[NMR paper] Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Nucleic Acids Res. 2013 Aug 27;
Authors: Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG
Abstract
Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the ?-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue ?,?-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.
PMID: 23982515 [PubMed - as supplied by publisher]
[NMR paper] Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance.
Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance.
Structure. 2013 Jan 8;21(1):32-41
Authors: Nyirenda J, Matsumoto S, Saitoh T, Maita N, Noda NN, Inagaki F, Kohda D
Abstract
Oligosaccharyltransferase (OST) is a membrane-bound...
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Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry
Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry
Alexander Kuhn, Puravankara Sreeraj, Rainer Po?ttgen, Hans-Dieter Wiemho?fer, Martin Wilkening and Paul Heitjans
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2020108/aop/images/medium/ja-2011-020108_0005.gif
Journal of the American Chemical Society
DOI: 10.1021/ja2020108
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
J Proteome Res. 2010 Dec 3;9(12):6729-39
Authors: Szeto SS, Reinke SN, Sykes BD, Lemire BD
Metabolomics is a powerful method of examining the intricate connections between mutations, metabolism, and disease. Metabolic...
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05-25-2011 07:01 PM
[NMR paper] NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.
NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.
Related Articles NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar.
J Mol Biol. 2005 Mar 25;347(2):277-85
Authors: Kitahara R, Yokoyama S, Akasaka K
Conformational fluctuation plays a key role in protein function, but we know little about the associated structural changes. Here we present a general method for elucidating, at the atomic level, a large-scale shape change of a protein molecule in solution undergoing conformational fluctuation....
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[NMR paper] The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic
The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic acid dehalogenase: a kinetic, NMR, and mutational analysis.
Related Articles The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic acid dehalogenase: a kinetic, NMR, and mutational analysis.
Biochemistry. 2004 Apr 13;43(14):4082-91
Authors: Azurmendi HF, Wang SC, Massiah MA, Poelarends GJ, Whitman CP, Mildvan AS
trans-3-Chloroacrylic acid dehalogenase (CaaD) converts trans-3-chloroacrylic acid to malonate semialdehyde by the...
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[NMR paper] Phosphate ions in bone: identification of a calcium-organic phosphate complex by 31P
Phosphate ions in bone: identification of a calcium-organic phosphate complex by 31P solid-state NMR spectroscopy at early stages of mineralization.
Related Articles Phosphate ions in bone: identification of a calcium-organic phosphate complex by 31P solid-state NMR spectroscopy at early stages of mineralization.
Calcif Tissue Int. 2003 May;72(5):610-26
Authors: Wu Y, Ackerman JL, Strawich ES, Rey C, Kim HM, Glimcher MJ
Previous 31P cross-polarization and differential cross-polarization magic angle spinning (CP/MAS and DCP/MAS) solid-state NMR...
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[NMR paper] NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Sa
NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Salmonella typhimurium.
Related Articles NMR investigation of the catalytic mechanism of arylamine N-acetyltransferase from Salmonella typhimurium.
Biochim Biophys Acta. 2003 Mar 17;1620(1-3):8-14
Authors: Delgoda R, Lian LY, Sandy J, Sim E
Arylamine N-acetyltransferases (NAT) are a family of enzymes found in both eucaryotes and procaryotes, which catalyse the N-acetylation of a range of arylamine and hydrazine drugs and carcinogenic arylamines, using acetyl...
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[NMR paper] Identification of reaction products and intermediates of aromatic-amine dehydrogenase
Identification of reaction products and intermediates of aromatic-amine dehydrogenase by 15N and 13C NMR.
Related Articles Identification of reaction products and intermediates of aromatic-amine dehydrogenase by 15N and 13C NMR.
Biochem J. 1998 Mar 15;330 ( Pt 3):1159-63
Authors: Bishop GR, Zhu Z, Whitehead TL, Hicks RP, Davidson VL
13C- and 15N-NMR studies of the reaction of aromatic amine dehydrogenase (AADH) with methylamine demonstrated that the products of the reductive half-reaction are an equivalent of formaldehyde hydrate and a reduced...
Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Linear Mode
