Abstract:
:NanGIR1 is a catalytic element inserted in the P6 loop of a group I intron (NanGIR2) in the small subunit rRNA precursor of the protist Naegleria andersoni [Einvik, C., Decatur, W. A., Embley, T. M., Vogt, V. M., and Johansen, S. (1997) RNA 3, 710-720]. It catalyzes site-specific hydrolysis at an internal processing site (IPS) after a G residue that immediately follows the P9 stem-loop. Functional and structural analyses were initiated to compare NanGIR1 to group I introns that carry out self-splicing. Chemical modification and site-directed mutagenesis studies showed that NanGIR1 shares many structural elements with other group I introns, but also contains a pseudoknot (P15), which is important for catalytic activity. Deletion analysis revealed the boundaries of the minimum self-cleaving unit (178 nucleotides). The rate of self-cleavage was measured as a function of mono- and divalent ion concentration, temperature, and pH. The reaction at the IPS yields 5'-phosphate and 3'-hydroxyl termini, requires Mg2+or Mn2+ ions, and is first-order in [OH-] between pH 5.0 and 8.5. The latter results suggest that the nucleophile in the reaction is hydroxide or possibly a Mg2+-coordinated hydroxide. With a second-order rate constant of 1 x 10(5) min-1 M-1, the self-cleavage reaction of NanGIR1 is 2 orders of magnitude faster than a similar site-specific hydrolysis reaction of the circular form of the Tetrahymena group I intron.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Jabri E,Aigner S,Cech TRdoi
10.1021/bi9718595subject
Has Abstractpub_date
1997-12-23 00:00:00pages
16345-54issue
51eissn
0006-2960issn
1520-4995pii
bi9718595journal_volume
36pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::The Ogg1 protein of Saccharomyces cerevisiae belongs to a family of DNA glycosylases and apurinic/apyrimidinic site (AP) lyases, the signature of which is the alpha-helix-hairpin-alpha-helix-Gly/Pro-Asp (HhH-GPD) active site motif together with a conserved catalytic lysine residue, to which we refer as the HhH-GPD/K f...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992262n
更新日期:2000-02-22 00:00:00
abstract::Two glutathione S-transferase (GST) activities have been identified and purified from etiolated corn tissue. The first, designated GST I enzyme, is constitutively present in corn tissue, and the second, designated GST II enzyme, is present only in tissue which has been treated with chemical antidotes which protect cor...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00274a011
更新日期:1983-03-01 00:00:00
abstract::Preprotein translocation in Escherichia coli is mediated by the translocase with SecA as peripheral ATPase and SecY, SecE, and SecG as membrane domain. To facilitate large-scale purification of the SecYEG heterotrimer, SecY was fused at its amino terminus with a hexahistidine tag and co-overexpressed with SecE and Sec...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi972105t
更新日期:1998-01-06 00:00:00
abstract::The substrate-bound form of the enzyme heme oxygenase (HO), which catalyzed the stereospecific alpha-meso bridge cleavage of hemin to yield biliverdin IX alpha, has been investigated by 1H NMR in both its primarily high-spin and its cyanide-inhibited low-spin forms. Both derivatives yield 1H NMR spectra indicative of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00187a033
更新日期:1994-05-31 00:00:00
abstract::The kinetics of Zn(2+) binding by two point-mutated forms of the HIV-1 NCp7 C-terminal zinc finger, each containing tridentate binding motif HCC [Ser49(35-50)NCp7] or CCC [Ala44(35-50)NCp7], has been studied by stopped-flow spectrofluorimetry. Both the formation and dissociation rate constants of the complexes between...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi047349+
更新日期:2005-05-17 00:00:00
abstract::The structure of the copper site in oxidized and reduced Rhus vernicifera stellacyanin has been studied by X-ray absorption (XAFS) spectroscopy at different pH values. Data for the oxidized protein are consistent with the fourth ligand being an O- or N-donating ligand rather than a cysteine from the disulfide bridge. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00001a026
更新日期:1995-01-10 00:00:00
abstract::A new fluorescence method to measure viscosity in cell cytosol [Fushimi, K., & Verkman, A. S. (1991) J. Cell Biol. 112, 719-725] has been applied to determine fluid-phase viscosity in sea urchin eggs. Freshly harvested eggs from Lytechinus pictus were loaded with the dyes 2,7-bis(2-carboxyethyl)-5-(and-6-)carboxyfluor...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00115a600
更新日期:1991-12-24 00:00:00
