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| Open AccessBiosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS–PKS hybrid enzyme
Tenuazonic acid is a mycotoxin produced by various plant pathogenic fungi but its biosynthetic gene is unknown to date. Here, the authors identify the tenuazonic acid biosynthetic gene encoding a protein with a unique KS domain that conducts cyclization step for tenuazonic acid release in Magnaporthe oryzae.
- Choong-Soo Yun
- , Takayuki Motoyama
- & Hiroyuki Osada
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Article
| Open AccessAutophagy and endosomal trafficking inhibition by Vibrio cholerae MARTX toxin phosphatidylinositol-3-phosphate-specific phospholipase A1 activity
The MARTX toxin of V. choleraeprocesses itself to deliver three distinct effector domains to the cytosol. Here the authors show that the third effector domain is a phosphatidylinositol-3-phosphate (PtdIns3P)-specific phospholipase that inhibits autophagy in target cells.
- Shivani Agarwal
- , Hyunjin Kim
- & Karla J. F. Satchell
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Article
| Open AccessStructural basis for phosphatidylinositol-phosphate biosynthesis
CDP-alcohol phosphotransferases (CDP-APs) are critical for the biosynthesis of glycerophospholipids. Here, Clarke et al.present the first structure of an enzymatically active CDP-AP in the presence of a bound lipid substrate and propose a mechanism for substrate binding and catalysis.
- Oliver B. Clarke
- , David Tomasek
- & Filippo Mancia
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| Open AccessATP binding to neighbouring subunits and intersubunit allosteric coupling underlie proteasomal ATPase function
The 26S proteasome contains a hexamer of ATPase subunits, which binds, unfolds and translocates substrates in an ATP-dependent manner. Kim et al. use FRET to show that ATP binding preferentially occurs at neighbouring subunits of the hexamer, and identify two allosteric systems that coordinate translocation.
- Young-Chan Kim
- , Aaron Snoberger
- & David M. Smith
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Article
| Open AccessThe thiostrepton A tryptophan methyltransferase TsrM catalyses a cob(II)alamin-dependent methyl transfer reaction
Cobalamin-dependent radical SAM enzymes are proposed as methyltransferases in many biosynthetic pathways. Here, the authors study a pathway involving the methylation of tryptophan, showing that methylcob(III)alamin is the most likely cofactor and propose a radical-based C-methylation mechanism.
- Alhosna Benjdia
- , Stéphane Pierre
- & Olivier Berteau
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Article
| Open AccessEnergetics of proton release on the first oxidation step in the water-oxidizing enzyme
The availability of crystal structures of photosystem II opens up the possibility of gaining insights into its mechanism. Here, the authors use a computational approach and propose a deprotonation event at O4 followed by long-range proton-transfer along a chain of strongly bonded water molecules.
- Keisuke Saito
- , A. William Rutherford
- & Hiroshi Ishikita
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Article
| Open AccessDetoxification of hostplant’s chemical defence rather than its anti-predator co-option drives β-glucosidase-mediated lepidopteran counteradaptation
During herbivory, deglycosylation of glycosylated phytochemicals may release aglycones which can be toxic when ingested. Here, Poreddy et al. show that ß-glucosidase in the tobacco hornworm midgut converts a toxic glycoside to a non-toxic form, a process which is crucial for larval development.
- Spoorthi Poreddy
- , Sirsha Mitra
- & Sagar S. Pandit
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Article
| Open AccessRedox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum
n-Butanol is a valuable biofuel that can be produced industrially by bacterial fermentation. Here the authors uncover a redox-switch within Clostridium acetobutylicum’s thiolase—a key enzyme involved in n-butanol biosynthesis—that controls the rate of fermentative butanol production.
- Sangwoo Kim
- , Yu-Sin Jang
- & Kyung-Jin Kim
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Article
| Open AccessEnhancing S-adenosyl-methionine catabolism extends Drosophila lifespan
Inhibiting the formation of S-adenosyl-methionine (SAM) increases worm but not fly lifespan. Here the authors show that humans and flies possess the SAM-consuming enzyme Gnmt, the activity of which is regulated by lifespan-extending interventions, and that knockdown of Gnmt extends fly lifespan.
