keyword
MENU ▼
Read by QxMD icon Read
search

AAA ATPase

keyword
https://www.readbyqxmd.com/read/28223493/crystal-structure-of-aquifex-aeolicus-%C3%AF-n-bound-to-promoter-dna-and-the-structure-of-%C3%AF-n-holoenzyme
#1
Elizabeth A Campbell, Shreya Kamath, Kanagalaghatta R Rajashankar, Mengyu Wu, Seth A Darst
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σ(N), is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA(+) ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σ(N) fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σ(N) The structure allowed us to build and refine an improved σ(N)-holoenzyme model based on previously published 3...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223361/covalently-linked-hslu-hexamers-support-a-probabilistic-mechanism-that-links-atp-hydrolysis-to-protein-unfolding-and-translocation
#2
Vladimir Baytshtok, Jiejen Chen, Steven E Glynn, Andrew R Nager, Robert A Grant, Tania A Baker, Robert T Sauer
The HslUV proteolytic machine consists of HslV, a double-ring self-compartmentalized peptidase, and one or two AAA+ HslU ring hexamers that hydrolyze ATP to power the unfolding of protein substrates and their translocation into the proteolytic chamber of HslV. Here, we use genetic-tethering and disulfide-bonding strategies to construct HslU pseudohexamers containing mixtures of ATPase active and inactive subunits at defined positions in the hexameric ring. Genetic tethering impairs HslV binding and degradation, even for pseudohexamers with six active subunits, but disulfide-linked pseudohexamers do not have these defects, indicating that the peptide tether interferes with HslV interactions...
February 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28205175/membrane-extraction-of-hmg-coa-reductase-as-determined-by-susceptibility-of-lumenal-epitope-to-in-vitro-protease-digestion
#3
Lindsey L Morris, Russell A DeBose-Boyd
Although many aspects of the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway have been elucidated, methods to detect and examine intermediate steps in the process are lacking. Here, we describe the use of a protease protection assay to study the metabolically regulated ERAD substrate HMG CoA reductase. Studies utilizing this assay reveal that ubiquitinated reductase becomes extracted across the ER membrane prior to its cytosolic release and proteasomal degradation through reactions mediated by distinct AAA-ATPases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28188183/variants-of-the-sir4-coiled-coil-domain-improve-binding-to-sir3-for-heterochromatin-formation-in-saccharomyces-cerevisiae
#4
Anke Samel, Adam Rudner, Ann E Ehrenhofer-Murray
Heterochromatin formation in the yeast Saccharomyces cerevisiae is characterized by the assembly of the Silent Information Regulator (SIR) complex, which consists of the histone deacetylase Sir2 and the structural components Sir3 and Sir4 and binds to unmodified nucleosomes to provide gene silencing. Sir3 contains an AAA(+) ATPase-like domain, and mutations in an exposed loop on the surface of this domain abrogate Sir3 silencing function in vivo as well in vitro binding to the Sir2/ Sir4 subcomplex. Here, we found that the removal of a single methyl group in the C-terminal coiled-coil domain (mutation T1314S) of Sir4 was sufficient to restore silencing at the silent mating-type loci HMR and HML to a Sir3 version with a mutation in this loop...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28157697/trip13-impairs-mitotic-checkpoint-surveillance-and-is-associated-with-poor-prognosis-in-multiple-myeloma
#5
Yi Tao, Guang Yang, Hongxing Yang, Dongliang Song, Liangning Hu, Bingqian Xie, Houcai Wang, Lu Gao, Minjie Gao, Hongwei Xu, Zhijian Xu, Xiaosong Wu, Yiwen Zhang, Weiliang Zhu, Fenghuang Zhan, Jumei Shi
AAA-ATPase TRIP13 is one of the chromosome instability gene recently established in multiple myeloma (MM), the second most common and incurable hematological malignancy. However, the specific function of TRIP13 in MM is largely unknown. Using sequential gene expression profiling, we demonstrated that high TRIP13 expression levels were positively correlated with progression, disease relapse, and poor prognosis in MM patients. Overexpressing human TRIP13 in myeloma cells prompted cell growth and drug resistance, and overexpressing murine TRIP13, which shares 93% sequence identity with human TRIP13, led to colony formation of NIH/3T3 fibroblasts in vitro and tumor formation in vivo...