abstract::A 39/34-kilodalton (kDa) monomeric dispase fragment of von Willebrand factor (vWF) has been purified by heparin affinity chromatography. Detailed structural analysis of the individual 39- and 34-kDa fragments indicated that they had identical amino acid sequences extending from Leu-480/Val-481 to Gly-718 with an intra...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00447a010
更新日期:1989-10-17 00:00:00
abstract::Fluorescent and photoactivatable fluorescent derivatives of tetrodotoxin (TTX) have been synthesized. N-Methylanthraniloylglycine hydrazide, anthraniloyl hydrazide, and 2-azidoanthraniloylglycine hydrazide were coupled to the carbonyl at C6 of oxidized tetrodotoxin to form stable fluorescent hydrazones. The C6 ketone ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00517a025
更新日期:1981-07-07 00:00:00
abstract::The initial hydrolysis of CaATP by chloroplast coupling factor 1 was studied with the quenched-flow method. The time course of hydrolysis can be described as a first-order conversion of the enzyme to an active form followed by steady-state formation of product. The rat constant for the first-order process is independe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00382a035
更新日期:1987-04-21 00:00:00
abstract::DNA sequences with repetitive G-rich structural motifs, which form special structures called G-quadruplexes, widely exist in the human genome. Here we report the general peroxidase activity of G-quadruplex-hemin complexes and discuss the connection between peroxidase activity and G-quadruplex structures. The high pero...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9006786
更新日期:2009-08-25 00:00:00
abstract::The binding of 8-anilino-1-naphthalenesulfonate (ANS) to ciliary dynein ATPase leads to a marked increase in the dye's fluorescence intensity, accompanied by a blue shift in the observed fluorescence emission maximum. We found that dynein has 37 +/- 3 ANS binding sites and that experimentally applied ANS concentration...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00347a012
更新日期:1985-12-17 00:00:00
abstract::Kinetic studies of the effect of addition of Co2+ or Mn2+ to a highly purified dipeptidase from Ehrlich-Lettré mouse ascites tumor cells show that these metals specifically activate the hydrolyses of certain classes of dipeptides. This enzyme was previously (S. Hayman and E. K. Patterson, 1971, J. Biol. Chem. 246, 660...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00690a018
更新日期:1975-09-23 00:00:00
abstract::We have previously suggested that folding of the SV40 attenuator RNA 1 into two hairpin elements leads to a block of transcription elongation. Using site-directed mutagenesis, we created three templates that either strengthened or weakened the proposed hairpin structures. The mutated and wild-type templates were clone...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00150a034
更新日期:1992-09-08 00:00:00
abstract::Treatment of human lymphoid cells with methyl methanesulfonate (MMS) results in discontinuities in cellular DNA. Discontinuities can be detected by sedimentation through neutral sucrose gradients after digestion with S1 nuclease on top of the gradient and by benzoylated naphthoylated diethylaminoethylcellulose (BND-ce...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00639a024
更新日期:1977-10-04 00:00:00
abstract::The X-ray crystal structures of the complexes of the recombinant kringle 1 domain of human plasminogen (Klpg) with the ligands epsilon-aminocaproic acid (EACA) and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA), which are representative of a class of in vivo antifibrinolytic agents, have been determined at...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9521351
更新日期:1996-02-27 00:00:00
abstract::We have studied the structure of the CuB site in the binuclear heme-copper center of the fully oxidized form of the quinol-oxidizing cytochrome aa3-600 from Bacillus subtilis by EXAFS and ENDOR spectroscopy. This enzyme is member of the large superfamily of heme-copper respiratory oxidases, which catalyze the reductio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00032a019
更新日期:1995-08-15 00:00:00
abstract::O-Aryloxycarbonyl hydroxamates have previously been shown to efficiently inactivate class C β-lactamases by cross-linking serine and lysine residues in the active site. A new analogue of these inhibitors, D-(R)-O-(phenoxycarbonyl)-N-[(4-amino-4-carboxy-1-butyl)oxycarbonyl]hydroxylamine, designed to inactivate certain ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01149
更新日期:2015-12-22 00:00:00
