Abstract:
:Restrictocin and related fungal endoribonucleases from the α-sarcin family site-specifically cleave the sarcin/ricin loop (SRL) on the ribosome to inhibit translation and ultimately trigger cell death. Previous studies showed that the SRL folds into a bulged-G motif and tetraloop, with restrictocin achieving a specificity of ∼1000-fold by recognizing both motifs only after the initial binding step. Here, we identify contacts within the protein-RNA interface and determine the extent to which each one contributes to enzyme specificity by examining the effect of protein mutations on the cleavage of the SRL substrate compared to a variety of other RNA substrates. As with other biomolecular interfaces, only a subset of contacts contributes to specificity. One contact of this subset is critical, with the H49A mutation resulting in quantitative loss of specificity. Maximum catalytic activity occurs when both motifs of the SRL are present, with the major contribution involving the bulged-G motif recognized by three lysine residues located adjacent to the active site: K110, K111, and K113. Our findings support a kinetic proofreading mechanism in which the active site residues H49 and, to a lesser extent, Y47 make greater catalytic contributions to SRL cleavage than to suboptimal substrates. This systematic and quantitative analysis begins to elucidate the principles governing RNA recognition by a site-specific endonuclease and may thus serve as a mechanistic model for investigating other RNA modifying enzymes.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Plantinga MJ,Korennykh AV,Piccirilli JA,Correll CCdoi
10.1021/bi1018336subject
Has Abstractpub_date
2011-04-12 00:00:00pages
3004-13issue
14eissn
0006-2960issn
1520-4995journal_volume
50pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::The role of acetylation on the conformation and association state of the inner core histone octamer isolated from HeLa cells was examined. Preparation of suitable quantities of pure acetylated and control inner core histones from HeLa cells required the development of a new preparative procedure. The results from size...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00384a041
更新日期:1987-05-19 00:00:00
abstract::Overall activation volumes for multistep reactions are not usually pressure independent. The present investigation gives a quantitative description of this effect under Theory. Simple relations are obtained which can easily be applied to experimental data and which allow more insight into the dynamics of enzyme reacti...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00405a024
更新日期:1988-03-08 00:00:00
abstract::Phosphorylation by ATP of E.*Ca2 (sarcoplasmic reticulum vesicles (SRV) with bound 45Ca2+) during 5-10 ms leads to the occlusion of 2 *Ca2+/EPtot [quench by ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) alone] in both "empty" (10 microM free Ca2+in) or "loaded" SRV (20-40 mM free Ca2+in)...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00408a041
更新日期:1988-04-19 00:00:00
abstract::The beta-glucosidase from Agrobacterium sp. catalyzes the hydrolysis of beta-glucosides via a covalent alpha-D-glucopyranosyl-enzyme intermediate involving Glu358. Hydrolysis of 2,4-dinitrophenyl beta-D-glucopyranoside by the low activity Glu358Asp mutant of Agrobacterium beta-glucosidase is accompanied by time-depend...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00044a033
更新日期:1995-11-07 00:00:00
abstract::One way to improve the economic feasibility of biomass conversion is to enhance the catalytic efficiency of cellulases through protein engineering. This requires that high-resolution structures of cellulases be available. Here we present the structure of E2cd, the catalytic domain of the thermophilic endocellulase E2 ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00089a006
更新日期:1993-09-28 00:00:00
abstract::A conserved, crystallographically defined bile acid binding site was originally identified in the membrane domain of mammalian and bacterial cytochrome c oxidase (CcO). Current studies show other amphipathic molecules including detergents, fatty acids, steroids, and porphyrins bind to this site and affect the already ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi3014505
更新日期:2013-02-26 00:00:00
abstract::The fluorescence of Eu(III) is used to study the nature of the Ca(II) binding sites in the central cavity of the two-zinc(II) insulin hexamer. The dependence of the Eu(III) fluorescence lifetime upon Eu(III) stoichiometry indicates that there are three identical Eu(III) binding sites present in the two-zinc(II) insuli...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00328a028
更新日期:1985-03-26 00:00:00
abstract::Lysine-146 of rabbit muscle aldolase (D-fructose-1,6-biphosphate aldolase, EC 4.1.2.13) is absolutely conserved in class I (Schiff base) aldolases and has been implicated previously in catalysis by protein modification. Site-directed mutagenesis was used to change lysine-146 to alanine, glutamine, leucine, or histidin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00206a036
更新日期:1994-10-11 00:00:00
abstract::Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that degrades the fatty acid amide family of signaling lipids, including the endocannabinoid anandamide. Genetic or pharmacological inactivation of FAAH leads to analgesic, anti-inflammatory, anxiolytic, and antidepressant phenotypes in rodents without s...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701378g
更新日期:2007-11-13 00:00:00
abstract::Islet-activating protein (IAP), pertussis toxin, is a hexameric protein composed of an A protomer and a B oligomer, the residual pentamer having such a subunit assembly that two different dimers, dimer 1 and dimer 2, are connected with each other by means of the smallest C subunit. Incubation of IAP with formaldehyde ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00354a025
更新日期:1986-03-25 00:00:00
abstract::The light harvesting 1 antenna (LH1) complex from Rhodobacter sphaeroides funnels excitation energy to the photosynthetic reaction center. Our ultimate goal is to build up the structure of LH1 from structures of its individual subunits, much as the antenna can self-assemble from its components in membrane-mimicking de...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011576j
