methylation of ribosomal and transfer RNAs. Fibrillarin has a conserved methyltransferase fold and employs S-adenosyl-L-methionine (AdoMet) as the cofactor in methyl transfer reactions. Comparison between recently determined crystal structures of free fibrillarin and fibrillarinNop5p-AdoMet tertiary complex revealed large conformational differences at the cofactor-binding site in fibrillarin. To identify the structural elements responsible for these large conformational differences, we refined a crystal structure of Archaeoglobus fulgidus fibrillarin-Nop5p binary complex at 3.5 Å. This structure exhibited a pre-formed backbone geometry at the cofactor binding site similar to that when the cofactor is bound, suggesting that binding of Nop5p alone to fibrillarin is sufficient to stabilize the AdoMet-binding pocket. Calorimetry studies of cofactor binding to fibrillarin alone and to fibrillarin-Nop5p binary complex provided further support for this role of Nop5p. Mutagenesis and thermodynamic data showed that a cationbridge formed between Tyr-89 of fibrillarin and Arg-169 of Nop5p, although dispensable for in vitro methylation activity, could partially account for the enhanced binding of cofactor to fibrillarin by Nop5p. Finally, assessment of cofactor-binding thermodynamics and catalytic activities of enzyme mutants identified three additional fibrillarin residues (Thr-70, Glu-88, and Asp-133) to be important for cofactor binding and for catalysis.

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mentioning

confidence: 80%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

Aittaleb¹,

Visone²,

Fenley

2004

Journal of Biological Chemistry

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“…Such interactions are common to nucleotide-binding proteins; anionic interaction with a nucleotide hydroxyl group, [30][31][32] and aromatic stacking against a nucleotide base occur in the DNA repair enzymes, 33,34 γ-tubulin, 35 the U1A spliceosomal protein, 36 the purine and pyrimidine phosphoribosyltransferases 32,37 and aspartyl-tRNA synthetase. 38 Indeed, the binding configuration at the SRP GTPase external nucleotide site is specifically reminiscent of similar arrangements in crystal structures of the editing complex of Klenow fragment 34,39 and AMP-bound adenine phosphoribosyltransferase (APRT) 40 ( Figure 6).…”

Section: Gmp Is Bound On the Surface Of The Gtpase Heterodimer At A Cmentioning

confidence: 99%

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Focia

Gawronski-Salerno

Coon

et al. 2006

Journal of Molecular Biology

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The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF 4 . This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.

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Nop5 interacts with the archaeal RNA exosome

et al. 2017

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The archaeal exosome, a protein complex responsible for phosphorolytic degradation and tailing of RNA, has an RNA-binding platform containing Rrp4, Csl4, and DnaG. Aiming to detect novel interaction partners of the exosome, we copurified Nop5, which is a part of an rRNA methylating ribonucleoprotein complex, with the exosome of Sulfolobus solfataricus grown to a late stationary phase. We demonstrated the capability of Nop5 to bind to the exosome with a homotrimeric Rrp4-cap and to increase the proportion of polyadenylated RNAin vitro, suggesting that Nop5 is a dual-function protein. Since tailing of RNA probably serves to enhance RNA degradation, association of Nop5 with the archaeal exosome in the stationary phase may enhance tailing and degradation of RNA as survival strategy.

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Structure and function of archaeal box C/D sRNP core proteins

Cited by 114 publications

References 34 publications

Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Nop5 interacts with the archaeal RNA exosome

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