EnzymesPub Date : 2021-01-01Epub Date: 2021-07-24DOI: 10.1016/bs.enz.2021.06.006
Nicolas Sluis-Cremer
{"title":"Retroviral reverse transcriptase: Structure, function and inhibition.","authors":"Nicolas Sluis-Cremer","doi":"10.1016/bs.enz.2021.06.006","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.06.006","url":null,"abstract":"<p><p>Reverse transcriptase (RT) is a multifunctional enzyme that has RNA- and DNA-dependent DNA polymerase activity and ribonuclease H (RNase H) activity, and is responsible for the reverse transcription of retroviral single-stranded RNA into double-stranded DNA. The essential role that RT plays in the human immunodeficiency virus (HIV) life cycle is highlighted by the fact that multiple antiviral drugs-which can be classified into two distinct therapeutic classes-are routinely used to treat and/or prevent HIV infection. This book chapter provides detailed insights into the three-dimensional structure of HIV RT, the biochemical mechanisms of DNA polymerization and RNase H activity, and the mechanisms by which nucleoside/nucleotide and nonnucleoside RT inhibitors block reverse transcription.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"179-194"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39958013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2021-01-01Epub Date: 2021-10-13DOI: 10.1016/bs.enz.2021.09.001
Rebeca Bocanegra, Ismael Plaza G A, Borja Ibarra
{"title":"In vitro single-molecule manipulation studies of viral DNA replication.","authors":"Rebeca Bocanegra, Ismael Plaza G A, Borja Ibarra","doi":"10.1016/bs.enz.2021.09.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.09.001","url":null,"abstract":"<p><p>Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"115-148"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39569528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2021-01-01DOI: 10.1016/S1874-6047(21)00045-7
Craig E Cameron, Jamie J Arnold, Laurie S Kaguni
{"title":"Preface.","authors":"Craig E Cameron, Jamie J Arnold, Laurie S Kaguni","doi":"10.1016/S1874-6047(21)00045-7","DOIUrl":"https://doi.org/10.1016/S1874-6047(21)00045-7","url":null,"abstract":"","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"50 ","pages":"xiii-xiv"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8630360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39802676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2021-01-01Epub Date: 2021-11-10DOI: 10.1016/bs.enz.2021.09.002
Jesse D Pyle, Sean P J Whelan, Louis-Marie Bloyet
{"title":"Structure and function of negative-strand RNA virus polymerase complexes.","authors":"Jesse D Pyle, Sean P J Whelan, Louis-Marie Bloyet","doi":"10.1016/bs.enz.2021.09.002","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.09.002","url":null,"abstract":"<p><p>Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"21-78"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39958014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2021-01-01Epub Date: 2021-07-24DOI: 10.1016/bs.enz.2021.06.005
Utz Fischer, Julia Bartuli, Clemens Grimm
{"title":"Structure and function of the poxvirus transcription machinery.","authors":"Utz Fischer, Julia Bartuli, Clemens Grimm","doi":"10.1016/bs.enz.2021.06.005","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.06.005","url":null,"abstract":"<p><p>Members of the Poxviridae family are large double-stranded DNA viruses that replicate exclusively in the cytoplasm of their hosts. This goes in hand with a high level of independence from the host cell, which supports transcription and replication events only in the nucleus or in DNA-containing organelles. Consequently, virus specific, rather than cellular enzymes mediate most processes involving DNA replication and mRNA synthesis. Recent technological advances allowed a detailed functional and structural investigation of the transcription machinery of the prototypic poxvirus vaccinia. The DNA-dependent RNA polymerase (RNAP) at its core displays distinct similarities to eukaryotic RNAPs. Strong idiosyncrasies, however, are apparent for viral factors that are associated with the viral RNAP during mRNA production. We expect that future studies will unravel more key aspects of poxvirus gene expression, helping also the understanding of nuclear transcription mechanisms.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"1-20"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39943075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2021-01-01Epub Date: 2021-11-02DOI: 10.1016/bs.enz.2021.09.003
Donald M Coen, Jessica L Lawler, Jonathan Abraham