February 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28118071/the-role-of-wrnip1-in-genome-maintenance
#6
Akari Yoshimura, Masayuki Seki, Takemi Enomoto
WRNIP1 interacts with WRN helicase, which is defective in the premature aging disease Werner syndrome. WRNIP1 belongs to the AAA+ ATPase family and is conserved from Escherichia coli to human. The protein contains an ubiquitin-binding zinc finger (UBZ) domain at the N terminus and an ATPase domain in the middle region. In addition to WRN, WRNIP1 interacts with proteins involved in multiple cellular pathways, including RAD18, monoubiquitylated PCNA, DNA polymerase δ, RAD51, and ATMIN. Mgs1, the yeast homolog of WRNIP1, may act downstream of ubiquitylation of PCNA to mobilize DNA polymerase δ...
January 24, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28115689/structural-insights-into-the-functional-cycle-of-the-atpase-module-of-the-26s-proteasome
#7
Marc Wehmer, Till Rudack, Florian Beck, Antje Aufderheide, Günter Pfeifer, Jürgen M Plitzko, Friedrich Förster, Klaus Schulten, Wolfgang Baumeister, Eri Sakata
In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA(+) ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4)...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28112645/structure-of-the-active-form-of-human-origin-recognition-complex-and-its-atpase-motor-module
#8
Ante Tocilj, Kin Fan On, Zuanning Yuan, Jingchuan Sun, Elad Elkayam, Huilin Li, Bruce Stillman, Leemor Joshua-Tor
Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer...
January 23, 2017: ELife
https://www.readbyqxmd.com/read/28106073/high-resolution-cryo-em-structure-of-the-proteasome-in-complex-with-adp-alfx
#9
Zhanyu Ding, Zhenglin Fu, Cong Xu, Yifan Wang, Yanxing Wang, Junrui Li, Liangliang Kong, Jinhuan Chen, Na Li, Rongguang Zhang, Yao Cong
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide...
January 20, 2017: Cell Research
https://www.readbyqxmd.com/read/28102317/time-resolved-neutron-scattering-provides-new-insight-into-protein-substrate-processing-by-a-aaa-unfoldase
#10
Ziad Ibrahim, Anne Martel, Martine Moulin, Henry S Kim, Michael Härtlein, Bruno Franzetti, Frank Gabel
We present a combination of small-angle neutron scattering, deuterium labelling and contrast variation, temperature activation and fluorescence spectroscopy as a novel approach to obtain time-resolved, structural data individually from macromolecular complexes and their substrates during active biochemical reactions. The approach allowed us to monitor the mechanical unfolding of a green fluorescent protein model substrate by the archaeal AAA+ PAN unfoldase on the sub-minute time scale. Concomitant with the unfolding of its substrate, the PAN complex underwent an energy-dependent transition from a relaxed to a contracted conformation, followed by a slower expansion to its initial state at the end of the reaction...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096334/role-of-cct-chaperonin-in-the-disassembly-of-mitotic-checkpoint-complexes
#11
Sharon Kaisari, Danielle Sitry-Shevah, Shirly Miniowitz-Shemtov, Adar Teichner, Avram Hershko
The mitotic checkpoint system prevents premature separation of sister chromatids in mitosis and thus ensures the fidelity of chromosome segregation. When this checkpoint is active, a mitotic checkpoint complex (MCC), composed of the checkpoint proteins Mad2, BubR1, Bub3, and Cdc20, is assembled. MCC inhibits the ubiquitin ligase anaphase promoting complex/cyclosome (APC/C), whose action is necessary for anaphase initiation. When the checkpoint signal is turned off, MCC is disassembled, a process required for exit from checkpoint-arrested state...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28088479/three-dimensional-structure-of-full-length-ntrx-an-unusual-member-of-the-ntrc-family-of-response-regulators
#12
Ignacio Fernández, Irina Cornaciu, Mariela Del Carmen Carrica, Emiko Uchikawa, Guillaume Hoffmann, Rodrigo Sieira, José Antonio Márquez, Fernando A Goldbaum
Bacteria sense and adapt to environmental changes using two-component systems. These signaling pathways are formed by a histidine kinase that phosphorylates a response regulator (RR), which finally modulates the transcription of target genes. The bacterium Brucella abortus codes for a two-component system formed by the histidine kinase NtrY and the RR NtrX that participates in sensing low oxygen tension and generating an adaptive response. NtrX is a modular protein with REC, AAA+, and DNA-binding domains, an architecture that classifies it among the NtrC subfamily of RRs...
January 12, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28064406/up-regulation-of-vps4a-promotes-neuronal-apoptosis-after-intracerebral-hemorrhage-in-adult-rats
#13
Jianbing Ren, Debin Yuan, Lili Xie, Xuelei Tao, Chenwei Duan, Yifeng Bao, Yunfeng He, Jianbin Ge, Hongjian Lu
Vps4, vacuolar protein sorting 4, belongs to ATPases Associated with diverse cellular Activities (AAA) protein family which is made up of Vps4A and Vps4B. Previous studies demonstrated that Vps4A plays vital roles in diverse aspects such as virus budding, the efficient transport of H-Ras to the PM (plasma membrane) and the involvement in the MVB (multivesiculate bodies) pathway. Interestingly, Vps4A is also expressed in the brain. However, the distribution and function of Vps4A in ICH diseases remain unclear...
