当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.

Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.

Abstract：

:In fosfomycin biosynthesis, the hydrolysis of cytidylyl ( S)-2-hydroxypropylphosphonate [( S)-HPP-CMP] to afford ( S)-HPP is the only uncharacterized step. Because FomD is an uncharacterized protein with a DUF402 domain that is encoded in the fosfomycin biosynthetic gene cluster, FomD was hypothesized to be responsible for this reaction. In this study, FomD was found to hydrolyze ( S)-HPP-CMP to give ( S)-HPP and CMP efficiently in the presence of Mn2+ or Co2+. FomD also hydrolyzed cytidylyl 2-hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation. The kcat/ KM value of FomD with ( S)-HPP-CMP was 10-fold greater than that with HEP-CMP, suggesting that FomD hydrolyzes ( S)-HPP-CMP rather than HEP-CMP in bacteria. The crystal structure of FomD showed that this protein adopts a barrel-like fold, which consists of a large twisted antiparallel β-sheet. This is a key structural feature of the DUF402 domain-containing proteins. Two metal cations are located between the FomD barrel and the two α-helices at the C-terminus and serve to presumably activate the phosphonate group of substrates for hydrolysis. Docking simulations with ( S)-HPP-CMP suggested that the methyl group at the C2 position of the HPP moiety is recognized by a hydrophobic interaction with Trp68. Further mutational analysis suggested that a conserved Tyr107 among the DUF402 domain family of proteins activates a water molecule to promote nucleophilic attack on the phosphorus atom of the phosphonate moiety. These findings provide mechanistic insights into the FomD reaction and lead to a complete understanding of the fosfomycin biosynthetic pathway in Streptomyces.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Sato S,Miyanaga A,Kim SY,Kuzuyama T,Kudo F,Eguchi T

doi

10.1021/acs.biochem.8b00690

subject

Has Abstract

pub_date

2018-08-14 00:00:00

pages

4858-4866

issue

32

eissn

0006-2960

issn

1520-4995

journal_volume

57

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Acylation of lysine 860 allows tight binding and cytotoxicity of Bordetella adenylate cyclase on CD11b-expressing cells.

    abstract：:The Bordetella adenylate cyclase toxin-hemolysin (CyaA, ACT, or AC-Hly) forms cation-selective membrane channels and delivers into the cytosol of target cells an adenylate cyclase domain (AC) that catalyzes uncontrolled conversion of cellular ATP to cAMP. Both toxin activities were previously shown to depend on post-t...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi050459b

    authors： Masin J,Basler M,Knapp O,El-Azami-El-Idrissi M,Maier E,Konopasek I,Benz R,Leclerc C,Sebo P

    更新日期：2005-09-27 00:00:00

  • SecA insertion into phospholipids is stimulated by negatively charged lipids and inhibited by ATP: a monolayer study.

    abstract：:SecA-lipid interactions are believed to be important for the translocation of precursor proteins across the inner membrane of Escherichia coli [Lill, R., Dowhan, W., & Wickner, W. (1990) Cell 60, 271-280]. SecA insertion into the phospholipid bilayer could a role in this process. We investigated this possibility by st...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00119a021

    authors： Breukink E,Demel RA,de Korte-Kool G,de Kruijff B

    更新日期：1992-02-04 00:00:00

  • Hydrogen exchange of individual amide protons in the F helix of cyanometmyoglobin.

    abstract：:Hydrogen exchange of the individual amide protons of alanine-90 (F5), glutamine-91 (F6), serine-92 (F7), and histidine-93 (F8) residues in cyanometmyoglobin of sperm whale has been studied by 1H nuclear magnetic resonance spectroscopy at 360 MHz. The amide proton resonance of F5, F6, and F7 have been assigned by use o...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00347a024

    authors： Kumar NV,Kallenbach NR

    更新日期：1985-12-17 00:00:00

  • Specific interaction of the [2Fe-2S] ferredoxin from Clostridium pasteurianum with the nitrogenase MoFe protein.

    abstract：:Putative physiological partners of the [2Fe-2S] ferredoxin from Clostridium pasteurianum have been searched by running crude soluble extracts of this bacterium through an affinity column to which the [2Fe-2S] ferredoxin had been covalently bound. Subsequent washing of the column with buffers of increasing ionic streng...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi970528p

    authors： Golinelli MP,Gagnon J,Meyer J

    更新日期：1997-09-30 00:00:00

  • Picosecond resolution of tyrosine fluorescence and anisotropy decays by 2-GHz frequency-domain fluorometry.

