当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1: A Familiar Binuclear Metal Center Embedded in a Seven-Bladed β-Propeller Protein Fold.

Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1: A Familiar Binuclear Metal Center Embedded in a Seven-Bladed β-Propeller Protein Fold.

Abstract：

:A novel phosphotriesterase was recently discovered and purified from Sphingobium sp. TCM1 (Sb-PTE) and shown to catalyze the hydrolysis of a broad spectrum of organophosphate esters with a catalytic efficiency that exceeds 10(6) M(-1) s(-1) for the hydrolysis of triphenyl phosphate. The enzyme was crystallized and the three-dimensional structure determined to a resolution of 2.1 Å using single-wavelength anomalous diffraction (Protein Data Bank entry 5HRM ). The enzyme adopts a seven-bladed β-propeller protein fold, and three disulfide bonds were identified between Cys-146 and Cys-242, Cys-411 and Cys-443, and Cys-542 and Cys-559. The active site of Sb-PTE contains a binuclear manganese center that is nearly identical to that of the structurally unrelated phosphotriesterase from Pseudomonas diminuta (Pd-PTE). The two metal ions in the active site are bridged to one another by Glu-201 and a water molecule. The α-metal ion is further coordinated to the protein by interactions with His-389, His-475, and Glu-407, whereas the β-metal ion is further liganded to His-317 and His-258. Computational docking of mimics of the proposed pentavalent reaction intermediates for the hydrolysis of organophosphates was used to provide a model for the binding of chiral substrates in the active site of Sb-PTE. The most striking difference in the catalytic properties of Sb-PTE, relative to those of Pd-PTE, is the enhanced rate of hydrolysis of organophosphate esters with substantially weaker leaving groups. The structural basis for this difference in the catalytic properties between Sb-PTE and Pd-PTE, despite the nearly identical binuclear metal centers for the activation of the substrate and nucleophilic water molecule, is at present unclear.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Mabanglo MF,Xiang DF,Bigley AN,Raushel FM

doi

10.1021/acs.biochem.6b00364

subject

Has Abstract

pub_date

2016-07-19 00:00:00

pages

3963-74

issue

28

eissn

0006-2960

issn

1520-4995

journal_volume

55

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Ribosome RNA assembly intermediates visualized in living cells.

    abstract：:In cells, RNAs likely adopt numerous intermediate conformations prior to formation of functional RNA-protein complexes. We used single-nucleotide resolution selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to probe the structure of Escherichia coli 16S rRNA in healthy growing bacteria. SHAPE-direct...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi500198b

    authors： McGinnis JL,Weeks KM

    更新日期：2014-05-20 00:00:00

  • Two-dimensional 1H NMR studies of cytochrome c: hydrogen exchange in the N-terminal helix.

    abstract：:The hydrogen exchange behavior of the N-terminal helical segment in horse heart cytochrome c was studied in both the reduced and the oxidized forms by use of two-dimensional nuclear magnetic resonance methods. The amide protons of the first six residues are not H bonded and exchange rapidly with solvent protons. The m...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00353a025

    authors： Wand AJ,Roder H,Englander SW

    更新日期：1986-03-11 00:00:00

  • Solvent isotope effects on the onset of inhibition of porcine pepsin by pepstatin.

    abstract：:Pepstatin is a slow and tight-binding inhibitor of pepsin. Preincubating enzyme and inhibitor in H2O and in D2O in the absence of substrate generates an inverse solvent isotope effect of Dk = 0.69 +/- 0.06 on the apparent first-order rate constant for the decay in enzymatic activity. Proton inventory analysis of the i...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00198a032

    authors： Cho YK,Rebholz KL,Northrop DB

    更新日期：1994-08-16 00:00:00

  • pH-dependent spectral and kinetic properties of cytochrome c peroxidase: comparison of freshly isolated and stored enzyme.

    abstract：:The effect of long-term storage on the electronic absorption spectrum and the kinetic properties of cytochrome c peroxidase has been investigated. No detectable differences were observed between freshly isolated enzyme and enzyme stored below -20 degrees C, in the crystalline state, for up to 41 months. The electronic...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00470a004

    authors： Vitello LB,Huang M,Erman JE

    更新日期：1990-05-08 00:00:00

  • Critical nature of a specific uridine O2-carbonyl for cleavage by the hammerhead ribozyme.

    abstract：:Three modified hammerhead ribozyme/substrate complexes have been prepared in which individual uridine O2-carbonyls have been eliminated. The modified complexes were chemically synthesized with the substitution of a single 2-pyridone (2P) base analogue for residues U4, U7, and U16.1. Steady-state kinetic analyses indic...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi982977a

    authors： Bevers S,Ha SB,McLaughlin LW

    更新日期：1999-06-15 00:00:00

  • Alamethicin incorporation in lipid bilayers: a thermodynamic study.

