Evolutionally Conserved Intermediates Between Ubiquitin and NEDD8

Kitahara, Ryo; Yamaguchi, Yoshiki; Sakata, Eri; Kasuya, Tadashi; Tanaka, Keiji; Kato, Koichi; Yokoyama, Shigeyuki; Akasaka, Kazuyuki

doi:10.1016/j.jmb.2006.07.074

Cited by 31 publications

(46 citation statements)

References 36 publications

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“…To test our hypothesis, a site-specific conformational fluctuation of the RRM1 domain was investigated using high pressure NMR spectroscopy; pressure perturbation was used to increase the population of partially disordered conformations, which have a potential risk of molecular association (29). Superposition of the 15 N/ 1 H HSQC spectra of the domain at 30 bars, before and after pressure treatment at 2000 bars, which usually induces transient conformational change in many proteins, revealed stable changes in the chemical shifts (Fig.…”

Section: Identification Of Core Regions Involved In Rrm1 Misfolding-mentioning

confidence: 99%

Aberrant Assembly of RNA Recognition Motif 1 Links to Pathogenic Conversion of TAR DNA-binding Protein of 43 kDa (TDP-43)

Shodai

Morimura

Ido

et al. 2013

Journal of Biological Chemistry

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Background:The role of RRM1 in the pathogenesis of TDP-43 proteinopathy is unclear. Results: RRM1 was aggregate-prone, mediated by a self-assembly at newly identified amyloidogenic ␤-strands containing cysteines; cysteine substitution(s) replicated diverse cytopathologies of TDP-43 in ALS. Conclusion: RRM1 misfolding may underlie TDP-43 proteinopathy. Significance: This study proposes a novel mechanism and a new in vitro model for TDP-43 proteinopathy.

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Section: Identification Of Core Regions Involved In Rrm1 Misfolding-mentioning

confidence: 99%

Aberrant Assembly of RNA Recognition Motif 1 Links to Pathogenic Conversion of TAR DNA-binding Protein of 43 kDa (TDP-43)

Shodai

Morimura

Ido

et al. 2013

Journal of Biological Chemistry

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“…64 It was subsequently detected in various cell lines and tissues, free and conjugated to proteins, and as a protein coined "related to ubiquitin-1" (RUB1) in yeast 65,66 Remarkably, NEDD8 could be processed by the ubiquitin system and incorporated into polyubiquitin chains if it was not for a difference in 7 residues of their amino acid sequences. 67,68 Furthermore, 1 single arginine residue in the heterodimeric E1-activating enzyme APPBP1-UBA3 determines specificity for NEDD8. 69 The 3 domains in the 3D structure of APPBP1-UBA3 facilitate the processing of NEDD8 in a way that is similar to an assembly line.…”

Section: Neural Precursor Cell-expressed Developmentally Downregulated-8mentioning

confidence: 99%

Ubiquitin and Ubiquitin-Like Proteins in Protein Regulation

Herrmann

Lerman

2007

Circulation Research

281

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Abstract-The discovery of the ubiquitin system was awarded with the Nobel Prize in Chemistry in 2004. Labeling of intracellular proteins for degradation by a multienzymatic complex, called the proteasome, was identified as the main function of this system. Subsequently, it was discovered that the attachment of ubiquitin to proteins can modify their function without degradation. Finally, a number of other molecules were recognized to be conjugated to proteins in a manner similar to ubiquitin and were henceforth called ubiquitin-like proteins. This review provides an overview of this class of molecules and its implication for function, subcellular location, and half-life of proteins. (Circ Res.

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“…Proteins generally undergo destabilization at low temperatures, which is also known as cold-denaturation (Privalov 1990;Nishii et al 1994;Nash and Jonas 1997a;Nash and Jonas 1997b;Kunugi and Tanaka 2002;Babu et al 2004;Kitahara et al 2006b). The partial molar volume difference between the folded and unfolded states is negatively larger at lower temperatures because the expansivity (temperature dependence of the partial molar volume) of the unfolded state is larger than that of the folded state (Mitra et al 2008).…”

Section: Locally Disordered Conformation Of Ubiquitinmentioning

confidence: 99%

“…Firstly, we discuss the N 1 to N 2 conformational fluctuation of NEDD8 and SUMO-2. We investigated the backbone dynamics of 15 N-labeled NEDD8 (Kitahara et al 2006b) and SUMO-2 (Kitahara et al 2008) using 15 N-spin relaxation measurements of individual amide groups and obtained values for the 15 N-longitudinal relaxation rate R 1 , the 15 N-transverse relaxation rate R 2 , and the heteronuclear steady-state 15 N-f 1 Hg NOE. In the case of NEDD8, the model-free analysis was performed (Lipari and Szabo 1982a;Lipari and Szabo 1982b).…”

Section: Evolutionally Conserved High-energy States Among Ubiquitin-lmentioning

confidence: 99%

High-Pressure NMR Spectroscopy Reveals Functional Sub-states of Ubiquitin and Ubiquitin-Like Proteins

Kitahara

2015

Subcellular Biochemistry

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High-pressure nuclear magnetic resonance (NMR) spectroscopy has revealed that ubiquitin has at least two high-energy states--an alternatively folded state N2 and a locally disordered state I--between the basic folded state N1 and totally unfolded U state. The high-energy states are conserved among ubiquitin-like post-translational modifiers, ubiquitin, NEDD8, and SUMO-2, showing the E1-E2-E3 cascade reaction. It is quite intriguing that structurally similar high-energy states are evolutionally conserved in the ubiquitin-like modifiers, and the thermodynamic stabilities vary among the proteins. To investigate atomic details of the high-energy states, a Q41N mutant of ubiquitin was created as a structural model of N2, which is 71% populated even at atmospheric pressure. The convergent structure of the "pure" N2 state was obtained by nuclear Overhauser effect (NOE)-based structural analysis of the Q41N mutant at 2.5 kbar, where the N2 state is 97% populated. The N2 state of ubiquitin is closely similar to the conformation of the protein bound to the ubiquitin-activating enzyme E1. The recognition of E1 by ubiquitin is best explained by conformational selection rather than by induced-fit motion.

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Evolutionally Conserved Intermediates Between Ubiquitin and NEDD8

Cited by 31 publications

References 36 publications

Aberrant Assembly of RNA Recognition Motif 1 Links to Pathogenic Conversion of TAR DNA-binding Protein of 43 kDa (TDP-43)

Aberrant Assembly of RNA Recognition Motif 1 Links to Pathogenic Conversion of TAR DNA-binding Protein of 43 kDa (TDP-43)

Ubiquitin and Ubiquitin-Like Proteins in Protein Regulation

High-Pressure NMR Spectroscopy Reveals Functional Sub-states of Ubiquitin and Ubiquitin-Like Proteins

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