当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Yeast pol eta holds a cis-syn thymine dimer loosely in the active site during elongation opposite the 3'-T of the dimer, but tightly opposite the 5'-T.

Yeast pol eta holds a cis-syn thymine dimer loosely in the active site during elongation opposite the 3'-T of the dimer, but tightly opposite the 5'-T.

Abstract：

:Polymerase eta is a member of the Y family of DNA polymerases which is able to bypass thymine dimers efficiently and in a relatively error-free manner. To elucidate the mechanism of dimer bypass, the efficiency of dAMP and pyrene nucleotide insertion opposite the thymine dimer and its N3-methyl derivatives was determined. Pol eta inserts pyrene nucleotide with greater efficiency than dAMP opposite the 3'-T of an undimerized or dimerized T and is an effective inhibitor of DNA synthesis by pol eta. Substitution of the N3H of the 3'-T of an undimerized T or a dimerized T with a methyl group has little effect on the insertion efficiency of pyrene nucleotide but greatly inhibits the insertion of dAMP. Together, these results suggest that the error-free insertion of dAMP opposite the 3'-T of the cis-syn thymine dimer happens by way of a loosely held dimer in the active site which can be displaced from the active site by pyrene nucleotide. In contrast, pol eta cannot insert pyrene nucleotide opposite the 5'-T of the dimer, whereas it can insert dAMP with efficiency comparable to that opposite the 3'-T. The inability to insert pyrene nucleotide opposite the 5'-T of the dimer is consistent with the idea that while the polymerase binds loosely to a templating nucleotide, it binds tightly to the nucleotide to its 3'-side. Overall, the results show a marked difference from similar studies on pol I family polymerases, and suggest mechanisms by which this Y family polymerase can process damaged DNA efficiently.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Sun L,Zhang K,Zhou L,Hohler P,Kool ET,Yuan F,Wang Z,Taylor JS

doi

10.1021/bi0345687

subject

Has Abstract

pub_date

2003-08-12 00:00:00

pages

9431-7

issue

31

eissn

0006-2960

issn

1520-4995

journal_volume

42

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Gangliosides as markers of cortisone-sensitive and cortisone-resistant rabbit thymocytes: characterization of thymus-specific gangliosides and preferential changes of particular gangliosides in the thymus of cortisone-treated rabbits.

    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

    authors： Iwamori M,Kiguchi K,Kanno J,Kitagawa M,Nagai Y

    更新日期：1986-02-25 00:00:00

  • HIV-1 protease: characterization of a catalytically competent enzyme-substrate intermediate.

    abstract：:The steady-state and pre-steady-state kinetic parameters for the interaction of E with the fluorogenic substrate 2-aminobenzoyl-Thr-Ile-Nle-Phe(p-NO(2))-Gln-Arg-NH(2) were determined in 1.25 M NaCl, 0.1 M MES-TRIS at pH 6.0 at 25 degrees C. At low concentrations of enzyme, the values of the K(m) and k(cat) calculated ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0116543

    authors： Porter DJ,Hanlon MH,Furfine ES

    更新日期：2002-01-29 00:00:00

  • Procatalytic ligand strain. Ionization and perturbation of 8-nitroxanthine at the urate oxidase active site.

    abstract：:The binding of the inhibitor 8-nitroxanthine to urate oxidase has been investigated by Raman and UV-visible absorption spectroscopy. The absorption maximum of 8-nitroxanthine shifts from 380 to 400 nm upon binding to the enzyme, demonstrating that the electronic structure of the ligand is perturbed. It has been propos...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0507837

    authors： Doll C,Bell AF,Power N,Tonge PJ,Tipton PA

    更新日期：2005-08-30 00:00:00

  • Serum Amyloid P Component (SAP) Interactome in Human Plasma Containing Physiological Calcium Levels.

    abstract：:The pentraxin serum amyloid P component (SAP) is secreted by the liver and found in plasma at a concentration of approximately 30 mg/L. SAP is a 25 kDa homopentamer known to bind both protein and nonprotein ligands, all in a calcium-dependent manner. The function of SAP is unclear but likely involves the humoral innat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.6b01027

    authors： Poulsen ET,Pedersen KW,Marzeda AM,Enghild JJ

    更新日期：2017-02-14 00:00:00

  • Effect of protein hydration on receptor conformation: decreased levels of bound water promote metarhodopsin II formation.

    abstract：:Neutral solutes were used to investigate the effects of osmotic stress both on the ability of rhodopsin to undergo its activating conformation change and on acyl chain packing in the rod outer segment (ROS) disk membrane. The equilibrium concentration of metarhodopsin II (MII), the conformation of photoactivated rhodo...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi990634m

    authors： Mitchell DC,Litman BJ

    更新日期：1999-06-15 00:00:00

  • Analysis of membrane-binding properties of dermaseptin analogues: relationships between binding and cytotoxicity.

    abstract：:To understand relationships between membrane-binding properties of cytolytic peptides and resulting cytotoxicity, we investigated interactions of dermaseptin analogues with model bilayers by means of surface plasmon resonance. First, we tested the system by comparing two native dermaseptins, S1 and S4, whose binding p...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi034514x

    authors： Gaidukov L,Fish A,Mor A

    更新日期：2003-11-11 00:00:00

  • Structural studies of acetylated and control inner core histones.

