scholarly journals Single-Atom Imino Substitutions at A9 and A10 Reveal Distinct Effects on the Fold and Function of the Hairpin Ribozyme Catalytic Core

Biochemistry ◽  
2009 ◽  
Vol 48 (33) ◽  
pp. 7777-7779 ◽  
Author(s):  
Robert C. Spitale ◽  
Rosaria Volpini ◽  
Michael V. Mungillo ◽  
Jolanta Krucinska ◽  
Gloria Cristalli ◽  
...  
Keyword(s):  
Single Atom ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
And Function

scholarly journals Biogenesis of NDUFS3-less complex I indicates TMEM126A/OPA7 as an assembly factor of the ND4-module

2020 ◽  
Author(s):  
Luigi D’Angelo ◽  
Elisa Astro ◽  
Monica De Luise ◽  
Ivana Kurelac ◽  
Nikkitha Umesh-Ganesh ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Optic Atrophy ◽  
Complex I ◽  
Disease Gene ◽  
Mitochondrial Respiratory Chain ◽  
Cell Types ◽  
Catalytic Core ◽  
Assembly Factor ◽  
Functional Consequences ◽  
And Function

ABSTRACTComplex I (CI) is the largest enzyme of the mitochondrial respiratory chain and its defects are the main cause of mitochondrial disease. To understand the mechanisms regulating the extremely intricate biogenesis of this fundamental bioenergetic machine, we analyzed the structural and functional consequences of the ablation of NDUFS3, a non-catalytic core subunit. We prove that in diverse mammalian cell types a small amount of functional CI can still be detected in the complete absence of NDUFS3. In addition, we have determined the dynamics of CI disassembly when the amount of NDUFS3 is gradually decreased. The process of degradation of the complex occurs in a hierarchical and modular fashion where the ND4-module remains stable and bound to TMEM126A. We have thus, uncovered the function of TMEM126A, the product of a disease gene causing recessive optic atrophy, as a factor necessary for the correct assembly and function of CI.

Sequence elements outside the catalytic core of natural hairpin ribozymes modulate the reactions differentially

2011 ◽  
Vol 392 (7) ◽  
Author(s):  
Preeti Bajaj ◽  
Gerhard Steger ◽  
Christian Hammann
Keyword(s):  
Mutational Analysis ◽  
Hammerhead Ribozyme ◽  
The Other ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
Arabis Mosaic Virus ◽  
Sequence Elements ◽  
Satellite Rnas ◽  
Hairpin Ribozymes

AbstractHairpin ribozymes occur naturally only in the satellite RNAs of tobacco ringspot virus (TRsV), chicory yellow mottle virus (CYMoV) and arabis mosaic virus (ArMV). The catalytic centre of the predominantly studied sTRsV hairpin ribozyme, and of sArMV is organised around a four-way helical junction. We show here that sCYMoV features a five-way helical junction instead. Mutational analysis indicates that the fifth stem does not influence kinetic parameters of the sCYMoV hairpin ribozymein vitroreactions, and therefore seems an appendix to that junction in the other ribozymes. We report further that all three ribozymes feature a three-way helical junction outside the catalytic core in stem A, with Watson-Crick complementarity to loop nucleotides in stem B. Kinetic analyses of cleavage and ligation reactions of several variants of the sTRsV and sCYMoV hairpin ribozymesin vitroshow that the presence of this junction interferes with their reactions, particularly the ligation. We provide evidence that this is not due to a presumed interaction of the afore-mentioned elements in stems A and B. The evolutionary survival of thiscis-inhibiting element seems rather to be caused by the coincidence of its position with that of the hammerhead ribozyme in the other RNA polarity.

Functional diversity of ISWI complexes

2004 ◽  
Vol 82 (4) ◽  
pp. 482-489 ◽  
Author(s):  
Sara S Dirscherl ◽  
Jocelyn E Krebs
Keyword(s):  
Chromatin Remodeling ◽  
Catalytic Core ◽  
Chromatin Remodelers ◽  
Form And Function ◽  
Curr Opin Cell Biol ◽  
Chromatid Cohesion ◽  
Chromatin Remodeling Complexes ◽  
And Function ◽  
Diverse Groups ◽  
Nuclear Processes

