当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase.

Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase.

Abstract：

:Photolyases reverse the effects of UV light on cells by converting cyclobutane dipyrimidine photoproducts (pyrimidine dimers, Pyr mean value of Pyr) into pyrimidine monomers in a light-dependent reaction. Previous work has suggested that, based on substrate preference, there are two classes of photolyase: DNA photolyase as exemplified by the Escherichia coli enzyme, and RNA photolyases found in plants such as Nicotiana tabacum and Phaseolus vulgaris. In experiments aimed at identifying substrate determinants, including the pentose ring, for binding and catalysis by E. coli DNA photolyase we tested several Pyr mean value of Pyr. We found that the enzyme has relative affinities for photodimers of T mean value of T greater than or equal to U mean value of T greater than U mean value of U much greater than C mean value of C and that the E-FADH2 form of the enzyme repairs these dimers at 366 nm with absolute quantum yields of 0.9 (T mean value of T), 0.8 (U mean value of T), 0.6 (U mean value of U), and 0.05 (C mean value of C). The enzyme also repairs an isolated thymine dimer and the synthetic substrate, 1,1'-trimethylene-bis (thymine) cyclobutane dimer. Unexpectedly, we found that this enzyme, previously thought to be specific for DNA, repairs uracil cyclobutane dimers in poly(rU). The affinity of photolyase for a uracil dimer in RNA is about 10(4)-fold lower than that for a U mean value of U in DNA; however, once bound, the enzyme repairs the photodimer with the same quantum yield whether the dimer is in ribonucleoside or deoxyribonucleoside form.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Kim ST,Sancar A

doi

10.1021/bi00099a019

subject

Has Abstract

pub_date

1991-09-03 00:00:00

pages

8623-30

issue

35

eissn

0006-2960

issn

1520-4995

journal_volume

30

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Elimination of the disulfide bridge in the Rieske iron-sulfur protein allows assembly of the [2Fe-2S] cluster into the Rieske protein but damages the ubiquinol oxidation site in the cytochrome bc1 complex.

    abstract：:The [2Fe-2S] cluster of the Rieske iron-sulfur protein is held between two loops of the protein that are connected by a disulfide bridge. We have replaced the two cysteines that form the disulfide bridge in the Rieske protein of Saccharomyces cerevisiae with tyrosine and leucine, and tyrosine and valine, to evaluate t...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi035344r

    authors： Merbitz-Zahradnik T,Zwicker K,Nett JH,Link TA,Trumpower BL

    更新日期：2003-11-25 00:00:00

  • Synthetic charybdotoxin-iberiotoxin chimeric peptides define toxin binding sites on calcium-activated and voltage-dependent potassium channels.

    abstract：:Charybdotoxin (ChTX) and iberiotoxin (IbTX) are highly charged peptidyl toxins which exhibit 68% sequence identity and share a similar three-dimensional structure. Despite these structural similarities, IbTX and ChTX differ in their selectivity for two types of potassium channels; large conductance calcium-activated p...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00060a030

    authors： Giangiacomo KM,Sugg EE,Garcia-Calvo M,Leonard RJ,McManus OB,Kaczorowski GJ,Garcia ML

    更新日期：1993-03-09 00:00:00

  • 2H and 31P NMR study of the interaction of general anesthetics with phosphatidylcholine membranes.

    abstract：:The effect of the general anesthetics alpha-chloralose and chloral hydrate as well as the nonanesthetic beta-chloralose on the order of phosphatidylcholine and phosphatidylcholine-cholesterol liposomes has been examined by 2H nuclear magnetic resonance. Chloral hydrate interacts with the hydrophilic head-group region,...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00346a019

    authors： Forrest BJ,Mattai J

    更新日期：1985-12-03 00:00:00

  • Minor groove orientation for the (1S,2R,3S,4R)-N2- [1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanosyl adduct in the N-ras codon 12 sequence.

    abstract：:The conformation of the trans-anti-(1S,2R,3S,4R)-N(2)-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanosyl adduct in d(G(1)G(2)C(3)A(4)G(5)X(6)T(7)G(8)G(9)T(10)G(11)).d(C(12)A(13)C(14)C(15)A(16)C(17)C(18)T(19)G(20)C(21)C(22)), bearing codon 12 of the human N-ras protooncogene (underlined), was ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi020462k

    authors： Kim HY,Wilkinson AS,Harris CM,Harris TM,Stone MP

    更新日期：2003-03-04 00:00:00

  • High-sensitivity scanning calorimetric study of mixtures of cholesterol with dimyristoyl- and dipalmitoylphosphatidylcholines.

    abstract：:A highly sensitive and stable scanning microcalorimeter is employed in a reinvestigation of the effect of cholesterol on multilamellar suspensions of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC). Below 20 mol % cholesterol the DPPC mixtures give heat-capacity curves each of which can...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00605a034

    authors： Mabrey S,Mateo PL,Sturtevant JM

    更新日期：1978-06-13 00:00:00

  • The effect of Mn2+ and Co2+ on the activities of a zinc metallodipeptidase from a mouse ascites tumor.

