Abstract：
:Some aminoacyl-tRNA synthetases (AARSs) employ an editing mechanism to ensure the fidelity of protein synthesis. Leucyl-tRNA synthetase (LeuRS), isoleucyl-tRNA synthetase (IleRS), and valyl-tRNA synthetase (ValRS) share a common insertion, called the CP1 domain, which is responsible for clearing misformed products. This discrete domain is connected to the main body of the enzyme via two beta-strand tethers. The CP1 hydrolytic editing active site is located approximately 30 A from the aminoacylation active site in the canonical core of the enzyme, requiring translocation of mischarged amino acids for editing. An ensemble of crystal and cocrystal structures for LeuRS, IleRS, and ValRS suggests that the CP1 domain rotates via its flexible beta-strand linkers relative to the main body along various steps in the enzyme's reaction pathway. Computational analysis suggested that the end of the N-terminal beta-strand acted as a hinge. We hypothesized that a molecular hinge could specifically direct movement of the CP1 domain relative to the main body. We introduced a series of mutations into both beta-strands in attempts to hinder movement and alter fidelity of LeuRS. Our results have identified specific residues within the beta-strand tethers that selectively impact enzyme activity, supporting the idea that beta-strand orientation is crucial for LeuRS canonical core and CP1 domain functions.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Mascarenhas AP,Martinis SAdoi
10.1021/bi702494qsubject
Has Abstractpub_date
2008-04-22 00:00:00pages
4808-16issue
16eissn
0006-2960issn
1520-4995journal_volume
47pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:The mechanism of the argininosuccinate lyase reaction has been probed by the measurement of the effects of isotopic substitution at the reaction centers. A primary deuterium isotope effect of 1.0 on both V and V/K is obtained with (2S,3R)-argininosuccinate-3-d, while a primary 15N isotope effect on V/K of 0.9964 +/- 0...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00365a004
更新日期：1986-08-26 00:00:00
abstract：:Neutral glycosphingolipids and gangliosides in rabbit thymus, spleen, bone marrow, and erythrocyte ghosts were analyzed by conventional chemical and enzymatic procedures and negative ion fast atom bombardment mass spectrometry (FABMS). Thymus gangliosides showed a characteristic composition. Major gangliosides compris...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00352a023
更新日期：1986-02-25 00:00:00
abstract：:The kinetic parameters (kpol, Kd app) for all possible correct and incorrect pairing between the A, T, G, and C bases were determined for wild-type (WT) rat DNA polymerase beta (pol beta) and the R283A mutant under pre-steady-state kinetic assay conditions. The base substitution fidelities of these two proteins were t...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi961653o
更新日期：1997-02-04 00:00:00
abstract：:PT-ACRAMTU ([PtCl(en)(ACRAMTU-S)](NO(3))(2), en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) is a cytotoxic platinum-acridine conjugate previously shown to form adducts with the N3 endocyclic nitrogen of adenine in the DNA minor groove. This unusual observation and our prior det...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi050745n
更新日期：2005-08-23 00:00:00
abstract：:A general understanding of how cytochromes evolve within a fixed structure to optimize redox potential for specific bioenergetic processes does not exist. Toward this end, a library approach is used to investigate the range and distribution of redox potential which occurs when all sequence space available through muta...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0001675
更新日期：2000-05-23 00:00:00
abstract：:The solvent accessibility of thrombin in its substrate-free and substrate-bound forms has been compared by amide hydrogen/deuterium (H/(2)H) exchange. The optimized inhibitor peptide dPhe-Pro-Arg chloromethyl ketone (PPACK) was used to simulate the substrate-bound form of thrombin. These studies were motivated by the ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0499718
更新日期：2004-05-11 00:00:00
abstract：:Soluble inorganic pyrophosphatase (PPase) is one of the better understood phosphoryl-transfer enzymes and is distinctive in having four divalent metal ions at the active site. Here we determine pH profiles for wild-type Saccharomyces cerevisiae PPase (Y-PPase) and for 14 of its active site variants and consider the ef...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi971771r
更新日期：1998-02-17 00:00:00