The yeast SWI/SNF ATP-dependent chromatin remodeling complex was first identified and characterized over 10 years ago (F. Winston and M. Carlson. 1992. Trends Genet. 8: 387–391.) Since then, the number of distinct ATP-dependent chromatin remodeling complexes and the variety of roles they play in nuclear processes have become dizzying (J.A. Martens and F. Winston. 2003. Curr. Opin. Genet. Dev. 13: 136–142; A. Vacquero et al. 2003. Sci. Aging Knowledge Environ. 2003: RE4) — and that does not even include the companion suite of histone modifying enzymes, which exhibit a comparable diversity in both number of complexes and variety of functions (M.J. Carrozza et al. 2003. Trends Genet. 19: 321–329; W. Fischle et al. 2003. Curr. Opin. Cell Biol. 15: 172–183; M. Iizuka and M.M. Smith. 2003. Curr. Opin. Genet. Dev. 13: 1529–1539). This vast complexity is hardly surprising, given that all nuclear processes that involve DNA — transcription, replication, repair, recombination, sister chromatid cohesion, etc. — must all occur in the context of chromatin. The SWI/SNF-related ATP-dependent remodelers are divided into a number of subfamilies, all related by the SWI2/SNF2 ATPase at their catalytic core. In nearly every species where researchers have looked for them, one or more members of each subfamily have been identified. Even the budding yeast, with its comparatively small genome, contains eight different chromatin remodelers in five different subfamilies. This review will focus on just one subfamily, the Imitation Switch (ISWI) family, which is proving to be one of the most diverse groups of chromatin remodelers in both form and function.

scholarly journals The SAM domain of mouse SAMHD1 is critical for its activation and regulation

2017 ◽  
Author(s):  
Olga Buzovetsky ◽  
Chenxiang Tang ◽  
Kirsten Knecht ◽  
Jenna M. Antonucci ◽  
Li Wu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bound States ◽  
Restriction Factor ◽  
Activation Process ◽  
Catalytic Core ◽  
Sam Domain ◽  
And Function ◽  
Hiv 1 ◽  
Viral Reverse Transcription

ABSTRACTHuman SAMHD1 (hSAMHD1) is a retroviral restriction factor that blocks HIV-1 infection by depleting the cellular nucleotides required for viral reverse transcription. SAMHD1 is allosterically activated by nucleotides that induce assembly of the active tetramer. Although the catalytic core of hSAMHD1 has been studied extensively, previous structures have not captured the regulatory SAM domain. In this study, we determined the first crystal structure of full-length SAMHD1 by capturing mouse SAMHD1 (mSAMHD1) structures in three different nucleotide bound states. Although mSAMHD1 and hSAMHD1 are highly similar in sequence and function, we found that mSAMHD1 possesses a more complex nucleotide-induced activation process, highlighting the regulatory role of the SAM domain. Our results provide new insights into the regulation of SAMHD1 activity, thereby will facilitate the improvement of HIV mouse models and the development of new therapies for certain cancers and autoimmune diseases.

The histidine phosphatase superfamily: structure and function

2007 ◽  
Vol 409 (2) ◽  
pp. 333-348 ◽  
Author(s):  
Daniel J. Rigden
Keyword(s):  
Sequence Similarity ◽  
Structure And Function ◽  
Proton Donor ◽  
Phosphoglycerate Mutase ◽  
Catalytic Core ◽  
Potential Applications ◽  
History Of ◽  
Histidine Phosphatase Superfamily ◽  
And Function ◽  
Functionally Diverse

The histidine phosphatase superfamily is a large functionally diverse group of proteins. They share a conserved catalytic core centred on a histidine which becomes phosphorylated during the course of the reaction. Although the superfamily is overwhelmingly composed of phosphatases, the earliest known and arguably best-studied member is dPGM (cofactor-dependent phosphoglycerate mutase). The superfamily contains two branches sharing very limited sequence similarity: the first containing dPGM, fructose-2,6-bisphosphatase, PhoE, SixA, TIGAR [TP53 (tumour protein 53)-induced glycolysis and apoptosis regulator], Sts-1 and many other activities, and the second, smaller, branch composed mainly of acid phosphatases and phytases. Human representatives of both branches are of considerable medical interest, and various parasites contain superfamily members whose inhibition might have therapeutic value. Additionally, several phosphatases, notably the phytases, have current or potential applications in agriculture. The present review aims to draw together what is known about structure and function in the superfamily. With the benefit of an expanding set of histidine phosphatase superfamily structures, a clearer picture of the conserved elements is obtained, along with, conversely, a view of the sometimes surprising variation in substrate-binding and proton donor residues across the superfamily. This analysis should contribute to correcting a history of over- and mis-annotation in the superfamily, but also suggests that structural knowledge, from models or experimental structures, in conjunction with experimental assays, will prove vital for the future description of function in the superfamily.

scholarly journals Real-time monitoring of peroxiredoxin oligomerization dynamics in living cells

2020 ◽  
Vol 117 (28) ◽  
pp. 16313-16323 ◽  
Author(s):  
Daniel Pastor-Flores ◽  
Deepti Talwar ◽  
Brandán Pedre ◽  
Tobias P. Dick
Keyword(s):  
Posttranslational Modifications ◽  
Structural Changes ◽  
Quaternary Structure ◽  
Redox Homeostasis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Living Cells ◽  
Single Atom ◽  
Oligomeric State ◽  
And Function