- Fumiaki Obata
- & Masayuki Miura
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Article
| Open AccessA novel thiol-reductase activity of Arabidopsis YUC6 confers drought tolerance independently of auxin biosynthesis
YUC6 is a flavin monooxygenase required for the synthesis of the plant hormone auxin. Chaet al. discover that in Arabidopsis, this enzyme also plays a role in combatting oxidative stress independently of auxin biosynthesis, by acting as a thiol-reductase.
- Joon-Yung Cha
- , Woe-Yeon Kim
- & Dae-Jin Yun
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Article
| Open AccessThe photochemical mechanism of a B12-dependent photoreceptor protein
Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al.present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.
- Roger J. Kutta
- , Samantha J. O. Hardman
- & Alex R. Jones
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Article
| Open AccessTwo enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis
Mycobacterium tuberculosis feeds on host fatty acids during infection, a process that requires a fructose bisphosphatase (FBPase) enzyme for gluconeogenesis. Here, Ganapathy et al.show that the bacterium has two different FBPases and that this enzymatic activity is required for full virulence.
- Uday Ganapathy
- , Joeli Marrero
- & Sabine Ehrt
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Article
| Open AccessStructure and vascular function of MEKK3–cerebral cavernous malformations 2 complex
The protein kinase MEKK3 interacts with CCM2, which is associated with the predominantly cerebrovascular CCM disease. Here the authors use structural, biochemical, cell biology and in vivotechniques to show that regulation of Rho signalling by the CCM2:MEKK3 complex is needed to maintain neurovascular integrity.
- Oriana S. Fisher
- , Hanqiang Deng
- & Bing Su
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Arginylation regulates purine nucleotide biosynthesis by enhancing the activity of phosphoribosyl pyrophosphate synthase
The phosphoribosyl pyrophosphate synthase PRPS2 catalyses the first step ofde novo purine nucleotide biosynthesis, and has recently been shown to couple protein and nucleotide metabolism. Zhang et al. demonstrate that PRPS2 activity is regulated by tRNA-dependent post-translational addition of arginine.
- Fangliang Zhang
- , Devang M. Patel
- & Anna Kashina
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Article
| Open Access9-O-Acetylation of sialic acids is catalysed by CASD1 via a covalent acetyl-enzyme intermediate
9-O-Acetylation is one of the most common modifications of sialic acids, implicated in sialoglycan recognition and ganglioside biology. Here, the authors show that the key enzyme for the biosynthesis of 9-O-acetylated sialoglycans is CASD1, which uses CMP-activated sialic acid as acceptor substrate.
- Anna-Maria T. Baumann
- , Mark J. G. Bakkers
- & Martina Mühlenhoff
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Article
| Open AccessA highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes
Synthetic engineering of complex pathways is often hindered by pathway branching and generation of non-target compounds. Here, the authors show that by judicious combination of moderately selective enzyme variants, a non-natural C50 carotenoid can be generated in bacteria with minimal production of unwanted compounds.
- Maiko Furubayashi
- , Mayu Ikezumi
- & Daisuke Umeno
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Article
| Open AccessDiscovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation
Mucosal sialoglycans contribute to host–microbe interactions at mucosal surfaces and impact bacterial colonization of the digestive system. Here the authors identify and characterize an intramolecular trans-sialidase produced by the gut bacterium R. gnavusATCC 29149 that may contribute to adaptation to the mucosal environment.
- Louise E. Tailford
- , C. David Owen
- & Nathalie Juge
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| Open AccessHuman Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities
Upf1 is a multifunctional helicase involved in various DNA- and RNA-related processes, including nonsense-mediated mRNA decay (NMD). Here the authors demonstrate that Upf1 is a highly processive ribonucleoprotein complex remodeler—a capability likely important for Upf1’s NMD function.
- Francesca Fiorini
- , Debjani Bagchi
- & Vincent Croquette
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| Open AccessStructural basis for catalytically restrictive dynamics of a high-energy enzyme state
Adenylate kinase (AdK) plays a key role in cellular energy homeostasis by catalysing the reversible magnesium-dependent formation of ADP from AMP and ATP. Here the authors present a detailed analysis of adenylate kinase’s conformational dynamics and characterize a high-energy state of AdK indispensable for catalysis.