{"title":"Herpesvirus DNA polymerase: Structures, functions, and mechanisms.","authors":"Donald M Coen, Jessica L Lawler, Jonathan Abraham","doi":"10.1016/bs.enz.2021.09.003","DOIUrl":"https://doi.org/10.1016/bs.enz.2021.09.003","url":null,"abstract":"<p><p>Herpesviruses comprise a family of DNA viruses that cause a variety of human and veterinary diseases. During productive infection, mammalian, avian, and reptilian herpesviruses replicate their genomes using a set of conserved viral proteins that include a two subunit DNA polymerase. This enzyme is both a model system for family B DNA polymerases and a target for inhibition by antiviral drugs. This chapter reviews the structure, function, and mechanisms of the polymerase of herpes simplex viruses 1 and 2 (HSV), with only occasional mention of polymerases of other herpesviruses such as human cytomegalovirus (HCMV). Antiviral polymerase inhibitors have had the most success against HSV and HCMV. Detailed structural information regarding HSV DNA polymerase is available, as is much functional information regarding the activities of the catalytic subunit (Pol), which include a DNA polymerization activity that can utilize both DNA and RNA primers, a 3'-5' exonuclease activity, and other activities in DNA synthesis and repair and in pathogenesis, including some remaining to be biochemically defined. Similarly, much is known regarding the accessory subunit, which both resembles and differs from sliding clamp processivity factors such as PCNA, and the interactions of this subunit with Pol and DNA. Both subunits contribute to replication fidelity (or lack thereof). The availability of both pharmacologic and genetic tools not only enabled the initial identification of Pol and the pol gene, but has also helped dissect their functions. Nevertheless, important questions remain for this long-studied enzyme, which is still an attractive target for new drug discovery.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":" ","pages":"133-178"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39943078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacterial luciferase: Molecular mechanisms and applications.","authors":"Ruchanok Tinikul, Paweenapon Chunthaboon, Jittima Phonbuppha, Tanakan Paladkong","doi":"10.1016/bs.enz.2020.06.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2020.06.001","url":null,"abstract":"<p><p>Bacterial luciferase is a flavin-dependent monooxygenase which is remarkable for its distinctive feature in transforming chemical energy to photons of visible light. The bacterial luciferase catalyzes bioluminescent reaction using reduced flavin mononucleotide, long-chain aldehyde and oxygen to yield oxidized flavin, corresponding acid, water and light at λ<sub>max</sub> around 490nm. The enzyme comprises of two non-identical α and β subunits, where α subunit is a catalytic center and β subunit is crucially required for maintaining catalytic function of the α subunit. The crystal structure with FMN bound and mutagenesis studies have assigned a number of amino acid residues that are important in coordinating critical reactions and stabilizing intermediates to attain optimum reaction efficiency. The enzyme achieves monooxygenation by generating C4a-hydroperoxyflavin intermediate that later changes its protonation status to become C4a-peroxyflavin, which is necessary for the nucleophilic attacking with aldehyde substrate. The decomposing of C4a-peroxyhemiacetal produces excited C4a-hydroxyflavin and acid product. The chemical basis regrading bioluminophore generation in Lux reaction remains an inconclusive issue. However, current data can, at least, demonstrate the involvement of electron transfer to create radical molecules which is the key step in this mechanism. Lux is a self-sufficient bioluminescent system in which all substrates can be recycled and produced by a group of enzymes from the lux operon. This makes Lux distinctively advantageous over other luciferases for reporter enzyme application. The progression of understanding of Lux catalysis is beneficial to improve light emitting efficiency in order to expand the robustness of Lux application.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"47 ","pages":"427-455"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.enz.2020.06.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38498524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2020-01-01Epub Date: 2020-07-18DOI: 10.1016/bs.enz.2020.06.002
Florian Csarman, Lena Wohlschlager, Roland Ludwig
