当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site.

Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site.

Abstract：

:We have used nucleobase substitution and kinetic analysis to test the hypothesis that hammerhead catalysis occurs by a general acid-base mechanism, in which nucleobases are directly involved in deprotonation of the attacking 2'-hydroxyl group and protonation of the 5'-oxygen that serves as the leaving group in the cleavage reaction. We demonstrate that simultaneous substitution of two important nucleobases, G8 and G12, with 2,6-diaminopurine shifts the pH optimum of the cleavage reaction from greater than 9.5 to approximately 6.8 in two different hammerhead constructs. Controls involving substitution with other nucleobases and combinations of nucleobases at G5, G8, and/or G12 do not show this behavior. The observed changes in the pH-rate behavior are consistent with a mechanism in which N1 protonation-deprotonation events of guanine or 2,6-diaminopurine at positions 8 and 12 are essential for catalysis. Further support for the participation of G8 and G12 comes from photochemical cross-linking experiments, which show that G8 and G12 can stack upon the two substrate nucleobases at the reactive linkage, G(or U)1.1 and C17 (Heckman, J. E., Lambert, D., and Burke, J. M. (2005) Photocrosslinking detects a compact active structure of the hammerhead ribozyme, Biochemistry 44, 4148-4156). Together, these results support a model in which the hammerhead undergoes a transient conformational change into a catalytically active structure, in which stacking of G8 and G12 upon the nucleobases spanning the cleavage site provides an appropriate architecture for general acid-base catalysis. The hammerhead and hairpin ribozymes may share similarities in the organization of their active sites and their catalytic mechanism.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Han J,Burke JM

doi

10.1021/bi047941z

subject

Has Abstract

pub_date

2005-05-31 00:00:00

pages

7864-70

issue

21

eissn

0006-2960

issn

1520-4995

journal_volume

44

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Dissection of porphyrin-induced conformational dynamics in the heme biosynthesis enzyme ferrochelatase.

    abstract：:Human ferrochelatase (EC 4.99.1.1) catalyzes the insertion ferrous iron into protoporphyrin IX as the last step in heme biosynthesis, an essential process to most organisms given the vast intracellular functions of heme. Even with multiple ferrochelatase structures available, the exact mechanism for iron insertion int...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi300704c

    authors： Asuru AP,An M,Busenlehner LS

    更新日期：2012-09-11 00:00:00

  • pH dependence of folding of iso-2-cytochrome c.

    abstract：:Starting from a standard unfolded state (3.0 M guanidine hydrochloride, pH 7.2), the kinetics of refolding of iso-2-cytochrome c have been investigated as a function of final pH between pH 3 and pH 10. Absorbance in the ultraviolet and visible spectral regions and tryptophan fluorescence are used to monitor folding. O...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00419a020

    authors： Nall BT,Osterhout JJ Jr,Ramdas L

    更新日期：1988-09-20 00:00:00

  • Engineering a Protein Binder Specific for p38α with Interface Expansion.

    abstract：:Protein binding specificities can be manipulated by redesigning contacts that already exist at an interface or by expanding the interface to allow interactions with residues adjacent to the original binding site. Previously, we developed a strategy, called AnchorDesign, for expanding interfaces around linear binding e...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.8b00408

    authors： Hussain M,Angus SP,Kuhlman B

    更新日期：2018-07-31 00:00:00

  • Expression, purification, and characterization of human factor XIII in Saccharomyces cerevisiae.

    abstract：:Factor XIII is the terminal enzyme of the clotting cascade. A cDNA sequence encoding human placental factor XIII was expressed in Saccharomyces cerevisiae with the yeast ADH2-4c promoter. Expression levels were a strong function of the noncoding flanking DNA content of the construction. When the terminal 3'-flanking n...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00459a028

    authors： Bishop PD,Teller DC,Smith RA,Lasser GW,Gilbert T,Seale RL

    更新日期：1990-02-20 00:00:00

  • Comparison of Pf1 and Fd gene 5 proteins and their single-stranded DNA complexes by NMR spectroscopy and differential scanning calorimetry.

    abstract：:The Pf1 gene 5 protein forms a large helical nucleoprotein complex (Mr = 3.1 x 10(7)) with single-stranded viral DNA, from which a 32 amino acid sequence rich in alanine, proline, and glutamine residues can be removed from the C-terminus by limited proteolysis. Sharp resonances in the 1H NMR spectrum of the Pf1 nucleo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00001a018

    authors： Davis KG,Plyte SE,Robertson SR,Cooper A,Kneale GG

    更新日期：1995-01-10 00:00:00

  • Phospholamban binds in a compact and ordered conformation to the Ca-ATPase.