- Michael Kovermann
- , Jörgen Ådén
- & Magnus Wolf-Watz
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Article
| Open AccessIdentification of Alp1U and Lom6 as epoxy hydrolases and implications for kinamycin and lomaiviticin biosynthesis
Kinamycins, fluostatins and lomaiviticins are naturally occurring antibiotics that possess unique diazofluorene structures and exhibit potent anti-tumour activity. Here the authors identify the epoxy hydrolases in the biosynthetic pathways of kinamycins and lomaiviticins, suggesting the existence of epoxy-intermediates in their biosynthesis.
- Bin Wang
- , Fang Guo
- & Keqian Yang
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Article
| Open AccessCrystallographic structure of a small molecule SIRT1 activator-enzyme complex
Sirtuins are NAD+-dependent deacylases implicated in the regulation of stress responses, bioenergetics and epigenetic control. Here the authors describe the crystal structure of a sirtuin-activating compounds (STAC)-sirtuin complex and begin to elucidate the mechanism of sirtuins activation by STACs.
- Han Dai
- , April W. Case
- & James L. Ellis
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Article
| Open AccessThe impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics
DNA intercalators, a type of fluorescent probes widely used to visualize DNA, can perturb DNA structure and stability. Here, the authors show how DNA-binding affinity can be tuned using DNA tension, ionic strength and dye species, and how this can be used to minimize DNA structural perturbations.
- Andreas S. Biebricher
- , Iddo Heller
- & Gijs J. L. Wuite
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The molecular origin of high DNA-repair efficiency by photolyase
Photolyase is an enzyme responsible for repairing DNA which is damaged after exposure to UV light. Here, the authors use site directed mutagenesis and femtosecond spectroscopy to study how photolyase achieves its maximal repair efficiency.
- Chuang Tan
- , Zheyun Liu
- & Dongping Zhong
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Article
| Open AccessInitial assembly steps of a translocase for folded proteins
The twin-arginine translocation complex consists of TatA, TatB and TatC subunits and transports folded proteins across cellular membranes. Here, using photocrosslinking, the authors show that TatB monomers form dome-like structures that are surrounded by TatC monomers enabling lateral access of TatA.
- Anne-Sophie Blümmel
- , Laura A. Haag
- & Julia Fröbel
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| Open AccessSite-specific processing of Ras and Rap1 Switch I by a MARTX toxin effector domain
V. vulnificus, a bacteria that cause life-threatening septicaemia following wound infections or tainted food consumption, utilizes MARTX toxins for toxic effector delivery. Here the authors show that the MARTX virulence factor DUF5 targets the cellular MAP kinase pathway as a Ras and Rap1 site-specific protease.
- Irena Antic
- , Marco Biancucci
- & Karla J. F. Satchell
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Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C
INO80-C and SWR-C are chromatin remodelling enzymes with roles in transcription pathways. Here, the authors show that they both have similar architectures displaying a ‘tail’ domain and a heterohexameric ‘head’ domain, with conformational changes influencing nucleosomal binding and enzyme activity.
- Shinya Watanabe
- , Dongyan Tan
- & Craig L. Peterson
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Article
| Open AccessThe low-affinity complex of cytochrome c and its peroxidase
The redox activity of cytochrome cin complex with its peroxidase has been rationalized by two possible models; a readily observable high-affinity complex and a more elusive but potentially more active low-affinity complex. Here, the authors provide an NMR-based structural mapping of this low-affinity complex.
- Karen Van de Water
- , Yann G. J. Sterckx
- & Alexander N. Volkov
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| Open AccessNon-canonical active site architecture of the radical SAM thiamin pyrimidine synthase
Most radical SAM enzymes use a [4Fe-4S] cluster to generate a 5′-deoxyadenosyl radical. Here the authors show the radical SAM thiamin pyrimidine synthase ThiC comprises an additional active site metal, probably representing an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.
