scholarly journals The missing link: allostery and catalysis in the anti-viral protein SAMHD1

2019 ◽  
Vol 47 (4) ◽  
pp. 1013-1027 ◽  
Author(s):  
Elizabeth R. Morris ◽  
Ian A. Taylor
Keyword(s):  
Allosteric Regulation ◽  
Active Form ◽  
Inflammatory Disorder ◽  
Dna Viruses ◽  
Allosteric Coupling ◽  
Allosteric Sites ◽  
Catalytically Active ◽  
Important Regulator ◽  
Hydrolysis Of ◽  
Vertebrate Protein

Abstract Vertebrate protein SAMHD1 (sterile-α-motif and HD domain containing protein 1) regulates the cellular dNTP (2′-deoxynucleoside-5′-triphosphate) pool by catalysing the hydrolysis of dNTP into 2′-deoxynucleoside and triphosphate products. As an important regulator of cell proliferation and a key player in dNTP homeostasis, mutations to SAMHD1 are implicated in hypermutated cancers, and germline mutations are associated with Chronic Lymphocytic Leukaemia and the inflammatory disorder Aicardi–Goutières Syndrome. By limiting the supply of dNTPs for viral DNA synthesis, SAMHD1 also restricts the replication of several retroviruses, such as HIV-1, and some DNA viruses in dendritic and myeloid lineage cells and resting T-cells. SAMHD1 activity is regulated throughout the cell cycle, both at the level of protein expression and post-translationally, through phosphorylation. In addition, allosteric regulation further fine-tunes the catalytic activity of SAMHD1, with a nucleotide-activated homotetramer as the catalytically active form of the protein. In cells, GTP and dATP are the likely physiological activators of two adjacent allosteric sites, AL1 (GTP) and AL2 (dATP), that bridge monomer–monomer interfaces to stabilise the protein homotetramer. This review summarises the extensive X-ray crystallographic, biophysical and molecular dynamics experiments that have elucidated important features of allosteric regulation in SAMHD1. We present a comprehensive mechanism detailing the structural and protein dynamics components of the allosteric coupling between nucleotide-induced tetramerization and the catalysis of dNTP hydrolysis by SAMHD1.

scholarly journals Thermal inactivation and chaperonin-mediated renaturation of mitochondrial aspartate aminotransferase

1998 ◽  
Vol 334 (1) ◽  
pp. 219-224 ◽  
Author(s):  
James M. LAWTON ◽  
Shawn DOONAN
Keyword(s):  
Escherichia Coli ◽  
Aspartate Aminotransferase ◽  
Thermal Inactivation ◽  
Active Form ◽  
Active Conformation ◽  
E Coli ◽  
Catalytically Active ◽  
Mitochondrial Aspartate Aminotransferase ◽  
Chaperonin 10 ◽  
Chaperonin 60

Mitochondrial aspartate aminotransferase is inactivated irreversibly on heating. The inactivated protein aggregates, but aggregation is prevented by the presence of the chaperonin 60 from Escherichia coli (GroEL). The chaperonin increases the rate of thermal inactivation in the temperature range 55–65 °C but not at lower temperatures. It has previously been shown [Twomey and Doonan (1997) Biochim. Biophys. Acta 1342, 37–44] that the enzyme switches to a modified, but catalytically active, conformation at approx. 55–60 °C and the present results show that this conformation is recognized by and binds to GroEL. The thermally inactivated protein can be released from GroEL in an active form by the addition of chaperonin 10 from E. coli (GroES)/ATP, showing that inactivation is not the result of irreversible chemical changes. These results suggest that the irreversibility of thermal inactivation is due to the formation of an altered conformation with a high kinetic barrier to refolding rather than to any covalent changes. In the absence of chaperonin the unfolded molecules aggregate but this is a consequence, rather than the cause, of irreversible inactivation.

scholarly journals The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1

2018 ◽  
Vol 115 (43) ◽  
pp. E10022-E10031 ◽  
Author(s):  
Kirsten M. Knecht ◽  
Olga Buzovetsky ◽  
Constanze Schneider ◽  
Dominique Thomas ◽  
Vishok Srikanth ◽  
...  
Keyword(s):  
Genome Stability ◽  
Structural Basis ◽  
Cancer Drug ◽  
Allosteric Site ◽  
Nucleotide Analogs ◽  
Antiviral Therapies ◽  
Allosteric Sites ◽  
Catalytically Active ◽  
Deoxynucleoside Triphosphate ◽  
Patient Responses

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in noncycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analog drugs important for treating a variety of cancers, including acute myeloid leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We found that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogs tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regard to nucleotide analogs, which can be used to improve current cancer and antiviral therapies.

scholarly journals Diversity and evolution of B-family DNA polymerases

2020 ◽  
Vol 48 (18) ◽  
pp. 10142-10156 ◽  
Author(s):  
Darius Kazlauskas ◽  
Mart Krupovic ◽  
Julien Guglielmini ◽  
Patrick Forterre ◽  
Česlovas Venclovas
Keyword(s):  
Structural Information ◽  
Dna Polymerases ◽  
Comprehensive Analysis ◽  
Metagenomic Data ◽  
Dna Viruses ◽  
Taxonomic Distribution ◽  
Binding Domains ◽  
Catalytically Active ◽  
Domains Of Life ◽  
Massive Accumulation

Abstract B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.