    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

    authors： Prevelige PE Jr,Fasman GD

    更新日期：1987-05-19 00:00:00

  • Molecular basis for the inhibition of HMGA1 proteins by distamycin A.

    abstract：:The molecular mechanism for the displacement of HMGA1 proteins from DNA is integral to disrupting their cellular function, which is linked to many metastatic cancers. Chemical shift and NOESY NMR experiments provide structural evidence for the displacement of an AT hook peptide (DNA binding motif of HMGA1 proteins) by...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi200822c

    authors： Smith AE,Buchmueller KL

    更新日期：2011-09-27 00:00:00

  • Differential scanning calorimetric study of the thermal unfolding of mutant forms of phage T4 lysozyme.

    abstract：:In two recent papers, we reported the effects of several point mutations on the thermodynamics of the thermal unfolding of the lysozyme of phage T4 as determined by differential scanning calorimetry. The mutants studied were R96H [Kitamura, S., & Sturtevant, J.M. (1989) Biochemistry 28, 3788-3792] and T157 replaced by...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00121a009

    authors： Hu CQ,Kitamura S,Tanaka A,Sturtevant JM

    更新日期：1992-02-18 00:00:00

  • Enzymatic assembly of epothilones: the EpoC subunit and reconstitution of the EpoA-ACP/B/C polyketide and nonribosomal peptide interfaces.

    abstract：:The biosynthesis of epothilones, a family of hybrid polyketide (PK)/nonribosomal peptide (NRP) antitumor agents, provides an ideal system to study a hybrid PK/NRP natural product with significant biomedical value. Here the third enzyme involved in epothilone production, the five domain 195 kDa polyketide synthase (PKS...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi020006w

    authors： O'Connor SE,Chen H,Walsh CT

    更新日期：2002-04-30 00:00:00

  • Interaction of profilin with G-actin and poly(L-proline).

    abstract：:The interaction of bovine spleen profilin with ATP- and ADP-G-actin and poly(L-proline) has been studied by spectrofluorimetry, analytical ultracentrifugation, and rapid kinetics in low ionic strength buffer. Profilin binding to G-actin is accompanied by a large quenching of tryptophan fluorescence, allowing the measu...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00194a011

    authors： Perelroizen I,Marchand JB,Blanchoin L,Didry D,Carlier MF

    更新日期：1994-07-19 00:00:00

  • Mechanism of inactivation of human leukocyte elastase by a chloromethyl ketone: kinetic and solvent isotope effect studies.

    abstract：:The mechanism of inactivation of human leukocyte elastase (HLE) by the chloromethyl ketone MeOSuc-Ala-Ala-Pro-Val-CH2Cl was investigated. The dependence of the first-order rate constant for inactivation on concentration of chloromethyl ketone is hyperbolic and suggests formation of a reversible "Michaelis complex" pri...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00367a011

    authors： Stein RL,Trainor DA

    更新日期：1986-09-23 00:00:00

  • Multiple enzyme activities of Escherichia coli MutT protein for sanitization of DNA and RNA precursor pools.

    abstract：:8-OxoGua (8-oxo-7,8-dihydroguanine) is produced in nucleic acids as well as in nucleotide pools of cells, by reactive oxygen species normally formed during cellular metabolic processes. MutT protein of Escherichia coli specifically degrades 8-oxoGua-containing deoxyribo- and ribonucleoside triphosphates to correspondi...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi047550k

    authors： Ito R,Hayakawa H,Sekiguchi M,Ishibashi T

    更新日期：2005-05-03 00:00:00

  • One-Enzyme Reverse Transcription qPCR Using Taq DNA Polymerase.

    abstract：:Taq DNA polymerase, one of the first thermostable DNA polymerases to be discovered, has been typecast as a DNA-dependent DNA polymerase commonly employed for PCR. However, Taq polymerase belongs to the same DNA polymerase superfamily as the Molony murine leukemia virus reverse transcriptase and has in the past been sh...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/acs.biochem.0c00778

    authors： Bhadra S,Maranhao AC,Paik I,Ellington AD

    更新日期：2020-12-15 00:00:00

  • Characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons.

    abstract：:In Sphingomonas CHY-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (PAHs) composed of up to five rings. The components of this enzyme were separately purified and characterized. The oxygenase component (ht-PhnI) was shown to contain one R...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0611311

    authors： Jouanneau Y,Meyer C,Jakoncic J,Stojanoff V,Gaillard J

    更新日期：2006-10-10 00:00:00

  • In silico mutation of cysteine residues in the ligand-binding domain of an N-methyl-D-aspartate receptor.