    abstract：:Interaction of the peptide antibiotic alamethicin with phospholipid vesicles has been monitored by changes in its circular dichroic and fluorescent properties. The data are consistent with an incorporation of the peptide in the lipid bilayer. Aggregation of alamethicin in the membrane phase is evident from a character...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00384a015

    authors： Rizzo V,Stankowski S,Schwarz G

    更新日期：1987-05-19 00:00:00

  • Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases.

    abstract：:Lysyl-tRNA synthetase, a class II enzyme, edits homocysteine by converting it into homocysteine thiolactone. In a similar reaction, the enzyme converts homoserine into homoserine lactone. Other class II enzymes, aspartyl-tRNA synthetase and seryl-tRNA synthetase, do not edit any of the amino acids tested. However, all...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi970589n

    authors： Jakubowski H

    更新日期：1997-09-16 00:00:00

  • Exchange rates at the lipid-protein interface of myelin proteolipid protein studied by spin-label electron spin resonance.

    abstract：:The electron spin resonance (ESR) spectra from spin-labeled phospholipids in recombinants of myelin proteolipid apoprotein with dimyristoylphosphatidylcholine have been simulated with the exchanged-coupled Bloch equations to obtain values for both the fraction of motionally restricted lipids and the exchange rate betw...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00401a009

    authors： Horváth LI,Brophy PJ,Marsh D

    更新日期：1988-01-12 00:00:00

  • Murine epidermal growth factor: structure and function.

    abstract：:Murine epidermal growth factor (EGF), a 53 amino acid protein, has been modified by enzymic digestion, site-specific chemical reactions, and recombinant DNA technology. After trypsin digestion the EGF derivatives EGF1-48 (called EGF-T) and EGF1-45 (called EGF-T2) were separated from the residual EGF and the C-terminal...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00414a005

    authors： Burgess AW,Lloyd CJ,Smith S,Stanley E,Walker F,Fabri L,Simpson RJ,Nice EC

    更新日期：1988-07-12 00:00:00

  • Partitioning of synaptotagmin I C2 domains between liquid-ordered and liquid-disordered inner leaflet lipid phases.

    abstract：:Synaptotagmin I is the calcium sensor in synchronous neurotransmitter release caused by fusion of synaptic vesicles with the presynaptic membrane in neurons. Synaptotagmin I interacts with acidic phospholipids, but also with soluble N-ethylmaleimide-sensitive factor attachment receptors (SNAREs), at various stages in ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi101864k

    authors： Wan C,Kiessling V,Cafiso DS,Tamm LK

    更新日期：2011-04-05 00:00:00

  • Molecular basis for the catalytic specificity of the CTX-M extended-spectrum β-lactamases.

    abstract：:Extended-spectrum β-lactamases (ESBLs) pose a threat to public health because of their ability to confer resistance to extended-spectrum cephalosporins such as cefotaxime. The CTX-M β-lactamases are the most widespread ESBL enzymes among antibiotic resistant bacteria. Many of the active site residues are conserved bet...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi501195g

    authors： Adamski CJ,Cardenas AM,Brown NG,Horton LB,Sankaran B,Prasad BV,Gilbert HF,Palzkill T

    更新日期：2015-01-20 00:00:00

  • A new bifunctional spin-label suitable for saturation-transfer EPR studies of protein rotational motion.

    abstract：:A new bifunctional spin-label (BSL) has been synthesized that can be immobilized on the surface of proteins, allowing measurement of rotational motion of proteins by saturation-transfer electron paramagnetic resonance (STEPR). The spin-label contains a photoactivatable azido moiety, a cleavable disulfide, and a nitrox...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00476a014

    authors： Wilcox MD,Parce JW,Thomas MJ,Lyles DS

    更新日期：1990-06-19 00:00:00

  • Partial purification and characterization of a neutral protease which cleaves type IV collagen.

    abstract：:A neutral protease has been extracted from the media of cultured metastatic tumor cells and purified approximately 1000 times after sequential ammonium sulfate fractionization, concanavalin A column chromatography, and molecular sieve chromatography. The protease has an apparent molecular weight of 70 000--80 000, is ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00504a017

    authors： Liotta LA,Tryggvason K,Garbisa S,Robey PG,Abe S

    更新日期：1981-01-06 00:00:00

  • Reconstitution of 5-hydroxytryptamine transport from cholate-disrupted platelet plasma membrane vesicles.