abstract：:Soluble guanylate cyclase isolated from bovine and rat lung is a heterodimeric hemoprotein composed of alpha1 and beta1 subunits. The heme binding region has been localized to residues 1-385 of the beta1 subunit [beta1(1-385)], while the catalytic site(s) have been localized to the C-terminal region of sGC. There are ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi972686m
更新日期：1998-03-31 00:00:00
abstract：:S-Adenosylmethionine decarboxylase is a pyruvate-dependent enzyme. The enzyme forms a Schiff base with substrate, S-adenosylmethionine, through the pyruvoyl moiety. This facilitates the release of CO2 from the substrate, which must then be protonated on the alpha carbon in order to permit hydrolysis of the Schiff base...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9825201
更新日期：1999-02-23 00:00:00
abstract：:A detailed kinetic analysis of the catalytic trimer of aspartate transcarbamoylase containing the active site substitution H134A was performed to investigate the role of His 134 in the catalytic mechanism. Replacement of histidine by alanine resulted in decreases in the affinities for the two substrates, carbamoyl pho...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00143a031
更新日期：1992-07-21 00:00:00
abstract：:We investigated the dependence of certain properties of bile salt/lecithin mixed micelles on the molar ratio of the two components. UV absorption suggested that the micellar system is fundamentally altered on passing through a bile salt:lecithin molar ratio of 1.8:1. Differential scanning calorimetry confirmed this tr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00505a029
更新日期：1981-01-20 00:00:00
abstract：:The increase of the proton motive force mediated by bacteriorhodopsin is compared to the intracellular ATP concentration under steady-state illumination. The membrane potential was measured via the accumulation of the lipophilic ion [14C]triphenylmethylphosphonium and the pH gradient via the accumulation of the weak a...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00561a012
更新日期：1980-09-30 00:00:00
abstract：:The human immunodeficiency virus utilizes its gp41 fusion protein to mediate virus-cell membrane fusion. The conserved disulfide loop region in the gp41 hairpin conformation reverses the protein chain, such that the N-terminal heptad repeat and the C-terminal heptad repeat regions interact to form the six-helix bundle...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi300868f
更新日期：2012-09-04 00:00:00
abstract：:Phosphofructokinase from Escherichia coli (EcPFK) is a homotetramer with four active sites and four allosteric sites. Understanding the allosteric activation of EcPFK by MgADP has been complicated by the complex web of possible interactions, including active site homotropic interactions, allosteric site homotropic int...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi048569q
更新日期：2004-11-09 00:00:00
abstract：:Aminoglycoside 2''-phosphotransferase IVa [APH(2'')-IVa] is a member of a family of bacterial enzymes responsible for medically relevant resistance to antibiotics. APH(2'')-IVa confers high-level resistance against several clinically used aminoglycoside antibiotics in various pathogenic Enterococcus species by phospho...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200747f
更新日期：2011-07-19 00:00:00
abstract：:1-Bromovinyl (I), Z-2-bromovinyl (II), 1,2-dibromoethyl (III), and a series of 4-(halomethyl)-2-nitrophenyl (IVa-c) diethyl phosphate esters were examined as substrates and mechanism-based inhibitors for the bacterial phosphotriesterase. All of these compounds were found to act as substrates for the enzyme. Inhibitor ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi970680r
更新日期：1997-07-22 00:00:00
abstract：:A Ca(2+)-activated thiol protease was purified from Drosophila melanogaster. The procedure involves Phenyl-Sepharose, Reactive Red-Agarose and Q-Sepharose fast flow (or MonoQ) chromatographic steps. The enzyme eluting from Q-Sepharose fast flow seems to be homogeneous as judged by silver staining on SDS-PAGE: it consi...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00150a012
更新日期：1992-09-08 00:00:00
abstract：:An improved procedure for the preparation of cobalt-cytochrome c has been developed. Various factors influencing the cobalt insertion process are discussed. The optical spectra of cobalt-cytochrome c suggest a six-coordinated species. The spectral shifts occurring with oxidation-reduction are compared with those obser...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00687a003
更新日期：1975-08-12 00:00:00
abstract：:(Z)-3-(Fluoromethyl)phosphoenolpyruvate has been synthesized in nine chemical steps from glyoxylic acid. The compound is stable at pH 3, but at pH 8 it decomposes within seconds to give 2-oxo-3-butenoate. When 3-(fluoromethyl)phosphoenolpyruvate is added to a solution of phosphoenolpyruvate carboxylase or pyruvate kin...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00404a039