January 7, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28053120/dna-flap-creation-by-the-rara-mgsa-protein-of-escherichia-coli
#14
Tyler H Stanage, Asher N Page, Michael M Cox
We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA(+) ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28049840/cytosolic-fc-receptor-trim21-inhibits-seeded-tau-aggregation
#15
William A McEwan, Benjamin Falcon, Marina Vaysburd, Dean Clift, Adrian L Oblak, Bernardino Ghetti, Michel Goedert, Leo C James
Alzheimer's disease (AD) and other neurodegenerative disorders are associated with the cytoplasmic aggregation of microtubule-associated protein tau. Recent evidence supports transcellular transfer of tau misfolding (seeding) as the mechanism of spread within an affected brain, a process reminiscent of viral infection. However, whereas microbial pathogens can be recognized as nonself by immune receptors, misfolded protein assemblies evade detection, as they are host-derived. Here, we show that when misfolded tau assemblies enter the cell, they can be detected and neutralized via a danger response mediated by tau-associated antibodies and the cytosolic Fc receptor tripartite motif protein 21 (TRIM21)...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28032027/valosin-containing-protein-is-a-target-of-5-l-fuligocandin%C3%A2-b-and-enhances-trail-resistance-in-cancer-cells
#16
Midori A Arai, Shota Taguchi, Kazuhiro Komatsuzaki, Kento Uchiyama, Ayaka Masuda, Mana Sampei, Mamoru Satoh, Sayaka Kado, Masami Ishibashi
Fuligocandin B (2) is a novel natural product that can overcome TRAIL resistance. We synthesized enatiomerically pure fuligocandin B (2) and its derivative 5'-I fuligocandin B (4), and found that the latter had an improved biological activity against the human gastric cancer cell line, AGS. We attached a biotin linker and photoactivatable aryl diazirine group to 5'-I fuligocandin B (4), and employed a pull-down assay to identify valosin-containing protein (VCP/p97), an AAA ATPase, as a 5'-I fuligocandin B (4) target protein...
December 2016: ChemistryOpen
https://www.readbyqxmd.com/read/28012053/transcriptomic-analysis-reveals-the-flooding-tolerant-mechanism-in-flooding-tolerant-line-and-abscisic-acid-treated-soybean
#17
Xiaojian Yin, Susumu Hiraga, Makita Hajika, Minoru Nishimura, Setsuko Komatsu
Soybean is highly sensitive to flooding stress and exhibits markedly reduced plant growth and grain yield under flooding conditions. To explore the mechanisms underlying initial flooding tolerance in soybean, RNA sequencing-based transcriptomic analysis was performed using a flooding-tolerant line and ABA-treated soybean. A total of 31 genes included 12 genes that exhibited similar temporal patterns were commonly changed in these plant groups in response to flooding and they were mainly involved in RNA regulation and protein metabolism...
December 23, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27990419/mutations-in-the-human-aaa-chaperone-p97-and-related-diseases
#18
REVIEW
Wai Kwan Tang, Di Xia
A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA(+) (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27979649/the-rava-viaa-chaperone-like-system-interacts-with-and-modulates-the-activity-of-the-fumarate-reductase-respiratory-complex
#19
Keith S Wong, Vaibhav Bhandari, Sarath Chandra Janga, Walid A Houry
Regulatory ATPase variant A (RavA) is a MoxR AAA+ protein that functions together with a partner protein that we termed VWA interacting with AAA+ ATPase (ViaA) containing a von Willebrand Factor A domain. However, the functional role of RavA-ViaA in the cell is not yet well established. Here, we show that RavA-ViaA are functionally associated with anaerobic respiration in Escherichia coli through interactions with the fumarate reductase (Frd) electron transport complex. Expression analysis of ravA and viaA genes showed that both proteins are co-expressed with multiple anaerobic respiratory genes, many of which are regulated by the anaerobic transcriptional regulator Fnr...
January 20, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27977397/atp-driven-processes-of-peroxisomal-matrix-protein-import
#20
Daniel Schwerter, Immanuel Grimm, Harald W Platta, Ralf Erdmann
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co- )receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+- proteins Pex1p and Pex6p...
December 15, 2016: Biological Chemistry
keyword
keyword
27198
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"