    abstract：:We extended the technique of frequency-domain fluorometry to an upper frequency limit of 2000 MHz. This was accomplished by using the harmonic content of a laser pulse train (3.76 MHz, 5 ps) from a synchronously pumped and cavity-dumped dye laser. We used a microchannel plate photomultiplier as the detector to obtain ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00375a012

    authors： Lakowicz JR,Laczko G,Gryczynski I

    更新日期：1987-01-13 00:00:00

  • The crystal structure of human procathepsin K.

    abstract：:Cathepsin K is a cysteine protease present in human osteoclasts that plays an important role in bone resorption. Cathepsin K is synthesized as an inactive proenzyme and activated under conditions of low pH. Autoproteolytic processing of the N-terminal 99 amino acid propeptide produces the active, mature form of cathep...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9822271

    authors： LaLonde JM,Zhao B,Janson CA,D'Alessio KJ,McQueney MS,Orsini MJ,Debouck CM,Smith WW

    更新日期：1999-01-19 00:00:00

  • Tyr275 and Lys279 stabilize NADPH within the catalytic site of NADPH:protochlorophyllide oxidoreductase and are involved in the formation of the enzyme photoactive state.

    abstract：:Fluorescence spectroscopic and kinetic analysis of photochemical activity, cofactor and substrate binding, and enzyme denaturation studies were performed with highly purified, recombinant pea NADPH:protochlorophyllide oxidoreductase (POR) heterologously expressed in Escherichia coli. The results obtained with an indiv...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0105025

    authors： Lebedev N,Karginova O,McIvor W,Timko MP

    更新日期：2001-10-23 00:00:00

  • Secondary binding sites for triplex-forming oligonucleotides containing bulges, loops, and mismatches in the third strand.

    abstract：:We have used DNase I footprinting to examine the binding of five different 17-mer oligonucleotides to a 53-base oligopurine tract containing four pyrimidine interruptions. Although all the expected triplexes formed with high affinity (K(d) approximately 10-50 nM), one oligonucleotide produced a footprint at a second s...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi992773+

    authors： Fox KR,Flashman E,Gowers D

    更新日期：2000-06-06 00:00:00

  • Isotropically shifted NMR resonances for the proximal histidyl imidazole NH protons in cobalt hemoglobin and iron-cobalt hybrid hemoglobins. Binding of the proximal histidine toward porphyrin metal ion in the intermediate state of cooperative ligand bindi

    abstract：:Exchangeable imidazole NH proton nuclear magnetic resonance (NMR) signals of the proximal histidine F8, which is directly coordinated to the paramagnetic porphyrin cobalt ion, have been measured for cobalt-substituted deoxyhemoglobins (deoxy-CoHb) and iron-cobalt hybrid hemoglobins, alpha (Co)2 beta (Fe)2 and alpha (F...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00281a019

    authors： Inubushi T,Ikeda-Saito M,Yonetani T

    更新日期：1983-06-07 00:00:00

  • Affinity selection of chemically modified proteins: role of lysyl residues in the binding of calmodulin to calcineurin.

    abstract：:In affinity selection, calcineurin selects from a population of randomly modified calmodulins those species with which it prefers to interact. The method shows that acetylation of lysines affects calmodulin so as to interfere with its ability to interact with calcineurin. Monoacetylation of any lysine of calmodulin re...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00379a026

    authors： Manalan AS,Klee CB

    更新日期：1987-03-10 00:00:00

  • Affinity of native kappa-bungarotoxin and site-directed mutants for the muscle nicotinic acetylcholine receptor.

    abstract：:kappa-Bungarotoxin (kappa-bgt) is a 66-residue peptide originally purified from snake venom that acts as an antagonist at certain acetylcholine receptors. It is one of four homologous kappa-neurotoxins that are distinguished from the structurally related alpha-neurotoxins by their ability to block the alpha 3-subunit-...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00248a004

    authors： Fiordalisi JJ,al-Rabiee R,Chiappinelli VA,Grant GA

    更新日期：1994-11-08 00:00:00

  • Interactions of Acanthamoeba profilin with actin and nucleotides bound to actin.

    abstract：:Three methods, fluorescence anisotropy of rhodamine-labeled profilin, intrinsic fluorescence and nucleotide exchange, give the same affinity, Kd = 0.1 microM, for Acanthamoeba profilins binding amoeba actin monomers with bound Mg-ATP. Replacement of serine 38 with cysteine created a unique site where labeling with rho...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi980093l

    authors： Vinson VK,De La Cruz EM,Higgs HN,Pollard TD

    更新日期：1998-08-04 00:00:00

  • Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability.

    abstract：:To investigate cytosine protonation and its influence on the sequence-dependent thermal stability of DNA triplexes in detail, we have employed homo- and heteronuclear NMR experiments on specifically (15)N-labeled oligodeoxynucleotides that were designed to fold into intramolecular triple helices of the pyrimidine moti...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi992630n

    authors： Leitner D,Schröder W,Weisz K

    更新日期：2000-05-16 00:00:00

  • Raman difference spectroscopic studies of the myosin S1.MgADP.vanadate complex.