On the roles of calcium and zinc ions in the formation of a catalytically active form of the metalloenzyme, l-alanyl-d-glutamate peptidase of the bacteriophage T5 (EndoT5)

2020 ◽  
Vol 164 ◽  
pp. 2711-2716 ◽  
Author(s):  
Victor P. Kutyshenko ◽  
Galina V. Mikoulinskaia ◽  
Dmitry A. Prokhorov ◽  
Nikolai V. Molochkov ◽  
Alexander Y. Yegorov ◽  
...  
Keyword(s):  
Active Form ◽  
Zinc Ions ◽  
Catalytically Active ◽  
Bacteriophage T5

scholarly journals The Anti-Tumor Agent Sodium Selenate Decreases Methylated PP2A, Increases GSK3βY216 Phosphorylation, Including Tau Disease Epitopes and Reduces Neuronal Excitability in SHSY-5Y Neurons

2019 ◽  
Vol 20 (4) ◽  
pp. 844 ◽  
Author(s):  
Wesal Habbab ◽  
Imad Aoudé ◽  
Freshteh Palangi ◽  
Sara Abdulla ◽  
Tariq Ahmed
Keyword(s):  
Neurological Disorders ◽  
Neuronal Excitability ◽  
Active Form ◽  
Close Correlation ◽  
Maximum Effect ◽  
Sodium Selenate ◽  
Dependent Manner ◽  
Maximum Increase ◽  
Electrophysiological Studies ◽  
Catalytically Active

Selenium application as sodium selenate was repeatedly shown to have anti-carcinogenic properties by increasing levels of the serine/ threonine protein phosphatase 2A (PP2A) in cancer cells. PP2A has a prominent role in cell development, homeostasis, and in neurons regulates excitability. PP2A, GSK3β and Tau reside together in a complex, which facilitates their interaction and (dys)-function as has been reported for several neurological disorders. In this study we recorded maximum increase in total PP2A at 3 µM sodium selenate in a neuron cell line. In conjunction with these data, whole-cell electrophysiological studies revealed that this concentration had maximum effect on membrane potentials, conductance and currents. Somewhat surprisingly, the catalytically active form, methylated PP2A (mePP2A) was significantly decreased. In close correlation to these data, the phosphorylation state of two substrate proteins, sensitive to PP2A activity, GSK3β and Tau were found to be increased. In summary, our data reveal that sodium selenate enhances PP2A levels, but reduces catalytic activity of PP2A in a dose dependent manner, which fails to reduce Tau and GSK3β phosphorylation under physiological conditions, indicating an alternative route in the rescue of cell pathology in neurological disorders.

scholarly journals Unraveling allosteric landscapes of allosterome with ASD

2019 ◽  
Author(s):  
Xinyi Liu ◽  
Shaoyong Lu ◽  
Kun Song ◽  
Qiancheng Shen ◽  
Duan Ni ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Protein Function ◽  
Target Identification ◽  
Allosteric Regulation ◽  
Biological Research ◽  
Missense Mutations ◽  
Allosteric Site ◽  
Comprehensive Information ◽  
Allosteric Sites ◽  
Human Proteins

Abstract Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an orthosteric site. The Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) was developed ten years ago to provide comprehensive information related to allosteric regulation. In recent years, allosteric regulation has received great attention in biological research, bioengineering, and drug discovery, leading to the emergence of entire allosteric landscapes as allosteromes. To facilitate research from the perspective of the allosterome, in ASD 2019, novel features were curated as follows: (i) >10 000 potential allosteric sites of human proteins were deposited for allosteric drug discovery; (ii) 7 human allosterome maps, including protease and ion channel maps, were built to reveal allosteric evolution within families; (iii) 1312 somatic missense mutations at allosteric sites were collected from patient samples from 33 cancer types and (iv) 1493 pharmacophores extracted from allosteric sites were provided for modulator screening. Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future.

scholarly journals Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases

2020 ◽  
Vol 295 (20) ◽  
pp. 6972-6982
Author(s):  
Dakshinamurthy Sivakumar ◽  
Vikash Kumar ◽  
Michael Naumann ◽  
Matthias Stein
Keyword(s):  
Active Site ◽  
Electrostatic Interactions ◽  
Active Form ◽  
Cysteine Proteases ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Catalytic Site ◽  
Dynamics Simulation ◽  
Active Site Residues ◽  
Catalytically Active

The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267. In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.