    abstract：:Mutagenesis and cross-linking measurements have identified specific contact interactions between the cytosolic and the transmembrane sequences of phospholamban (PLB) and the Ca-ATPase, and in conjunction with the high-resolution structures of PLB and the Ca-ATPase, have been used to construct models of the PLB-ATPase ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi035424v

    authors： Li J,Xiong Y,Bigelow DJ,Squier TC

    更新日期：2004-01-20 00:00:00

  • Dynamics of light-induced conformational changes of the phoborhodopsin/transducer complex formed in the n-dodecyl beta-D-maltoside micelle.

    abstract：:A complex of photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) and its cognate halobacterial transducer II (pHtrII) existing in the plasma membrane mediates the light signal to the cytoplasm in the earliest step of negative phototaxis in Natronomonas pharaonis. We have investigated the dynamics of t...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi602482s

    authors： Taniguchi Y,Ikehara T,Kamo N,Yamasaki H,Toyoshima Y

    更新日期：2007-05-08 00:00:00

  • Hydrogen-deuterium substitution and solvent effects on the nitrogen-15 nuclear magnetic resonance of gramicidin S: evaluation of secondary structure.

    abstract：:Complete assignments of nitrogen-15 resonances of gramicidin S have been made in dimethyl sulfoxide, trifluoroethanol, and in a solvent mixture of dimethyl sulfoxide (50%) and methanol (50%). The assignments are achieved by utilizing the secondary structure of gramicidin S, by comparing the nitrogen-15 spectrum of gra...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00606a005

    authors： Khaled MA,Urry DW,Sugano H,Miyoshi M,Izumiya N

    更新日期：1978-06-27 00:00:00

  • Solution structure of the first intracellular loop of prostacyclin receptor and implication of its interaction with the C-terminal segment of G alpha s protein.

    abstract：:The amino acids (residues 39-51) responsible for the interaction between the first intracellular loop (iLP1) of the human prostacyclin receptor (IP) and G alpha s protein have been identified [Zhang, L., Huang, G., Wu, J., and Ruan, K. H. (2005) Biochemistry 44, 11389-11401]. To further characterize the structural/fun...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0515669

    authors： Zhang L,Wu J,Ruan KH

    更新日期：2006-02-14 00:00:00

  • Antisera specific for the alpha 1, alpha 2, alpha 3, and beta subunits of the Na,K-ATPase: differential expression of alpha and beta subunits in rat tissue membranes.

    abstract：:We have developed a panel of antibodies specific for the alpha 1, alpha 2, alpha 3, and beta subunits of the rat Na,K-ATPase. TrpE-alpha subunit isoform fusion proteins were used to generate three antisera, each of which reacted specifically with a distinct alpha subunit isotype. Western blot analysis of rat tissue mi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00437a002

    authors： Shyjan AW,Levenson R

    更新日期：1989-05-30 00:00:00

  • Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism.

    abstract：:Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.7b00851

    authors： Castaneda CA,Lopez JE,Joseph CG,Scholle MD,Mrksich M,Fierke CA

    更新日期：2017-10-24 00:00:00

  • Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.

    abstract：:In a large number of plant species hydroxynitrile lyases catalyze the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as a deterrent against herbivores and fungi. In vitro hydroxynitrile lyases are proficient biocatalysts for the stereospecific synthesis ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi802162s

    authors： Dreveny I,Andryushkova AS,Glieder A,Gruber K,Kratky C

    更新日期：2009-04-21 00:00:00

  • Kinetics and mechanism of transitions involving the lamellar, cubic, inverted hexagonal, and fluid isotropic phases of hydrated monoacylglycerides monitored by time-resolved X-ray diffraction.

    abstract：:A study of the dynamics and mechanism of the various thermotropic phase transitions undergone by the hydrated monoacylglycerides monoolein and monoelaidin, in the temperature range of 20-120 degrees C and from 0 to 5 M NaCl, has been undertaken. Measurements were made by using time-resolved X-ray diffraction at the Co...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00394a008

    authors： Caffrey M

    更新日期：1987-10-06 00:00:00

  • Ethanol-perturbed amyloidogenic self-assembly of insulin: looking for origins of amyloid strains.

    abstract：:A model cosolvent, ethanol, has profound and diversified effects on the amyloidogenic self-assembly of insulin, yielding spectroscopically and morphologically distinguishable forms of beta-aggregates. The alcohol reduces hydrodynamic radii of insulin molecules, decreases enthalpic costs associated with aggregation-pro...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi050281t

    authors： Dzwolak W,Grudzielanek S,Smirnovas V,Ravindra R,Nicolini C,Jansen R,Loksztejn A,Porowski S,Winter R