    abstract：:The Raman spectra of the nonbridging V--O bonds in the myosin S1.MgADP.Vi complex, often believed to be a transition-state analogue for the phosphotransfer reaction catalyzed by myosin, and in a vanadate solution model compound have been obtained using Raman difference spectroscopic techniques. A symmetric/asymmetric ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi980556n

    authors： Deng H,Wang J,Callender RH,Grammer JC,Yount RG

    更新日期：1998-08-04 00:00:00

  • Biochemical and kinetic characteristics of the interaction of the antitumor antibiotic sparsomycin with prokaryotic and eukaryotic ribosomes.

    abstract：:Using 125I-labeled phenol-alanine sparsomycin, an analogue of sparsomycin having higher biological activity than the unmodified antibiotic, we studied the requirements and the characteristics of its interaction with the ribosome. The drug does not bind to either isolated ribosomal subunits or reconstituted whole ribos...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00104a011

    authors： Lazaro E,van den Broek LA,San Felix A,Ottenheijm HC,Ballesta JP

    更新日期：1991-10-08 00:00:00

  • Modification of ribonuclease T1 specificity by random mutagenesis of the substrate binding segment.

    abstract：:Attempts to modify the guanine specificity of ribonuclease T1 (RNase T1) by rationally designed amino acid substitutions failed so far. Therefore, we applied a semirational approach by randomizing the guanine binding site. A combinatorial library of approximately 1.6 million RNase T1 variants containing permutations o...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9817515

    authors： Hubner B,Haensler M,Hahn U

    更新日期：1999-01-26 00:00:00

  • Quantitation of lateral stress in lipid layer containing nonbilayer phase preferring lipids by frequency-domain fluorescence spectroscopy.

    abstract：:Frequency-resolved fluorescence measurements have been performed to quantitate the lateral stress of the lipid layer containing nonbilayer phase preferring dioleoylphosphatidylethanolamine (DOPE). On the basis of a new rotational diffusion model, the wobbling diffusion constant (Dw), the curvature-related hopping diff...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00130a005

    authors： Chen SY,Cheng KH,Van der Meer BW

    更新日期：1992-04-21 00:00:00

  • An atomic-level mechanism for molybdenum nitrogenase. Part 1. Reduction of dinitrogen.

    abstract：:The properties of the Fe and Mo sites of the iron-molybdenum cofactor of nitrogenase with respect to binding and activation of N(2) have been studied by molecular mechanics calculations on the local protein environment and by density functional theory (DFT) calculations on subsections of the cofactor. The DFT calculat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi025623z

    authors： Durrant MC

    更新日期：2002-11-26 00:00:00

  • Intramolecular disulfide loop formation in a peptide containing two cysteines.

    abstract：:The cyanogen bromide fragment comprising residues 115-181 of Kunitz soybean trypsin inhibitor is a soluble random-coil peptide at pH 7 containing two cysteines separated by eight other amino acids in the primary sequence. Four of the six rate constants have been determined for the three disulfide exchange reactions be...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00377a005

    authors： Snyder GH

    更新日期：1987-02-10 00:00:00

  • Insights into the inhibition of the p90 ribosomal S6 kinase (RSK) by the flavonol glycoside SL0101 from the 1.5 Å crystal structure of the N-terminal domain of RSK2 with bound inhibitor.

    abstract：:The p90 ribosomal S6 family of kinases (RSK) are potential drug targets, due to their involvement in cancer and other pathologies. There are currently only two known selective inhibitors of RSK, but the basis for selectivity is not known. One of these inhibitors is a naturally occurring kaempferol-α-L-diacetylrhamnosi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi300620c

    authors： Utepbergenov D,Derewenda U,Olekhnovich N,Szukalska G,Banerjee B,Hilinski MK,Lannigan DA,Stukenberg PT,Derewenda ZS

    更新日期：2012-08-21 00:00:00

  • Nonphotochemical quenching of excitation energy in photosystem II. A picosecond time-resolved study of the low yield of chlorophyll a fluorescence induced by single-turnover flash in isolated spinach thylakoids.

    abstract：:Chlorophyll a fluorescence emission is widely used as a noninvasive measure of a number of parameters related to photosynthetic efficiency in oxygenic photosynthetic organisms. The most important component for the estimation of photochemistry is the relative increase in fluorescence yield between dark-adapted samples ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9806854

    authors： Vasil'ev S,Bruce D

    更新日期：1998-08-04 00:00:00

  • Fidelity of HIV-1 reverse transcriptase copying RNA in vitro.

