scholarly journals Molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Keijun Kakihara ◽  
Kengo Asamizu ◽  
Kei Moritsugu ◽  
Masahide Kubo ◽  
Tetsuya Kitaguchi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Membrane Trafficking ◽  
Cushing’S Disease ◽  
Molecular Basis ◽  
Binding Pocket ◽  
Cushing's Disease ◽  
Binding Motif ◽  
Single Molecule Fret ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

AbstractUbiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins. Mutations in the 14-3-3-binding motif in USP8 are related to Cushing’s disease. However, the molecular basis of USP8 activity regulation remains unclear. This study identified amino acids 645–684 of USP8 as an autoinhibitory region, which might interact with the catalytic USP domain, as per the results of pull-down and single-molecule FRET assays performed in this study. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 inhibited USP8 activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushing’s disease due to USP8 mutations.

scholarly journals The molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain

2021 ◽  
Author(s):  
Keijun Kakihara ◽  
Kengo Asamizu ◽  
Kei Moritsugu ◽  
Masahide Kubo ◽  
Tetsuya Kitaguchi ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Single Molecule ◽  
Membrane Trafficking ◽  
Molecular Basis ◽  
Binding Pocket ◽  
Binding Motif ◽  
Deubiquitinating Enzyme ◽  
Single Molecule Fret ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins, and mutations of the 14-3-3 binding motif in USP8 are related to Cushing′s disease. However, the molecular basis of USP8 enzyme activity regulation remains unclear. Here, we identified amino acids 645–684 of USP8 as an autoinhibitory region, which our pull-down and single-molecule FRET assay results suggested interacts with the catalytic USP domain. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 was found to inhibit USP8 enzyme activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushing′s disease caused by USP8 mutations.

The ubiquitin-specific protease 8 gene is frequently mutated in adenomas causing Cushing's disease

2015 ◽  
Author(s):  
Luis Gustavo Perez Rivas ◽  
Marily Theodoropoulou ◽  
Francesco Ferrau ◽  
Clara Nusser ◽  
Kohei Kawaguchi ◽  
...  
Keyword(s):  
Cushing’S Disease ◽  
Cushing's Disease ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

scholarly journals The Gene of the Ubiquitin-Specific Protease 8 Is Frequently Mutated in Adenomas Causing Cushing's Disease

2015 ◽  
Vol 100 (7) ◽  
pp. E997-E1004 ◽  
Author(s):  
Luis G. Perez-Rivas ◽  
Marily Theodoropoulou ◽  
Francesco Ferraù ◽  
Clara Nusser ◽  
Kohei Kawaguchi ◽  
...  
Keyword(s):  
Cushing’S Disease ◽  
Cushing's Disease ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

scholarly journals The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor

2019 ◽  
Author(s):  
Michael V. LeVine ◽  
Daniel S. Terry ◽  
George Khelashvili ◽  
Zarek S. Siegel ◽  
Matthias Quick ◽  
...  
Keyword(s):  
Single Molecule ◽  
Substrate Binding ◽  
Md Simulations ◽  
Binding Pocket ◽  
Coupled Transport ◽  
Single Molecule Fret ◽  
Allosteric Mechanism ◽  
Specific Transport ◽  
Slc6 Family ◽  
The Stability

AbstractNeurotransmitter:sodium symporters (NSS) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. While a combination of structural, functional, and computational studies on LeuT, a bacterial NSS homolog, has provided critical insight into the mechanism of sodium-coupled transport, the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of MD simulations, single-molecule FRET imaging, and measurements of Na+ binding and substrate transport that reveal an allosteric mechanism in which residues F259 and I359 in the substrate binding pocket couple substrate binding to Na+ release from the Na2 site through allosteric modulation of the stability of a partially-open, inward-facing state. We propose a new model for transport selectivity in which the two residues act as a volumetric sensor that inhibits the transport of bulky amino acids.

scholarly journals Implementation of single molecule FRET for visualizing intramolecular movement in CRISPR-Cas9

2020 ◽  
Author(s):  
Haruka Narita ◽  
Hiroshi Ebata ◽  
Karibu Sakai ◽  
Katsuhiko Minami ◽  
Sotaro Uemura ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Dna Sequence ◽  
Single Molecule ◽  
Fluorescence Anisotropy ◽  
Molecular Basis ◽  
Catalytic Process ◽  
Single Molecule Fret ◽  
Protospacer Adjacent Motif ◽  
A Genome ◽  
Cas9 Protein