    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

    authors： Patterson EK,Gatmaitan JS,Hayman S

    更新日期：1975-09-23 00:00:00

  • Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme.

    abstract：:Group I intron RNAs contain a core of highly conserved helices flanked by peripheral domains that stabilize the core structure. In the Tetrahymena group I ribozyme, the P4, P5, and P6 helices of the core pack tightly against a three-helix subdomain called P5abc. Chemical footprinting and the crystal structure of the T...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi982113p

    authors： Doherty EA,Herschlag D,Doudna JA

    更新日期：1999-03-09 00:00:00

  • NMR study of isoleucine transfer RNA from Thermus thermophilus.

    abstract：:An NMR and nuclear Overhauser effect (NOE) analysis of Thermus thermophilus tRNAIle1a is presented. This species contains modifications including s2T54 and s4U8 [Horie, N., Hara-Yokoyama, M., Yokoyama, S., Watanabe, K., Kuchino, Y., Nishimura, S., & Miyazawa, T. (1985) Biochemistry 24, 5711-5715]. All the expected sec...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00355a010

    authors： Choi BS,Redfield AG

    更新日期：1986-04-08 00:00:00

  • Characterization of unique DNA-binding and transcriptional-activation functions in the carboxyl-terminal extension of the zinc finger region in the human vitamin D receptor.

    abstract：:The vitamin D receptor (VDR) binds 1,25-dihydroxyvitamin D(3) and mediates its actions on gene transcription by heterodimerizing with retinoid X receptors (RXRs) on direct repeat (DR+3) vitamin D responsive elements (VDREs) located in target genes. The VDRE binding function of VDR has been primarily ascribed to the zi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9916574

    authors： Hsieh JC,Whitfield GK,Oza AK,Dang HT,Price JN,Galligan MA,Jurutka PW,Thompson PD,Haussler CA,Haussler MR

    更新日期：1999-12-07 00:00:00

  • Deletion of the Mitochondrial Protein VWA8 Induces Oxidative Stress and an HNF4α Compensatory Response in Hepatocytes.

    abstract：:von Willebrand A domain-containing protein 8 (VWA8) is a poorly characterized, mitochondrial matrix-targeted protein with an AAA ATPase domain and ATPase activity that increases in livers of mice fed a high-fat diet. This study was undertaken to use CRISPR/Cas9 to delete VWA8 in cultured mouse hepatocytes and gain ins...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b00863

    authors： Luo M,Willis WT,Coletta DK,Langlais PR,Mengos A,Ma W,Finlayson J,Wagner GR,Shi CX,Mandarino LJ

    更新日期：2019-12-10 00:00:00

  • Energetics of internal GU mismatches in ribooligonucleotide helixes.

    abstract：:Thermodynamic parameters of helix formation were measured spectroscopically for 16 oligoribonucleotides containing either internal GU mismatches or the corresponding AU pairs. Internal GU mismatches stabilize each helix, but not as much as the corresponding AU pairs. The differences in the enthalpy and entropy changes...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00367a061

    authors： Sugimoto N,Kierzek R,Freier SM,Turner DH

    更新日期：1986-09-23 00:00:00

  • Analyzing topography of membrane-inserted diphtheria toxin T domain using BODIPY-streptavidin: at low pH, helices 8 and 9 form a transmembrane hairpin but helices 5-7 form stable nonclassical inserted segments on the cis side of the bilayer.

    abstract：:Low pH-induced membrane insertion by diphtheria toxin T domain is crucial for A chain translocation into the cytoplasm. To define the membrane topography of the T domain, the exposure of biotinylated Cys residues to the cis and trans bilayer surfaces was examined using model membrane vesicles containing a deeply inser...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi049354j

    authors： Rosconi MP,Zhao G,London E

    更新日期：2004-07-20 00:00:00

  • Glutathione Directly Intercepts DNA Radicals To Inhibit Oxidative DNA-Protein Cross-Linking Induced by the One-Electron Oxidation of Guanine.