    abstract：:The genomic hypervariation of human immunodeficiency virus 1 (HIV-1) could result from misincorporations by the viral reverse transcriptase. We developed an assay for reverse transcriptase fidelity during RNA-dependent as well as DNA-dependent DNA polymerization in vitro. A lacZ alpha RNA fragment transcribed by T3 RN...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00119a002

    authors： Ji JP,Loeb LA

    更新日期：1992-02-04 00:00:00

  • Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies.

    abstract：:Transcarboxylase (TC) is a multisubunit enzyme that catalyzes the transfer of a carboxylate group from methylmalonyl-CoA (MMCoA) to pyruvate. The CO2- group is shuttled between the MMCoA and pyruvate binding sites by a biotin cofactor, covalently linked to the 1.3S subunit. Fully carboxylated 1.3S can be prepared in v...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0116442

    authors： Rivera-Hainaj RE,Pusztai-Carey M,Venkat Reddy D,Choowongkomon K,Sönnichsen FD,Carey PR

    更新日期：2002-02-19 00:00:00

  • Free energy rhythms in Saccharomyces cerevisiae: a dynamic perspective with implications for ribosomal biogenesis.

    abstract：:To describe the time course of cellular systems, we integrate ideas from thermodynamics and information theory to discuss the work needed to change the state of the cell. The biological example analyzed is experimental microarray transcription level oscillations of yeast in the different phases as characterized by oxy...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi3016982

    authors： Gross A,Li CM,Remacle F,Levine RD

    更新日期：2013-03-05 00:00:00

  • Resonance Raman evidence for the presence of two heme pocket conformations with varied activities in CO-bound bovine soluble guanylate cyclase and their conversion.

    abstract：:Resonance Raman (RR) spectra of soluble guanylate cyclase (sGC) reported by five independent research groups have been classified as two types: sGC(1) and sGC(2). Here we demonstrate that the RR spectra of sGC isolated from bovine lung contain only sGC(2) while both species are observed in the spectra of the CO-bound ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0489208

    authors： Li Z,Pal B,Takenaka S,Tsuyama S,Kitagawa T

    更新日期：2005-01-25 00:00:00

  • Cryoelectron microscopy of Escherichia coli F1 adenosinetriphosphatase decorated with monoclonal antibodies to individual subunits of the complex.

    abstract：:Monoclonal antibodies directed against epitopes on each of the five subunits (alpha, beta, gamma, delta, and epsilon) of the Escherichia coli F1 ATPase (ECF1) have been prepared and used to localize the subunits in the enzyme complex. Fab' fragments, prepared by pepsin digestion of the antibodies, were bound to ECF1 a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00437a031

    authors： Gogol EP,Aggeler R,Sagermann M,Capaldi RA

    更新日期：1989-05-30 00:00:00

  • Role of isomerization of initial complexes in the binding of inhibitors to dihydrofolate reductase.

    abstract：:Stopped-flow measurements of protein fluorescence quenching when methotrexate (MTX) binds to dihydrofolate reductase (isoenzyme II) of Streptococcus faecium (SFDHFR II) analyze as the sum of two differentials: a rapid binding phase and a second phase for which the observed rate constant is independent of methotrexate ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00339a010

    authors： Blakley RL,Cocco L

    更新日期：1985-08-27 00:00:00

  • Internal architecture of the core nucleosome: fluorescence energy transfer studies at methionine-84 of histone H4.

    abstract：:Chicken histone H4, labeled separately at Met-84 with N-[[(iodoacetyl)amino]ethyl]-5-naphthylamine-1-sulfonic acid and 5-(iodoacetamido)fluorescein, was reassociated with unlabeled histones H2A, H2B, and H3 and 146 base pairs of DNA to produce fluorescently labeled nucleosomes having physical characteristics virtually...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00366a010

    authors： Chung DG,Lewis PN

    更新日期：1986-09-09 00:00:00

  • Chemical modification of prostaglandin H synthase with diethyl pyrocarbonate.

    abstract：:The role of histidine in catalysis by prostaglandin H synthase has been investigated using chemical modification with diethyl pyrocarbonate (DEPC), an agent that has been found to rather selectively derivatize histidine residues in proteins under mild conditions. Incubation of the synthase apoprotein with DEPC at pH 7...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00124a013

    authors： Zhang X,Tsai AL,Kulmacz RJ

    更新日期：1992-03-10 00:00:00

  • Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction.

    abstract：:The iron storage protein bacterioferritin (Bfr) binds up to 12 hemes b at specific sites in its protein shell. The heme b can be substituted with the photosensitizer Zn(II)-protoporphyrin IX (ZnPP), and photosensitized reductive iron release from the ferric oxyhydroxide {[FeO(OH)] n ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b01103

    authors： Benavides BS,Valandro S,Cioloboc D,Taylor AB,Schanze KS,Kurtz DM Jr

    更新日期：2020-04-28 00:00:00