    更新日期：2005-06-28 00:00:00

  • The study of pH-dependent stability shows that the TPLH-mediated hydrogen-bonding network is important for the conformation and stability of human gankyrin.

    abstract：:Ankyrin repeat (AR) proteins possess a distinctive modular and repetitive architecture, and their global folds are maintained by short-range interactions in terms of the primary sequence. In this work, we extended our previous study on the highly conserved TPLH tetrapeptide and investigated the impact of a solvent-exp...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi4005717

    authors： Yuan C,Guo Y,Zhu L,Guo W,Mahajan A,Weghorst CM,Li J

    更新日期：2013-07-16 00:00:00

  • Dynamic structure of a highly ordered beta-sheet molten globule: multiple conformations with a stable core.

    abstract：:The structure of [14-38]Abu, a variant of bovine pancreatic trypsin inhibitor (BPTI) with only the 14-38 disulfide bridge intact, has been analyzed by two-dimensional 1H and 1H-15N NMR. Except for the 18-24, 29-35 antiparallel beta-sheet, residues in all regions of the molecule give two exchange cross peaks for each 1...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00036a015

    authors： Barbar E,Barany G,Woodward C

    更新日期：1995-09-12 00:00:00

  • Protochlorophyllide oxidoreductase: "dark" reactions of a light-driven enzyme.

    abstract：:The light-driven enzyme NADPH:protochlorophyllide oxidoreductase (POR) catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key regulatory step in the chlorophyll biosynthesis pathway. As POR is light activated, it allows intermediates in the reaction pathway to be observed by initiat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0268448

    authors： Heyes DJ,Ruban AV,Hunter CN

    更新日期：2003-01-21 00:00:00

  • “Locked onto the target”: increasing the efficiency of antagomirzymes using locked nucleic acid modifications.

    abstract：:This study highlights the effect of incorporation of locked nucleic acid (LNA) on improving the functional efficacy of DNAzymes against microRNAs (antagomirzymes). DNAzymes were designed against two different sites of miR-27a, which were encompassed both within the precursor and mature form of miRNA. The cleavage and ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi101185k

    authors： Kaur H,Scaria V,Maiti S

    更新日期：2010-11-09 00:00:00

  • Correlation of beta-amyloid aggregate size and hydrophobicity with decreased bilayer fluidity of model membranes.

    abstract：:beta-amyloid peptide (Abeta) is the primary constituent of senile plaques, a defining feature of Alzheimer's disease. Aggregated Abeta is toxic to neurons, but the mechanism of toxicity remains unproven. One proposal is that Abeta toxicity results from relatively nonspecific Abeta-membrane interactions. We hypothesize...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0001980

    authors： Kremer JJ,Pallitto MM,Sklansky DJ,Murphy RM

    更新日期：2000-08-22 00:00:00

  • Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding.

    abstract：:c-Myc is a member of a family of sequence specific-DNA binding proteins that are thought to regulate the transcription of genes involved in normal cell growth, differentiation, and apoptosis. In order to understand how human c-myc functions as a transcription factor, we have studied the mechanism of action and structu...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi960793v

    authors： McEwan IJ,Dahlman-Wright K,Ford J,Wright AP

    更新日期：1996-07-23 00:00:00

  • Orientation of paramagnetic probes attached to gizzard regulatory light chain bound to myosin heads in rabbit skeletal muscle.

    abstract：:The orientation of the myosin neck was monitored using electron paramagnetic resonance (EPR) spectroscopy. Gizzard regulatory light chain was labeled with a nitroxide spin probe and exchanged for the native subunit, located in the myosin neck, in rabbit psoas muscle fibers. The EPR spectra of rigor fibers indicated a ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi960505v

    authors： Zhao L,Gollub J,Cooke R

    更新日期：1996-08-06 00:00:00

  • Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV.

    abstract：:The inhibitory effect of phosphorothioate residues, located within one strand of double-stranded DNA, on the hydrolytic activity of the restriction endonuclease EcoRV was investigated. Specific incorporation of a phosphorothioate group at the site of cleavage yielded the sequence 5'-GATsATC-3'. This modified sequence ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00493a008

    authors： Olsen DB,Kotzorek G,Eckstein F

    更新日期：1990-10-16 00:00:00

  • In vitro interaction between ceruloplasmin and human serum transferrin.