Peroxiredoxins are central to cellular redox homeostasis and signaling. They serve as peroxide scavengers, sensors, signal transducers, and chaperones, depending on conditions and context. Typical 2-Cys peroxiredoxins are known to switch between different oligomeric states, depending on redox state, pH, posttranslational modifications, and other factors. Quaternary states and their changes are closely connected to peroxiredoxin activity and function but so far have been studied, almost exclusively, outside the context of the living cell. Here we introduce the use of homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization to monitor dynamic changes in peroxiredoxin quaternary structure inside the crowded environment of living cells. Using the approach, we confirm peroxide- and thioredoxin-related quaternary transitions to take place in cellulo and observe that the relationship between dimer–decamer transitions and intersubunit disulfide bond formation is more complex than previously thought. Furthermore, we demonstrate the use of the approach to compare different peroxiredoxin isoforms and to identify mutations and small molecules affecting the oligomeric state inside cells. Mutagenesis experiments reveal that the dimer–decamer equilibrium is delicately balanced and can be shifted by single-atom structural changes. We show how to use this insight to improve the design of peroxiredoxin-based redox biosensors.

scholarly journals Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 Å resolution

2000 ◽  
Vol 348 (1) ◽  
pp. 201-207 ◽  
Author(s):  
Gideon J. DAVIES ◽  
A. Marek BRZOZOWSKI ◽  
Miroslawa DAUTER ◽  
Annabelle VARROT ◽  
Martin SCHÜLEIN
Keyword(s):  
Active Site ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Crystalline Cellulose ◽  
Glycoside Hydrolase Family ◽  
Catalytic Core ◽  
Humicola Insolens ◽  
Cellobiohydrolase Ii ◽  
And Function

Cellulases are traditionally classified as either endoglucanases or cellobiohydrolases on the basis of their respective catalytic activities on crystalline cellulose, which is generally hydrolysed more efficiently only by the cellobiohydrolases. On the basis of the Trichoderma reesei cellobiohydrolase II structure, it was proposed that the active-site tunnel of cellobiohydrolases permitted the processive hydrolysis of cellulose, whereas the corresponding endoglucanases would display open active-site clefts [Rouvinen, Bergfors, Teeri, Knowles and Jones (1990) Science 249, 380-386]. Glycoside hydrolase family 6 contains both cellobiohydrolases and endoglucanases. The structure of the catalytic core of the family 6 endoglucanase Cel6B from Humicola insolens has been solved by molecular replacement with the known T. reesei cellobiohydrolase II as the search model. Strangely, at the sequence level, this enzyme exhibits the highest sequence similarity to family 6 cellobiohydrolases and displays just one of the loop deletions traditionally associated with endoglucanases in this family. However, this enzyme shows no activity on crystalline substrates but a high activity on soluble substrates, which is typical of an endoglucanase. The three-dimensional structure reveals that the deletion of just a single loop of the active site, coupled with the resultant conformational change in a second ‘cellobiohydrolase-specific’ loop, peels open the active-site tunnel to reveal a substrate-binding groove.

A Base Change in the Catalytic Core of the Hairpin Ribozyme Perturbs Function but Not Domain Docking†

Biochemistry ◽  
2001 ◽  
Vol 40 (8) ◽  
pp. 2580-2587 ◽  
Author(s):  
Nils G. Walter ◽  
Philip A. Chan ◽  
Ken J. Hampel ◽  
David P. Millar ◽  
John M. Burke
Keyword(s):  
Base Change ◽  
Hairpin Ribozyme ◽  
Catalytic Core ◽  
Domain Docking

Towards understanding the catalytic core structure of the spliceosome

2005 ◽  
Vol 33 (3) ◽  
pp. 447-449 ◽  
Author(s):  
S.E. Butcher ◽  
D.A. Brow
Keyword(s):  
Structure And Function ◽  
Mrna Splicing ◽  
Catalytic Core ◽  
Coding Regions ◽  
High Resolution Structure ◽  
Associated Proteins ◽  
And Function ◽  
Mrna Precursor ◽  
Precursor Mrna ◽  
Resolution Structure

The spliceosome catalyses the splicing of nuclear pre-mRNA (precursor mRNA) in eukaryotes. Pre-mRNA splicing is essential to remove internal non-coding regions of pre-mRNA (introns) and to join the remaining segments (exons) into mRNA before translation. The spliceosome is a complex assembly of five RNAs (U1, U2, U4, U5 and U6) and many dozens of associated proteins. Although a high-resolution structure of the spliceosome is not yet available, inroads have been made towards understanding its structure and function. There is growing evidence suggesting that U2 and U6 RNAs, of the five, may contribute to the catalysis of pre-mRNA splicing. In this review, recent progress towards understanding the structure and function of U2 and U6 RNAs is summarized.

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