    abstract：:The bile acid cholate disrupts platelet plasma membrane vesicles and inactivates 5-hydroxytryptamine transport activity. The transporter appears not to be solubilized by this procedure, but remains associated with a high molecular weight aggregate. Merely removing cholate does not restore the vesicular structure or tr...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00617a033

    authors： Rudnick G,Nelson PJ

    更新日期：1978-11-28 00:00:00

  • Three small ribooligonucleotides with specific arginine sites.

    abstract：:Arginine-binding RNA motifs are important to protein-RNA interaction and perhaps also for Archean biochemistry. Selection-amplification was used to isolate three RNAs that are eluted by free arginine from an L-arginine affinity column (Kd approximately 0.2-0.4 mM). The binding sites contain specific internal and bulge...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00072a002

    authors： Connell GJ,Illangesekare M,Yarus M

    更新日期：1993-06-01 00:00:00

  • Changes in conformation at the cytoplasmic ends of the fifth and sixth transmembrane helices of a yeast G protein-coupled receptor in response to ligand binding.

    abstract：:The third intracellular loop (IL3) of G protein-coupled receptors (GPCRs) is an important contact domain between GPCRs and their G proteins. Previously, the IL3 of Ste2p, a Saccharomyces cerevisiae GPCR, was suggested to undergo a conformational change upon activation as detected by differential protease susceptibilit...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi200254h

    authors： Umanah GK,Huang LY,Maccarone JM,Naider F,Becker JM

    更新日期：2011-08-16 00:00:00

  • Differential DNA recognition and cleavage by EcoRI dependent on the dynamic equilibrium between the two forms of the malondialdehyde-deoxyguanosine adduct.

    abstract：:DNA damage may alter the outcome of protein-nucleic acid interactions. The malondialdehyde-deoxyguanosine adduct, 3-(2'-deoxy-beta-d-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10-(3H)-one (M(1)dG), miscodes in vivo and in vitro. M(1)dG is an exocyclic adduct that undergoes ring-opening in duplex DNA to form the a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0472898

    authors： VanderVeen LA,Druckova A,Riggins JN,Sorrells JL,Guengerich FP,Marnett LJ

    更新日期：2005-04-05 00:00:00

  • Determinants of high-affinity DNA binding by the glucocorticoid receptor: evaluation of receptor domains outside the DNA-binding domain.

    abstract：:In this study, we have investigated the influence of regions outside the DNA-binding domain of the human glucocorticoid receptor on high-affinity DNA binding. We find that the DNA-binding domain shows a 10-fold lower affinity for a palindromic DNA-binding site than the intact receptor. The N-terminal part of the recep...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00152a047

    authors： Dahlman-Wright K,Wright AP,Gustafsson JA

    更新日期：1992-09-22 00:00:00

  • Identification and assignment of base pairs in three helical stems of Torulopsis utilis ribosomal 5S RNA and its RNase T1 and RNase T2 cleaved fragments via 500-MHz proton homonuclear overhauser enhancements.

    abstract：:Imino proton resonances in the downfield region (10-14 ppm) of the 500-MHz 1H NMR spectrum of Torulopsis utilis 5S RNA are identified (A X U, G X C, or G X U) and assigned to base pairs in helices I, IV, and V via analysis of homonuclear Overhauser enhancements (NOE) from intact T. utilis 5S RNA, its RNase T1 and RNas...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00366a021

    authors： Chen SM,Marshall AG

    更新日期：1986-09-09 00:00:00

  • Misfolding of the cystic fibrosis transmembrane conductance regulator and disease.

    abstract：:Understanding the structural basis for defects in protein function that underlie protein-based genetic diseases is the fundamental requirement for development of therapies. This situation is epitomized by the cystic fibrosis transmembrane conductance regulator (CFTR)-the gene product known to be defective in CF patien...

    journal_title：Biochemistry

    pub_type： 杂志文章,评审

    doi：10.1021/bi702209s

    authors： Cheung JC,Deber CM

    更新日期：2008-02-12 00:00:00

  • Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids.

    abstract：:In an earlier study, β³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different β-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate β-amino acids into DHFR, in spite of...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00389

    authors： Maini R,Chowdhury SR,Dedkova LM,Roy B,Daskalova SM,Paul R,Chen S,Hecht SM

    更新日期：2015-06-16 00:00:00

  • Integration of the thylakoid membrane protein cytochrome b6 in the cytoplasmic membrane of Escherichia coli.