更新日期：1988-02-23 00:00:00
abstract：:The highly processive motor, myosin V, has an extremely long neck containing six calmodulin-binding IQ motifs that allows it to take multiple 36 nm steps corresponding to the pseudo-repeat of actin. To further investigate how myosin V moves processively on actin filaments, we altered the length of the neck by adding o...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0512086
更新日期：2005-12-13 00:00:00
abstract：:The effect of RNA secondary structure on the kinetics of DNA synthesis catalyzed by HIV-1 RT was determined using a 66 nucleotide RNA template containing a stable 12 base pair hairpin structure. Prior to reaching the hairpin structure, the primer elongation by RT was fast and the kinetics of polymerization was not aff...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi971217h
更新日期：1997-10-14 00:00:00
abstract：:Electrophilic halogenating agents, including hypohalous acids and haloamines, oxidize free methionine and the N-terminal methionines of peptides and proteins (e.g., Met-1 of anti-inflammatory peptide 1 and ubiquitin) to produce dehydromethionine (a five-membered isothiazolidinium heterocycle). Amide derivatives of met...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901343d
更新日期：2009-11-24 00:00:00
abstract：:The DNA of Novikoff hepatoma ascites cells was found to contain a 3.6-megadalton EcoRI restriction fragment, referred to as EcoRI fragment A (Parker et al., 1979). C0t analyses demonstrated an enrichment of fragment A sequences in Novikoff hepatoma genome relative to normal rat liver DNA. This fragment was cloned in l...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00507a017
更新日期：1981-02-17 00:00:00
abstract：:Maduropeptin (MDP) is a recently isolated antitumor antibiotic, consisting of an enediyne-containing chromophore embedded in a highly acidic protein. This holoantibiotic damages duplex DNA in vitro, producing a mixture of single- and double-strand breaks at selected sites. The chromophore, isolated as the methanol add...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00036a035
更新日期：1995-09-12 00:00:00
abstract：:Because of the conflicting conclusions that have been reached regarding the location of the two putative membrane-spanning segments from cysteine 911 through isoleucine 929 and from isoleucine 946 through cysteine 964 in the alpha subunit of native ovine Na+/K(+)-transporting ATPase, the disposition of lysine 943 with...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00029a027
更新日期：1995-07-25 00:00:00
abstract：:Steric constraints in the retinal binding pocket of sensory rhodopsin I (SR-I) are analyzed by studying effects of sample temperature and retinal analogs. The flash-induced yield of the earliest detected intermediate S610, which corresponds to the K intermediate in the bacteriorhodopsin (BR) photocycle, decreases belo...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00089a044
更新日期：1993-09-28 00:00:00
abstract：:Despite significant progress in the elucidation of the genetic basis of early-onset familial Alzheimer's disease (AD), the etiology of sporadic cases remains elusive. Although certain genetic loci play a role in conferring susceptibility in some sporadic AD cases, it is likely that the etiology is multifactorial; henc...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi000029f
更新日期：2000-05-23 00:00:00
abstract：:The micellar properties of mixed, bovine gangliosides and purified galactosyl-N-acetylacetylgalactosaminyl (N-acetylneuraminyl) galactosylglucosylceramide were studied by gel filtration, equilibrium dialysis, and band and boundary centrifugation in sucrose gradients. The dissociation of micelles is very slow (days) in...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00573a028
更新日期：1979-03-20 00:00:00
abstract：:Interaction between aggregates of amyloid beta protein (Abeta) and membranes has been hypothesized by many to be a key event in the mechanism of neurotoxicity associated with Alzheimer's disease (AD). Proposed membrane-related mechanisms of neurotoxicity include ion channel formation, membrane disruption, changes in m...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9006397
更新日期：2009-09-22 00:00:00
abstract：:We have used time-resolved phosphorescence anisotropy to investigate the effects of essential light chain (ELC) isoforms (A1 and A2) on the interaction of skeletal muscle myosin with actin, to relate structural dynamics to previously reported functional effects. Actin was labeled with a phosphorescent probe at C374, a...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi3014467
更新日期：2013-03-05 00:00:00