更新日期:2002-01-08 00:00:00
abstract::Choline oxidase catalyzes the oxidation of choline to glycine betaine through a two-step, four-electron reaction with betaine aldehyde as an intermediate. Oxygen is the final electron acceptor. Alcohol oxidation is initiated by the removal of the substrate hydroxyl proton by an unknown active site residue with a pKa v...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi500982y
更新日期:2015-01-20 00:00:00
abstract::Hepatic microsomal NADPH-cytochrome P-450 reductase was solubilized from rabbit liver microsomes in the presence of detergents and purified to homogeneity by column chromatography. The purified reductase had a molecular weight of 78 000 and contained 1 mol each of FAD and FMN per mol of enzyme. On reduction with NADPH...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00604a032
更新日期:1978-05-30 00:00:00
abstract::We have studied the effects of site-directed mutations in Escherichia coli nitrate reductase A (NarGHI) on heme reduction by a menaquinol analogue (menadiol) using the stopped-flow method. For NarGHI(H66Y) and NarGHI(H187Y), both lacking heme b(L) but having heme b(H), the heme reduction by menadiol is abolished. For ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0350856
更新日期:2003-12-09 00:00:00
abstract::We have studied the tridecadeoxynucleotide CGCGAATTACGCG (I), which contains an additional A at position 9 compared to the dodecanucleotide of which the crystal structure has been determined. Sequence I exhibits no distinct melting curve and also has a concentration-dependent pattern of peaks on reverse-phase chromato...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00371a025
更新日期:1986-11-18 00:00:00
abstract::The association of membrane and cytoplasmic proteins with the cytoskeleton of resting and activated platelets was studied. Glycoproteins were identified by labeling with 125I-labeled lectins (concanavalin A, wheat germ agglutinin, and Lens culinaris). Polypeptides, which are embedded in the lipid bilayer, have been id...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00537a002
更新日期:1982-04-13 00:00:00
abstract::Specific lysine residues on the ubiquitin surface were selected during the course of evolution to form different polyubiquitin chain structures that signal diverse cellular processes. A vast number of ubiquitin receptors specifically recognize and decode the signals conferred by these polyubiquitin chains. The mechani...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00498
更新日期:2015-08-04 00:00:00
abstract::The respiratory chain in the cytochrome d deficient mutant Escherichia coli GR19N is a relatively simple, linear system consisting of primary dehydrogenases, ubiquinone 8, cytochrome b-556, and cytochrome o oxidase. By use of right-side-out and inside-out membrane vesicles from this strain, various oxidase activities ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00357a004
更新日期:1986-05-06 00:00:00
abstract::The X-ray crystal structure of human soluble epoxide hydrolase (sEH) has been determined at 2.6 A resolution, revealing a domain-swapped quaternary structure identical to that observed for the murine enzyme [Argiriadi, M. A., Morisseau, C., Hammock, B. D., and Christianson, D. W. (1999) Proc. Natl. Acad. Sci. U.S.A. 9...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi036189j
更新日期:2004-04-27 00:00:00
abstract::The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201092q
更新日期:2011-11-22 00:00:00
abstract::The binding of Sp1 transcription factor to DNA is considered a potential target for small ligands designed to interfere with gene transcription. We attempted to distinguish the direct inhibition of the Sp1-binding to DNA in vivo (cell culture) from more indirect effects due to the network of pathways that modulate cel...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi036185e
更新日期:2004-06-15 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::In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understood. Here, we use evolutionary sequence variation in the α-lytic protease (αLP) p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00720
更新日期:2021-01-26 00:00:00
abstract::The structure/function properties of functional groups in the leadzyme have been studied by assaying the activity of analog ribozymes generated by the systematic substitution of modified nucleotides in the internal loop region of the ribozyme. Guanosine analogs introduced at positions 4 and 7 occupied by guanosine in ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi962219p
更新日期:1997-03-18 00:00:00
abstract::The distribution of one-disulfide bonds in the two-disulfide intermediates in the oxidative refolding of bovine pancreatic ribonuclease A has been characterized. These two-disulfide intermediates were formed from the fully reduced denatured protein by oxidation with dithiothreitol, then blocked with AEMTS, purified by...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990570f
更新日期:1999-06-01 00:00:00
abstract::The ability of avian-specific linker histone H5, and the globular domains of H5 (GH5) and H1(0) (GH1(0), to self-associate either free in solution or when bound to DNA was investigated. All three proteins underwent a salt-dependent increase in turbidity that may be indicative of nonspecific interactions. Dithiobis(suc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi980716v
更新日期:1998-09-08 00:00:00
abstract::It has been suggested that the down-regulation of hepatic HMG-CoA reductase by dietary cholesterol requires modification of the cholesterol molecule before it can exert its suppressive action. In a recent study [Lund, E., Breuer, O., & Björkhem, I. (1992) J. Biol. Chem. 267, 25092-25097], we showed that side-chain hyd...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00167a038
更新日期:1994-01-11 00:00:00
abstract::The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800134y
更新日期:2008-07-15 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::Modification of pig kidney fructose-1,6-bisphosphatase with 2,3-butanedione in borate buffer (pH 7.8) leads to the loss of the activation of the enzyme by monovalent cations, as well as to the loss of allosteric adenosine 5'-monophosphate (AMP) inhibition. In agreement with the results obtained for the butanedione mod...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00661a017
更新日期:1976-08-10 00:00:00