    abstract：:Oxidative DNA damage can lead to cancer, and as enzymatic DNA repair systems become compromised during the aging process, the role of exogenous antioxidants becomes more critical. Here, we examined whether such non-enzymatic DNA repair can be effected by the common cellular antioxidant glutathione, investigating both ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b00697

    authors： Safaeipour M,Jauregui J,Castillo S,Bekarian M,Esparza D,Sanchez M,Stemp EDA

    更新日期：2019-11-19 00:00:00

  • Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by phosphonate monoesters.

    abstract：:The class C serine beta-lactamase of Enterobacter cloacae P99 was inhibited by a series of aryl methylphosphonate monoester monoanions. The effectiveness of these inhibitors was promoted by an acylamido substituent on the methyl group and a good leaving group at phosphorus. The former preference suggests that noncoval...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00140a024

    authors： Rahil J,Pratt RF

    更新日期：1992-06-30 00:00:00

  • Exchange mechanisms for hydrogen bonding protons of cytidylic and guanylic acids.

    abstract：:The pH dependence of buffer catalysis of exchange of the C-4 amino protons of cyclic cytosine 2',3'-monophosphate (cCMP) and the N-1 proton of cyclic guanosine 2',3'-monophosphate (cGMP) conforms to an exchange mechanism, in which protonation of the nucleobases at C(N-3) AND G(N-7) establishes the important intermedia...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00608a035

    authors： McConnell B

    更新日期：1978-07-25 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

  • Energetics of coiled coil folding: the nature of the transition states.

    abstract：:Coiled coils are simple models for studying the association of two polypeptide chains to form a folded protein. Previous work has shown that the folding of a coiled coil can be described by a two-state transition between two unfolded monomeric peptide chains and a folded coiled coil dimer. Here we report the thermodyn...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi002161l

    authors： Bosshard HR,Dürr E,Hitz T,Jelesarov I

    更新日期：2001-03-27 00:00:00

  • Surface proton donors for the D-pathway of cytochrome c oxidase in the absence of subunit III.

    abstract：:The major proton-transfer pathway into the buried active site of cytochrome c oxidase (CcO) is the D-pathway that begins with the subunit I residue Asp-132 on the inner protein surface (the cytoplasmic surface of the aa3-type CcO of Rhodobacter sphaeroides). Asp-132 is surrounded by residues from both subunits I and I...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0605843

    authors： Adelroth P,Hosler J

    更新日期：2006-07-11 00:00:00

  • Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding.

    abstract：:Applications of sensitive new technologies, in particular, two-dimensional NMR spectroscopy, have allowed detection of folded structures in short peptide fragments of proteins in aqueous solution under conditions where native proteins fold. These structures are in rapid dynamic exchange with unfolded states. These obs...

    journal_title：Biochemistry

    pub_type： 杂志文章,评审

    doi：10.1021/bi00419a001

    authors： Wright PE,Dyson HJ,Lerner RA

    更新日期：1988-09-20 00:00:00

  • Evidence that catalysis by yeast inorganic pyrophosphatase proceeds by direct phosphoryl transfer to water and not via a phosphoryl enzyme intermediate.

    abstract：:In this work, we show that adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S) is a substrate for yeast inorganic pyrophosphatase (PPase) (EC 3.6.1.1) and further, using chirally labeled [gamma-17O,18O]ATP gamma S, that enzyme-catalyzed hydrolysis to produce chiral inorganic thio[17O,18O]phosphate proceeds with inversio...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00300a002

    authors： Gonzalez MA,Webb MR,Welsh KM,Cooperman BS

    更新日期：1984-02-28 00:00:00

  • Role of proximal His93 in nitric oxide binding to metmyoglobin. Application of continuum solvation in Monte Carlo protein simulations.

    abstract：:Monte Carlo protein simulations with continuum solvation were used to explore the conformational mobility of NO within the active site of metmyoglobin. To the best of our knowledge this is the first application of a continuum solvation model for exploring protein binding sites. The usefulness of the Monte Carlo confor...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi981611v

    authors： Keserü GM,Menyhárd DK

    更新日期：1999-05-18 00:00:00

  • Investigating the cause of the alkaline transition of phytocyanins.