SHORT ABSTRACTThis paper summarizes how to visualize the flexible inter-domain movements of CRISPR-associated protein Cas9 using single molecule FRETLONG ABSTRACTThe CRISPR-associated protein Cas9 is widely used as a genome editing tool because of its ability to be programmed to cleave any DNA sequence that is followed by a protospacer adjacent motif. The continuing expansion of Cas9 technologies has stimulated studies regarding the molecular basis of the Cas9 catalytic process. Here we summarize methods for single molecule FRET (smFRET) to visualize the inter-domain movements of Cas9 protein. Our measurements and analysis demonstrate flexible and reversible movements of the Cas9 domains. Such flexible movements allow Cas9 to adopt transient conformations beyond those solved by crystal structures and play important roles in the Cas9 catalytic process. In addition to the smFRET measurement itself, to obtain precise results, it is necessary to validate Cas9 catalytic activity. Also, fluorescence anisotropy data are required to interpret smFRET data properly. Thus, in this paper, we describe the details of these important additional experiments for smFRET measurements.

scholarly journals Ubiquitin-specific Protease 7 Is a Regulator of Ubiquitin-conjugating Enzyme UbE2E1

2013 ◽  
Vol 288 (23) ◽  
pp. 16975-16985 ◽  
Author(s):  
Feroz Sarkari ◽  
Keith Wheaton ◽  
Anthony La Delfa ◽  
Majda Mohamed ◽  
Faryal Shaikh ◽  
...  
Keyword(s):  
Dynamic Balance ◽  
Ubiquitin Proteasome System ◽  
Binding Motif ◽  
Deubiquitinating Enzyme ◽  
Interacting Protein ◽  
Identical Manner ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme found in all eukaryotes that catalyzes the removal of ubiquitin from specific target proteins. Here, we report that UbE2E1, an E2 ubiquitin conjugation enzyme with a unique N-terminal extension, is a novel USP7-interacting protein. USP7 forms a complex with UbE2E1 in vitro and in vivo through the ASTS USP7 binding motif within its N-terminal extension in an identical manner with other known USP7 binding proteins. We show that USP7 attenuates UbE2E1-mediated ubiquitination, an effect that requires the N-terminal ASTS sequence of UbE2E1 as well as the catalytic activity of USP7. Additionally, USP7 is critical in maintaining the steady state levels of UbE2E1 in cells. This study reveals a new cellular mechanism that couples the opposing activities of the ubiquitination machinery and a deubiquitinating enzyme to maintain and modulate the dynamic balance of the ubiquitin-proteasome system.

Molecular basis of pharmacological therapy in Cushing’s disease

Endocrine ◽  
2013 ◽  
Vol 46 (2) ◽  
pp. 181-198 ◽  
Author(s):  
Diego Ferone ◽  
Claudia Pivonello ◽  
Giovanni Vitale ◽  
Maria Chiara Zatelli ◽  
Annamaria Colao ◽  
...  
Keyword(s):  
Cushing’S Disease ◽  
Molecular Basis ◽  
Pharmacological Therapy ◽  
Cushing's Disease

scholarly journals Structural basis of recognition and destabilization of histone H2B ubiquitinated nucleosome by DOT1L histone H3 Lys79 methyltransferase

2018 ◽  
Author(s):  
Seongmin Jang ◽  
Chanshin Kang ◽  
Han-Sol Yang ◽  
Taeyang Jung ◽  
Hans Hebert ◽  
...  
Keyword(s):  
Single Molecule ◽  
Cross Talk ◽  
Molecular Basis ◽  
Histone H3 ◽  
Structural Basis ◽  
Histone H2b ◽  
Single Molecule Fret ◽  
Catalytic Function ◽  
Histone H3 Methylation ◽  
Hydrophobic Helix

AbstractDOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B-ubiquitination. Here, we present cryo-EM structures of DOT1L complex with unmodified and H2B-ubiquitinated nucleosomes, showing that DOT1L recognizes H2B-ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L respectively. Furthermore, the structures combined with single-molecule FRET experiment show that H2B-ubiquitination enhances a non-catalytic function of DOT1L destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.

scholarly journals NSF-mediated disassembly of on- and off-pathway SNARE complexes and inhibition by complexin

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Ucheor B Choi ◽  
Minglei Zhao ◽  
K Ian White ◽  
Richard A Pfuetzner ◽  
Luis Esquivies ◽  
...  
Keyword(s):  
Quality Control ◽  
Ionic Strength ◽  
Single Molecule ◽  
Membrane Trafficking ◽  
Neurotransmitter Release ◽  
Single Step ◽  
High Ionic Strength ◽  
Snare Complex ◽  
Single Molecule Fret ◽  
Cis And Trans

SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of NSF-mediated disassembly and reassembly of individual SNARE complexes. For ternary neuronal SNARE complexes, disassembly proceeds in a single step within 100 msec. We observed short- (<0.32 s) and long-lived (≥0.32 s) disassembled states. The long-lived states represent fully disassembled SNARE complex, while the short-lived states correspond to failed disassembly or immediate reassembly. Either high ionic strength or decreased αSNAP concentration reduces the disassembly rate while increasing the frequency of short-lived states. NSF is also capable of disassembling anti-parallel ternary SNARE complexes, implicating it in quality control. Finally, complexin-1 competes with αSNAP binding to the SNARE complex; addition of complexin-1 has an effect similar to that of decreasing the αSNAP concentration, possibly differentially regulating cis and trans SNARE complexes disassembly.

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