- Michael K. Fenwick
- , Angad P. Mehta
- & Steven E. Ealick
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| Open AccessCrystallographic and spectroscopic snapshots reveal a dehydrogenase in action
Aldehydes are common intermediates in enzymatic pathways, but their high reactivity can make them difficult to observe. Here, the authors study the mechanism of aldehyde deactivation in a dehydrogenase, showing a key E/Zisomerization and observing a thiohemiacetal intermediate by crystal structure analysis.
- Lu Huo
- , Ian Davis
- & Aimin Liu
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Article
| Open AccessCentromeric binding and activity of Protein Phosphatase 4
Many cellular processes, including the cell division cycle, require concerted action of protein kinases and phosphatases. Here Lipinszki et al. present a crystal structure of the Drosophilaphosphoprotein phosphatase 4 subunit, Falafel, in complex with the centromeric protein CENP-C, and reveal a new recognition mode for this phosphatase.
- Zoltan Lipinszki
- , Stephane Lefevre
- & Marcin R. Przewloka
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A dynamic supramolecular polymer with stimuli-responsive handedness for in situ probing of enzymatic ATP hydrolysis
Interesting changes in physical and optical properties can result from the binding of small molecules to supramolecular polymers. Here, the authors present an ATP assay, using a supramolecular helix to switch between left- and right-handed conformations on binding different adenosine phosphates.
- Mohit Kumar
- , Patrick Brocorens
- & Subi J. George
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Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins
Tyrosinases mediate the initial two catalytic steps in the conversion of tyrosine into melanin, and mutations in these enzymes are leading causes of albinism. Goldfeder et al.present tyrosinase crystal structures and reveal that both of its substrates orient identically in the active site.
- Mor Goldfeder
- , Margarita Kanteev
- & Ayelet Fishman
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Family-wide analysis of poly(ADP-ribose) polymerase activity
The poly(ADP-ribose) polymerase family of enzymes control many aspects of cellular signalling by covalently modifying proteins with either poly- or mono-(ADP-ribose). Vyas et al.catalogue the catalytic specificity of this family, and reveal that the majority of these enzymes generate only mono(ADP-ribose).
- Sejal Vyas
- , Ivan Matic
- & Paul Chang
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| Open AccessImpact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase
Residues within the catalytic site of enzymes are important for activity, but whether more distant residues are also sensitive to mutation is unclear. Here, Leferink et al.show that mutation of residues in copper nitrate reductase that are 12Å away from the active site perturb enzyme function.
- Nicole G. H. Leferink
- , Svetlana V. Antonyuk
- & S. Samar Hasnain
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A role for DNA polymerase θ in the timing of DNA replication
DNA polymerase θ (Pol θ) exhibits properties typical of translesion and repair synthesis; however, its physiological function remains elusive. Here, the authors show that Pol θ plays a role in the initiation and timing of DNA replication during human cell division.
- Anne Fernandez-Vidal
- , Laure Guitton-Sert
- & Jean-Sébastien Hoffmann
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Article
| Open AccessStructure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis
Cytidine-diphosphate diacylglycerol (CDP-DAG) is a central liponucleotide intermediate required for the biosynthesis of some phospholipids and is synthesized by CDP-DAG synthetase (Cds). Here, Liu et al. report the structure of a Cds that shows how it can accept hydrophilic and hydrophobic substrates, and suggest a mechanism that requires two metal ions.
- Xiuying Liu
- , Yan Yin
- & Zhenfeng Liu
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X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism
The CDP-alcohol phosphatidyltransferase family is involved in phospholipid biosynthesis. Here, Nogly et al.report the crystal structure of a bifunctional enzyme from this family, show that magnesium is required for enzymatic activity, and propose a structure-based catalytic mechanism.
- Przemyslaw Nogly
- , Ivan Gushchin
- & Margarida Archer
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Two-way traffic of glycoside hydrolase family 18 processive chitinases on crystalline chitin
The degradation of chitin and cellulose is dependent on the processivity of degrading enzymes. Here, Igarashi et al. use high-speed atomic force microscopy to visualize the movement of two chitinases (ChiA and ChiB) and show them to move in opposite directions, allowing a molecular mechanism to be proposed.