{"title":"Cellobiose dehydrogenase.","authors":"Florian Csarman, Lena Wohlschlager, Roland Ludwig","doi":"10.1016/bs.enz.2020.06.002","DOIUrl":"https://doi.org/10.1016/bs.enz.2020.06.002","url":null,"abstract":"<p><p>Cellobiose dehydrogenase (CDH) is an extracellular hemoflavoenzyme secreted by fungi to assist lignocellulolytic enzymes in biomass degradation. Its catalytic flavodehydrogenase (DH) domain is a member of the glucose-methanol-choline oxidoreductase family similar to glucose oxidase. The catalytic domain is linked to an N-terminal electron transferring cytochrome (CYT) domain which interacts with lytic polysaccharide monooxygenase (LPMO) in oxidative cellulose and hemicellulose depolymerization. Based on CDH sequence analysis, four phylogenetic classes were defined. CDHs in these classes exhibit different structural and catalytic properties in regard to cellulose binding, substrate specificity, and the pH optima of their catalytic reaction or the interdomain electron transfer between the DH and CYT domain. The structure, reaction mechanism and kinetics of CDHs from Class-I and Class-II have been characterized in detail and recombinant expression allows the application in many areas, such as biosensors, biofuel cells biomass hydrolysis, biosynthetic processes, and the antimicrobial functionalization of surfaces.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"47 ","pages":"457-489"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.enz.2020.06.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38498525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EnzymesPub Date : 2020-01-01Epub Date: 2020-09-08DOI: 10.1016/bs.enz.2020.08.001
Lluís Ribas de Pouplana
{"title":"The evolution of aminoacyl-tRNA synthetases: From dawn to LUCA.","authors":"Lluís Ribas de Pouplana","doi":"10.1016/bs.enz.2020.08.001","DOIUrl":"https://doi.org/10.1016/bs.enz.2020.08.001","url":null,"abstract":"<p><p>The origin of all extant life on earth is intimately linked to the establishment of the principal components of the Genetic Code. Aminoacyl-tRNA synthetases (aaRS), by virtue of their universality and essential functions in protein synthesis, count among the biomolecules that evolved to a level of complexity comparable to their extant state before the advent of the Last Universal Common Ancestor (LUCA). Despite the enormous technical difficulties in analyzing such an ancient process, proposals have been put forward to describe the emergence and evolution of the two aaRS families. In this chapter, I critically review some of these proposals and place them along a hypothetical timeline based on other essential aspects of the origin of life. This chapter focuses on the evolution of the aaRS prior to LUCA. Readers will be referred to excellent literature that covers the phylogeny of aaRS in the three extant domains of life.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"48 ","pages":"11-37"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.enz.2020.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25576700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structure and function relationships of sugar oxidases and their potential use in biocatalysis.","authors":"Kanokkan Sriwaiyaphram, Pangrum Punthong, Jeerus Sucharitakul, Thanyaporn Wongnate","doi":"10.1016/bs.enz.2020.05.006","DOIUrl":"https://doi.org/10.1016/bs.enz.2020.05.006","url":null,"abstract":"<p><p>Several sugar oxidases that catalyze the oxidation of sugars have been isolated and characterized. These enzymes can be classified as flavoenzyme due to the presence of flavin adenine dinucleotide (FAD) as a cofactor. Sugar oxidases have been proposed to be the key biocatalyst in biotransformation of carbohydrates which can potentially convert sugars to provide a pool of intermediates for synthesis of rare sugars, fine chemicals and drugs. Moreover, sugar oxidases have been applied in biosensing of various biomolecules in food industries, diagnosis of diseases and environmental pollutant detection. This review provides the discussions on general properties, current mechanistic understanding, structural determination, biocatalytic application, and biosensor integration of representative sugar oxidase enzymes, namely pyranose 2-oxidase (P2O), glucose oxidase (GO), hexose oxidase (HO), and oligosaccharide oxidase. The information regarding the relationship between structure and function of these sugar oxidases points out the key properties of this particular group of enzymes that can be modified by engineering, which had resulted in a remarkable economic importance.</p>","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"47 ","pages":"193-230"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.enz.2020.05.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38401146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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