BIOCHEMISTRY OF THE USTILAGINALES: VIII. THE STRUCTURES AND CONFIGURATIONS OF THE USTILIC ACIDS

1953 ◽  
Vol 31 (4) ◽  
pp. 396-417 ◽  
Author(s):  
R. U. Lemieux
Keyword(s):  
Methyl Esters ◽  
Active Form ◽  
Aluminum Hydride ◽  
Optically Active ◽  
Lithium Aluminum ◽  
Acid Oxidation ◽  
Chromic Acid Oxidation ◽  
Pure Compounds ◽  
Hydrolysis Of ◽  
Derivatives Of

Methanolysis of ustilagic acid and hydrolysis of the methyl esters formed yielded a crystalline acidic fraction which was essentially a mixture of two substances termed the ustilic acids A and B. The acids were separated as their iso-propylidene derivatives. The ustilic acids cocrystallize to mixtures with melting points intermediate between those of the pure compounds. Conversion of ustilic acid A, m.p. 112–113 °C, [α]D −8° in methanol, which made up about 70% of the mixture, by hydrogenolysis to palmitic acid, by oxidation with chromic oxide to pentadecanedioic acid, and by lead tetraacetate oxidation followed by hydrogenation to 15-hydroxypentadecanoic acid showed the substance to be an optically active form of 15,16-dihydroxyhexadecanoic acid. Conversion of ustilic acid B, m.p. 140–141 °C, [α]D−10° in methanol, by sodium bismuthate oxidation followed by hydrogenation to 1,14-dihydroxytetradecane, by chromic acid oxidation of its methyl ester followed by hydrolysis of the product, and peroxide oxidation of the α-keto acid thus formed to tetradecanedioic acid, and by hydrogenolysis of the C2-carbon atom through a series of reactions to ustilic acid A, showed the substance to be an optically active form of 2,15,16-trihydroxy-hexadecanoic acid. Optically active forms of 2,15-dihydroxypentadecanoic and 2-hydroxypentadecanoic acids were prepared from ustilic acid B. Application of certain empirical rules of rotation to derivatives of these 2-hydroxyacids showed them to possess the D-configuration. Reduction of ustilic acid B with lithium aluminum hydride gave meso-1,2,15,16-tetrahydroxyhexadecane. Thus, ustilic acid B was the 2D,15D,16-trihydroxyhexadecanoic acid and the ustilic acid A was the 15D,16-dihydroxyhexadecanoic acid. Several derivatives of the above described acids were prepared.

scholarly journals The action of progesterone and diethylstilboestrol on the dehydrogenase and esterase activities of a purified aldehyde dehydrogenase from rabbit liver

1977 ◽  
Vol 161 (1) ◽  
pp. 123-130 ◽  
Author(s):  
R J S Julian
Keyword(s):  
Aldehyde Dehydrogenase ◽  
Sodium Dodecyl Sulphate ◽  
Sodium Dodecyl ◽  
Rabbit Liver ◽  
Polyacrylamide Gels ◽  
Catalytically Active ◽  
Steroid Sensitive ◽  
Hydrolysis Of Esters ◽  
Hydrolysis Of ◽  
Esterase Activities

A steroid-sensitive aldehyde dehydrogenase (EC 1.2.1.3) was purified from rabbit liver and is homogeneous by the criterion of electrophoresis in polyacrylamide gels with or without sodium dodecyl sulphate. The enzyme is tetrameric, of subunit mo.wt. 48 300, and contains no tightly bound zinc. The fluorescence of the protein is decreased in the presence of progesterone, which is inhibitory to the reactions catalysed by the enzyme. When NADH is bound to the enzyme, the fluorescence of the coenzyme is augmented to an extent independent of the presence of steroids or acetaldehyde. The purified enzyme catalyses the oxidation of acetaldehyde and glucuronolactone, and the hydrolysis of 4-nitrophenyl acetate. Each of these reactions is inhibited by progesterone in such a manner as to suggest the formation of a catalytically active enzyme-hormone complex. Diethylstilboestrol inhibits the hydrolysis of esters by this enzyme, but stimulates the oxidation of aldehydes, except at low aldehyde concentrations; the ligand is then inhibitory. NADH inhibits the hydrolysis of 4-nitrophenyl acetate by the enzyme in a partially competitive fashion.

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