    abstract：:The thermodynamics of the interactions of serum apotransferrin (T) and holotransferrin (TFe(2)) with ceruloplasmin (Cp), as well as those of human lactoferrin (Lf), were assessed by fluorescence emission spectroscopy. Cp interacts with two Lf molecules. The first interaction depends on pH and μ, whereas the second doe...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi1014503

    authors： Ha-Duong NT,Eid C,Hémadi M,El Hage Chahine JM

    更新日期：2010-12-07 00:00:00

  • Chemistry Is Dead. Long Live Chemistry!

    abstract：:Chemistry, once king of fluorescence microscopy, was usurped by the field of fluorescent proteins. The increased demands of modern microscopy techniques on the "photon budget" require better and brighter fluorophores, causing a renewed interest in synthetic dyes. Here, we review the recent advances in biochemistry, pr...

    journal_title：Biochemistry

    pub_type： 杂志文章,评审

    doi：10.1021/acs.biochem.7b00529

    authors： Lavis LD

    更新日期：2017-10-03 00:00:00

  • Reactions of glutamate 1-semialdehyde aminomutase with R- and S-enantiomers of a novel, mechanism-based inhibitor, 2,3-diaminopropyl sulfate.

    abstract：:Glutamate semialdehyde aminomutase is a recognized target for selective herbicides and antibacterial agents because it provides the aminolevulinate from which tetrapyrroles are synthesized in plants and bacteria but not in animals. The reactions of the enzyme with R- and S-enantiomers of a novel compound, diaminopropy...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi992307k

    authors： Contestabile R,Jenn T,Akhtar M,Gani D,John RA

    更新日期：2000-03-21 00:00:00

  • Phosphorylation-dependent regulation of the guanylyl cyclase-linked natriuretic peptide receptor B: dephosphorylation is a mechanism of desensitization.

    abstract：:C-type natriuretic peptide (CNP) binds the guanylyl cyclase-linked natriuretic peptide receptor B (NPR-B) and stimulates marked elevations of the intracellular signaling molecule, cGMP. Here, the essential role of phosphorylation in the hormonal activation and deactivation of this receptor is described. Exposure of NI...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi972303k

    authors： Potter LR

    更新日期：1998-02-24 00:00:00

  • Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants.

    abstract：:The influenza M2 proton channel is a major drug target, but unfortunately, the acquisition of resistance mutations greatly reduces the functional life span of a drug in influenza treatment. New M2 inhibitors that inhibit mutant M2 channels otherwise resistant to the early adamantine-based drugs have been reported, but...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.8b00722

    authors： Santner P,Martins JMDS,Kampmeyer C,Hartmann-Petersen R,Laursen JS,Stein A,Olsen CA,Arkin IT,Winther JR,Willemoës M,Lindorff-Larsen K

    更新日期：2018-10-16 00:00:00

  • Photoinduced reactivity of the HIV-1 envelope glycoprotein with a membrane-embedded probe reveals insertion of portions of the HIV-1 Gp41 cytoplasmic tail into the viral membrane.

    abstract：:The interactions of HIV-1 Env (gp120-gp41) with CD4 and coreceptors trigger a barrage of conformational changes in Env that drive the membrane fusion process. Various regions of gp41 have profound effects on HIV entry and budding. However, the precise interactions between gp41 and the membrane have not been elucidated...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi701920f

    authors： Viard M,Ablan SD,Zhou M,Veenstra TD,Freed EO,Raviv Y,Blumenthal R

    更新日期：2008-02-19 00:00:00

  • Human ferrochelatase is an iron-sulfur protein.

    abstract：:Recombinant human ferrochelatase has been expressed in Escherichia coli and purified to homogeneity. Metal analyses revealed approximately 2 mol of non-heme Fe per mol of the purified enzyme (M(r) = 40,000). The UV-visible absorption spectrum of the purified enzyme consists of a protein absorption at 278 nm (epsilon a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00168a003

    authors： Dailey HA,Finnegan MG,Johnson MK

    更新日期：1994-01-18 00:00:00

  • Reconstitution and further characterization of the cholesterol transport activity of the small-intestinal brush border membrane.

    abstract：:The sterol (free and esterified cholesterol) transport activity of the small-intestinal brush border membrane was solubilized with the short-chain detergent diheptanoylphosphatidylcholine and reconstituted to an artificial membrane system (proteoliposomes). The resulting proteoliposomes were identified as unilamellar ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi970625i

    authors： Boffelli D,Weber FE,Compassi S,Werder M,Schulthess G,Hauser H

    更新日期：1997-09-02 00:00:00