abstract::The effects of structural modifications of the flavin mononucleotide (FMN) prosthetic group of Clostridium pasteurianum flavodoxin on the kinetics of electron transfer to the oxidized form (from 5-deazariboflavin semiquinone produced by laser flash photolysis) and from the semiquinone form (to horse heart cytochrome c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00281a034
更新日期:1983-06-07 00:00:00
abstract::The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201181q
更新日期:2011-10-18 00:00:00
abstract::The EcoRV restriction/modification system consists of two enzymes that recognize the DNA sequence GATATC. The EcoRV restriction endonuclease cleaves DNA at this site, but the DNA of Escherichia coli carrying the EcoRV system is protected from this reaction by the EcoRV methyltransferase. However, in vitro, the EcoRV n...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00500a003
更新日期:1990-12-04 00:00:00
abstract::The specific deamidation of asparagine-71 of triosephosphate isomerase increases upon substrate binding and catalysis. This deamidation at the dimer interface initiates subunit dissociation, unfolding, and protein degradation. The apparent connection between catalysis and terminal marking supports the concept of "mole...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00188a027
更新日期:1994-06-07 00:00:00
abstract::Calmodulin (CaM) is composed of two EF-hand domains tethered by a flexible linker. Upon Ca2+-binding, a fragment of CaM encompassing EF-hands 2 and 3 (CaM2/3; residues 46-113) folds into a structure remarkably similar to the N- and C-domains of CaM. In this study, we demonstrate that Ca2+-ligated CaM2/3 can also bind ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700265j
更新日期:2007-07-24 00:00:00
abstract::The effect of anions on the stability of different functional conformations of Hb is examined through the determination of the dependence of O(2) affinity on water activity (a(w)). The control of a(w) is effected by varying the sucrose osmolal concentration in the bathing solution according to the "osmotic stress" met...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9905361
更新日期:1999-09-07 00:00:00
abstract::Inexpensive, straightforward, and rapid medical diagnostics are becoming increasingly important for disease identification in time- and resource-limited settings. Previous attempts to link oligonucleotide-based aptamers and hammerhead ribozymes to form ligand-induced ribozymes have been successful in identifying a var...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00523
更新日期:2018-08-28 00:00:00
abstract::The activation of adenosine-5'-monophosphate aminohydrolase from rabbit skeletal muscle by H+ has been demonstrated. Evidence is presented which indicates that the binding of H+ and K+ is linked, in that the dissociation constant (KA) for K+ activation is reduced as the pH is lowered. Concomitantly, the pK of several ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00641a013
更新日期:1977-11-01 00:00:00
abstract::Some ascidians sequester vanadium and other metal ions that are bound and transported in higher organisms by transferrin. The ascidian Ciona intestinalis has a monolobal transferrin (nicatransferrin) in its plasma. The binding of vanadium(V) to nicatransferrin was investigated by using isothermal titration calorimetry...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901630j
更新日期:2009-12-15 00:00:00
abstract::The ligation state of hemoglobin during its cross-linking by glycolaldehyde influences the ultimate oxygen affinity of the cross-linked protein. Thus, if the cross-linking is performed with carbonmonoxy-hemoglobin, the oxygen affinity increases slightly to a P50 of 7 mmHg from a P50 of 9 mmHg for unmodified hemoglobin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00417a064
更新日期:1988-08-23 00:00:00
abstract::One of the distinctive features of eubacterial retinal-based proton pumps, proteorhodopsins, xanthorhodopsin, and others, is hydrogen bonding of the key aspartate residue, the counterion to the retinal Schiff base, to a histidine. We describe properties of the recently found eubacterium proton pump from Exiguobacteriu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi300409m
更新日期:2012-07-24 00:00:00
abstract::We have examined the ability of the Escherichia coli single-stranded DNA binding protein (SSB) tetramer to form its different binding modes on poly(dC), poly(U), and poly(A) over a range of NaCl and NaF concentrations for comparison with previous studies with poly(dT). In reverse titrations with poly(U) and poly(A) at...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00186a016
更新日期:1994-05-24 00:00:00