Backbone and side chain NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis

Veith, Thomas; Wurm, Jan Philip; Duchardt‐Ferner, Elke; Weis, Benjamin L.; Martin, Roman; Safferthal, Charlotta; Bohnsack, Markus T.; Schleiff, Enrico; Wöhnert, Jens

doi:10.1007/s12104-011-9323-4

Cited by 3 publications

(4 citation statements)

References 12 publications

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“…S10). In contrast, the addition of unlabeled PhFap7 to 15 N-PhNob1 led to significant chemical shift changes for numerous PhNob1 backbone signals (28) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 94%

Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA–protein interactions during small ribosomal subunit biogenesis

Hellmich¹,

Weis²,

Lioutikov³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Significance Ribosomes are complex macromolecular machines universal to all domains of life that synthesize all cellular proteins. They consist of many different protein and RNA building blocks. Their biogenesis—a paradigm for the assembly of macromolecular machines in general—is a highly complex and tightly regulated process in eukaryotes requiring the concerted action of many ribosome assembly factors. In this study we analyze the cross-talk between two of these assembly factors and ribosomal building blocks with biophysical methods and show how it might contribute to the fidelity and efficiency of ribosome assembly.

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“…S10). In contrast, the addition of unlabeled PhFap7 to 15 N-PhNob1 led to significant chemical shift changes for numerous PhNob1 backbone signals (28) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 94%

Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA–protein interactions during small ribosomal subunit biogenesis

Hellmich¹,

Weis²,

Lioutikov³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Isotopically labeled PhNob1 was expressed and purified and yielded high-quality 1 H, 15 N-HSQC spectra containing the expected number of backbone amide signals ( Figure 4 A). Essentially complete NMR assignments were obtained for the backbone and side chain resonances of full-length PhNob1 (deposited in BioMagResBank (BMRB)—accession number 17595) ( 48 ). Chemical shift-based prediction of secondary structure elements using the programs PECAN ( 70 ) and TALOS+ ( 52 ) revealed an alternating pattern of five β-strands and six α-helices in the first 120 residues of PhNob1 and the presence of 2–3 short β-strands in the C-terminal part of the protein ( 48 ).…”

Section: Resultsmentioning

confidence: 99%

“…Essentially complete NMR assignments were obtained for the backbone and side chain resonances of full-length PhNob1 (deposited in BioMagResBank (BMRB)—accession number 17595) ( 48 ). Chemical shift-based prediction of secondary structure elements using the programs PECAN ( 70 ) and TALOS+ ( 52 ) revealed an alternating pattern of five β-strands and six α-helices in the first 120 residues of PhNob1 and the presence of 2–3 short β-strands in the C-terminal part of the protein ( 48 ). The alternating pattern of five β-strands and 6 α-helices in the N-terminal portion of PhNob1 is in agreement with the presence of a PIN domain in PhNob1 as predicted based on sequence homologies.…”

Section: Resultsmentioning

confidence: 99%

“…Chemical shifts were referenced to an external trimethylsilylpropionate standard dissolved in NMR-buffer. The standard set of triple resonance experiments was used for the assignment of PhNob1 backbone and side chain resonances as described elsewhere ( 48 ). In addition, the assignments for the backbone amide groups of lysines were verified using 15 N-heteronuclear single quantum correlation (HSQC) spectra of an amino acid selectively labeled PhNob1 sample prepared as described ( 49 ).…”

Section: Methodsmentioning

confidence: 99%

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Structural and functional analysis of the archaeal endonuclease Nob1

Veith

Martin

Wurm

et al. 2011

Nucleic Acids Research

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Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.

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NOB1: A Potential Biomarker or Target in Cancer

Zhao

2019

CDT

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Human NIN1/RPN12 binding protein 1 homolog (NOB1), an RNA binding protein, is expressed ubiquitously in normal tissues such as the lung, liver, and spleen. Its core physiological function is to regulate protease activities and participate in maintaining RNA metabolism and stability. NOB1 is overexpressed in a variety of cancers, including pancreatic cancer, non-small cell lung cancer, ovarian cancer, prostate carcinoma, osteosarcoma, papillary thyroid carcinoma, colorectal cancer, and glioma. Although existing data indicate that NOB1 overexpression is associated with cancer growth, invasion, and poor prognosis, the molecular mechanisms behind these effects and its exact roles remain unclear. Several studies have confirmed that NOB1 is clinically relevant in different cancers, and further research at the molecular level will help evaluate the role of NOB1 in tumors. NOB1 has become an attractive target in anticancer therapy because it is overexpressed in many cancers and mediates different stages of tumor development. Elucidating the role of NOB1 in different signaling pathways as a potential cancer treatment will provide new ideas for existing cancer treatment methods. This review summarizes the research progress made into NOB1 in cancer in the past decade; this information provides valuable clues and theoretical guidance for future anticancer therapy by targeting NOB1.

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Backbone and side chain NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis

Cited by 3 publications

References 12 publications

Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA–protein interactions during small ribosomal subunit biogenesis

Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA–protein interactions during small ribosomal subunit biogenesis

Structural and functional analysis of the archaeal endonuclease Nob1

NOB1: A Potential Biomarker or Target in Cancer

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