- Kiyohiko Igarashi
- , Takayuki Uchihashi
- & Masahiro Samejima
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Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system
Lactate racemase is an enzyme that interconverts the L and D isomers of the common metabolite lactate. Here, the authors show that lactate racemase represents a new type of nickel-dependent enzyme, which is activated by accessory proteins that are widespread among prokaryotic microbes.
- Benoît Desguin
- , Philippe Goffin
- & Pascal Hols
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Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases
Studies have identified that mutations to metabolic enzymes can lead to abnormal biological activity and disease. Here, the authors show that in addition to this, non-enzymatic chemistry could also influence abnormal metabolic processes and disease development.
- Hanna Tarhonskaya
- , Anna M. Rydzik
- & Christopher J. Schofield
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A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods
Allosteric sites are an increasingly used target for drug design. Here, the authors computationally predict an allosteric site in cathepsin K and subsequently identify a small-molecule allosteric modifier.
- Marko Novinec
- , Matevž Korenč
- & Antonio Baici
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Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer
Vitamin K epoxide reductase (VKOR) catalyses the formation of protein disulphide bonds and is the pharmacological target of the anticoagulant drug warfarin. Liu et al. present crystal structures of a bacterial VKOR in two different conformations and reveal how motions of a helix ensure unidirectional electron transfer.
- Shixuan Liu
- , Wei Cheng
- & Weikai Li
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Unexpected reactivity and mechanism of carboxamide activation in bacterial N-linked protein glycosylation
Oligosaccharyltransferases catalyse the transfer of lipid-anchored glycans onto acceptor asparagine residues in substrate proteins. By assaying chemically modified peptide substrate analogues, Lizak et al. rule out all but one of the currently postulated catalytic mechanisms for this enzyme.
- Christian Lizak
- , Sabina Gerber
- & Kaspar P. Locher
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Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction
The post-translational protein modification tyrosine sulfation is catalysed by tyrosylprotein sulfotransferase (TPST). Teramoto et al. present the first crystal structure of the human TPST isoform 2 complexed with a substrate peptide derived from complement C4 and 3′phosphoadenosine-5′-phosphate, revealing the molecular basis of catalysis.
- Takamasa Teramoto
- , Yukari Fujikawa
- & Yoshimitsu Kakuta
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Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors
New influenza neuramidase inhibitors may increase preparedness against influenza outbreaks. Vavricka et al.confirm the catalytic mechanism of neuramidase and show that it can be inhibited irreversibly with covalent inhibitors.
- Christopher J. Vavricka
- , Yue Liu
- & George F. Gao
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| Open AccessSupporting conditional mouse mutagenesis with a comprehensive cre characterization resource
The cre-loxP system is widely used for the generation of conditional gene knockouts. Here Heffner et al.systematically characterize cre recombinase activity in tissues of embryonic and adult cre-driver mouse strains and provide an online resource for scientists.
- Caleb S. Heffner
- , C. Herbert Pratt
- & Stephen A. Murray
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Spectroscopic observation of iodosylarene metalloporphyrin adducts and manganese(V)-oxo porphyrin species in a cytochrome P450 analogue
Metalloporphyrin compounds are studied as models of cytochrome P450, which is capable of catalysing oxidative reactions. Here, reaction conditions are varied to allow spectroscopic observation of oxidant-metalloporphyrin adducts and metal-oxo intermediates, which may elucidate reaction mechanisms.
- Mian Guo
- , Hang Dong
- & Aiwen Lei
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Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase
Poly(ADP-ribose) glycohydrolase catabolises poly(ADP-ribose), which is covalently attached to proteins following post-translational modification. In this study, the structure of poly(ADP-ribose) glycohydrolase fromTetrahymena thermophilais reported in complex with the small molecule inhibitor RBPI-3.
- Mark S. Dunstan
- , Eva Barkauskaite
- & Ivan Ahel
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Casein kinase 2 reverses tail-independent inactivation of kinesin-1
Kinesin-1 is a motor protein that transports cargo along microtubules and defects in this process can result in neurodegeneration. In this study, a role for casein kinase 2 in regulating the activity of Kinesin-1 is reported, suggesting that signalling molecules can modulate this transport process.
- Jing Xu
- , Babu J. N. Reddy
- & Steven P. Gross