    abstract：:An overexpression system for spinach apocytochrome b(6) as a fusion protein to a maltose-binding protein in Escherichia coli was established using the expression vector pMalp2. The fusion of the cytochrome b(6) to the periplasmic maltose-binding protein directs the cytochrome on the Sec-dependent pathway. The cytochro...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi047422w

    authors： Króliczewski J,Hombek-Urban K,Szczepaniak A

    更新日期：2005-05-24 00:00:00

  • Understanding functional divergence in proteins by studying intragenomic homologues.

    abstract：:Studies of intragenomic homologues in bacterial genomes can provide valuable insights into functional divergence. Three GTP cyclohydrolase II homologues in the Streptomyces coelicolor genome have been shown to catalyze two related but distinct reactions [Spoonamore, J. E., Dahlgran, A. L., Jacobsen, N. E., and Bandari...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi702263z

    authors： Spoonamore JE,Bandarian V

    更新日期：2008-02-26 00:00:00

  • Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment.

    abstract：:The effects of nearest neighbor interactions between a nucleotide base at the primer 3'-terminus and an incoming deoxyribonucleoside triphosphate on DNA polymerase catalyzed insertion were examined. Kinetics of inserting the fluorescent nucleotide analog 2-aminopurine deoxyribonucleotide (dAPMP) and dAMP opposite a te...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00092a039

    authors： Bloom LB,Otto MR,Beechem JM,Goodman MF

    更新日期：1993-10-19 00:00:00

  • Monoclonal antibodies to poly(adenosine diphosphate ribose) recognize different structures.

    abstract：:Two hybridomas producing monoclonal antibodies to poly(adenosine diphosphate ribose) [poly(ADP-Rib)] were established. One antibody, 10H (IgG3, kappa), bound to most of the poly(ADP-Rib) preparation, which consisted of molecules of various sizes of more than 20 ADP-Rib residues. The binding of this antibody was inhibi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00311a032

    authors： Kawamitsu H,Hoshino H,Okada H,Miwa M,Momoi H,Sugimura T

    更新日期：1984-07-31 00:00:00

  • Role of lysines in human angiogenin: chemical modification and site-directed mutagenesis.

    abstract：:The role of lysines in the ribonucleolytic and angiogenic activities of human angiogenin has been examined by chemical modification and site-directed mutagenesis. It was demonstrated previously [Shapiro, R., Weremowicz, S., Riordan, J.F., & Vallee, B.L. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8783-8787] that extensiv...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00430a045

    authors： Shapiro R,Fox EA,Riordan JF

    更新日期：1989-02-21 00:00:00

  • Copper-induced conformational changes in the N-terminal domain of the Wilson disease copper-transporting ATPase.

    abstract：:The Wilson disease copper-transporting ATPase plays a critical role in the intracellular trafficking of copper. Mutations in this protein lead to the accumulation of a toxic level of copper in the liver, kidney, and brain followed by extensive tissue damage and death. The ATPase has a novel amino-terminal domain ( app...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi992222j

    authors： DiDonato M,Hsu HF,Narindrasorasak S,Que L Jr,Sarkar B

    更新日期：2000-02-22 00:00:00

  • Influence of N-cap mutations on the structure and stability of Escherichia coli HPr.

    abstract：:This paper describes the effect of N-capping substitutions on the structure and stability of histidine-containing protein (HPr). We have used NMR spectroscopy and conformational stability studies to quantify changes in local and global free energy due to mutagenesis at Ser46, the N-cap for helix B in HPr. Previous NMR...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi960349s

    authors： Thapar R,Nicholson EM,Rajagopal P,Waygood EB,Scholtz JM,Klevit RE

    更新日期：1996-09-03 00:00:00

  • DNA repair catalyzed by Escherichia coli DNA photolyase containing only reduced flavin: elimination of the enzyme's second chromophore by reduction with sodium borohydride.

    abstract：:DNA photolyase from Escherichia coli contains FAD plus a partially characterized, second chromophore. In vivo, the flavin is fully reduced (FADH2), but oxidation to a stable, blue radical (FADH.) occurs during enzyme isolation. The second chromophore is irreversibly reduced by reaction of the enzyme with sodium borohy...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00395a034

    authors： Jorns MS,Wang B,Jordan SP

    更新日期：1987-10-20 00:00:00

  • Isolation and characterization of bovine factor VII.

    abstract：:Factor VII (proconvertin) has been purified approximately 5 x 10(5)-fold from bovine plasma with an overall yield of 30%. The isolation procedure involves barium sulfate adsorption and elution, DEAE-Sephadex batchwise adsorption and elution, benzamidine-agarose column chromatography, heparin-agarose column chromatogra...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00693a023

    authors： Kisiel W,Davie EW

    更新日期：1975-11-04 00:00:00