    abstract：:The phytocyanins are a family of plant cupredoxins that have been subdivided into the stellacyanins, plantacyanins, and uclacyanins. All of these proteins possess the typical type 1 His(2)Cys equatorial ligand set at their mononuclear copper sites, but the stellacyanins have an axial Gln ligand in place of the weakly ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi048256v

    authors： Harrison MD,Yanagisawa S,Dennison C

    更新日期：2005-03-01 00:00:00

  • Site-directed mutagenesis of intersubunit boundary residues in histidine decarboxylase, a pH-dependent allosteric enzyme.

    abstract：:Histidine decarboxylase (HDC) from Lactobacillus 30a forms a trimer around a central cavity or well. Three active sites are formed around the well at the interface of each of two adjacent molecules. HDC exhibits cooperative kinetics at pH 7.6 and can be described in terms of a two-state, T and R, model. At pH 4.8, pro...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00018a009

    authors： Pishko EJ,Potter KA,Robertus JD

    更新日期：1995-05-09 00:00:00

  • An Efficient Viologen-Based Electron Donor to Nitrogenase.

    abstract：:Nitrogenase catalyzes the reduction of N2 to NH3, supporting all biological nitrogen fixation. Electron donors to this enzyme are ferredoxin or flavodoxin (in vivo) and sodium dithionite (in vitro). Features of these electron donors put a limit on spectrophotometric studies and electrocatalytic applications of nitroge...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.9b00844

    authors： Badalyan A,Yang ZY,Hu B,Luo J,Hu M,Liu TL,Seefeldt LC

    更新日期：2019-11-19 00:00:00

  • Reactivity at the substrate activation site of yeast pyruvate decarboxylase: inhibition by distortion of domain interactions.

    abstract：:The residue C221 on pyruvate decarboxylase (EC. 4.1.1.1) from Saccharomyces cerevisiae has been shown to be the site where the substrate activation cascade is triggered [Baburina et al. (1994) Biochemistry 33, 5630-5635] and is located on the beta domain [Arjunan et al. (1996) J. Mol. Biol. 256, 590], while the active...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9709912

    authors： Baburina I,Dikdan G,Guo F,Tous GI,Root B,Jordan F

    更新日期：1998-02-03 00:00:00

  • Molecular Basis for Fe(III)-Independent Curcumin Potentiation of Cystic Fibrosis Transmembrane Conductance Regulator Activity.

    abstract：:Curcumin potentiates the phosphorylation-dependent activity of human cystic fibrosis transmembrane conductance regulator (CFTR) in Fe(3+)-dependent and Fe(3+)-independent manners. Although the Fe(3+)-dependent curcumin potentiation results from removal of endogenous inhibitory Fe(3+) at the interface of the regulatory...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.5b00219

    authors： Wang G

    更新日期：2015-05-12 00:00:00

  • A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain.

    abstract：:The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spectroscopy and restrained molecular dynamics. The molecule contained the highly conserved modification ribothymidine at its naturally occurring position. The ribothymidine-modified T Psi C stem-loop is the product of the m...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi990118w

    authors： Koshlap KM,Guenther R,Sochacka E,Malkiewicz A,Agris PF

    更新日期：1999-07-06 00:00:00

  • Hydrolysis of tri- and monoacylglycerol by lipoprotein lipase: evidence for a common active site.

    abstract：:The relationship between triacylglycerol and monoacylglycerol hydrolyzing activities of purified rat heart lipoprotein lipase was studied using emulsified trioleoylglycerol and micellar or albumin-bound monooleoylglycerol as substrates. The maximal reaction rates obtained with the two substrates were similar (650 and ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00654a017

    authors： Twu JS,Nilsson-Ehle P,Schotz MC

    更新日期：1976-05-04 00:00:00

  • Deamidation Slows Curli Amyloid-Protein Aggregation.

    abstract：:Nonenzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the majo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.7b00241

    authors： Wang H,Shu Q,Frieden C,Gross ML

    更新日期：2017-06-13 00:00:00

  • Formation of radiation-induced cross-links between thymine and tyrosine: possible model for cross-linking of DNA and proteins by ionizing radiation.

    abstract：:A model for radiation-induced cross-linking of DNA and proteins has been developed. It is based on initial formation of free radicals on a DNA base, i.e., thymine, and on an amino acid, i.e., tyrosine. It was demonstrated that interaction of these radicals is highly favored as measured by their kinetics and the cross-...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00322a034

    authors： Simic MG,Dizdaroglu M

    更新日期：1985-01-01 00:00:00