    abstract：:The precise nature of redox modulation of N-methyl-d-aspartate (NMDA) receptors is still unclear, although it is thought to be related to the formation and breaking of disulfide bonds. Recent structural data demonstrated the way in which disulfide bonds in the ligand-binding core of the NR1 subunit are arranged. Howev...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi061462d

    authors： Kaye SL,Sansom MS,Biggin PC

    更新日期：2007-02-27 00:00:00

  • Specific stimulation of the T7 gene 6 exonuclease by the phage T7 coded deoxyribonucleic acid binding protein.

    abstract：:Bacteriophage T7 codes for a single-stranded DNA binding protein. This protein is the product of gene 2.5 and has been found previously to stimulate specifically the activity of the phage-coded DNA polymerase. We report here that the T7 DNA binding protein also stimulates the activity of the phage-coded exonuclease. T...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00266a042

    authors： Roberts L,Sadowski P,Wong JT

    更新日期：1982-11-09 00:00:00

  • Mechanistic and stereochemical studies of glycine oxidase from Bacillus subtilis strain R5.

    abstract：:Glycine oxidase gene from a strain of Bacillus subtilis was cloned and expressed in Escherichia coli. The purified enzyme was found, by mass spectrometry, to have a protein M(r) of 40763 (value of 40761.6 predicted from DNA sequence) and a FAD prosthetic group M(r) of 785.1 (theoretical value of 785.5). Glycine oxidas...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi100553n

    authors： Jamil F,Gardner QA,Bashir Q,Rashid N,Akhtar M

    更新日期：2010-08-31 00:00:00

  • Kinetic, spectroscopic, and X-ray crystallographic characterization of the functional E151H aminopeptidase from Aeromonas proteolytica.

    abstract：:Glutamate151 (E151) has been shown to be catalytically essential for the aminopeptidase from Vibrio proteolyticus (AAP). E151 acts as the general acid/base during the catalytic mechanism of peptide hydrolysis. However, a glutamate residue is not the only residue capable of functioning as a general acid/base during cat...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi0505823

    authors： Bzymek KP,Moulin A,Swierczek SI,Ringe D,Petsko GA,Bennett B,Holz RC

    更新日期：2005-09-13 00:00:00

  • Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit.

    abstract：:F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, bet...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi052592+

    authors： Boltz KW,Frasch WD

    更新日期：2006-09-19 00:00:00

  • Chromomycin dimer-DNA oligomer complexes. Sequence selectivity and divalent cation specificity.

    abstract：:This paper reports on a solution NMR characterization of the sequence selectivity and metal ion specificity in chromomycin-DNA oligomer complexes in the presence of divalent cations. The sequence selectivity studies have focused on chromomycin complexes with the self-complementary d(A1-A2-G3-G4-C5-C6-T7-T8) duplex con...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00501a012

    authors： Gao XL,Patel DJ

    更新日期：1990-12-11 00:00:00

  • Analysis of peptides for helical prediction.

    abstract：:Two terminally blocked peptides, acetylAETAAAKFLRQHMamide and acetylAETSSSRYLRQHMamide, were obtained by solid-phase synthesis, purified by reversed-phase chromatography, and characterized by fast atom bombardment mass spectrometry. Both peptides were soluble in aqueous solutions and remained monomeric over the concen...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00427a048

    authors： Merutka G,Stellwagen E

    更新日期：1989-01-10 00:00:00

  • Regulatory mechanisms of tumor suppressor P16(INK4A) and their relevance to cancer.

    abstract：:P16(INK4A) (also known as P16 and MTS1), a protein consisting exclusively of four ankyrin repeats, is recognized as a tumor suppressor mainly because of the prevalence of genetic inactivation of the p16(INK4A) (or CDKN2A) gene in virtually all types of human cancers. However, it has also been shown that an elevated le...

    journal_title：Biochemistry

    pub_type： 杂志文章,评审

    doi：10.1021/bi200642e

    authors： Li J,Poi MJ,Tsai MD

    更新日期：2011-06-28 00:00:00

  • Conformational characteristics of luliberin. Luminescence properties at liquid-nitrogen temperature.

    abstract：:The luminescence properties (fluorescence and phosphorescence) of luliberin have been investigated at liquid-nitrogen temperature (77 K) in 50% ethylene glycolaqueous buffer at various pH's. Calculation of the energy-transfer efficiency between Trp and Tyr residues leads to an evaluation of the distance separating the...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00671a009

    authors： Marche P,Montenay-Garestier T,Fromageot P,Hélène C

    更新日期：1976-12-28 00:00:00

  • Either the carboxyl- or the amino-terminal region of the human ecto-ATPase (E-NTPDase 2) confers detergent and temperature sensitivity to the chicken ecto-ATP-diphosphohydrolase (E-NTPDase 8).

    abstract：:Human ecto-ATPase (E-NTPDase 2) and chicken ecto-ATP-diphosphohydrolase (E-NTPDase 8) are cell surface nucleotidases with two transmembranous domains, one each at the N- and C-termini. Hydrolysis of substrates occurs in active sites residing in their extracellular domains. Human ecto-ATPase activity is decreased by NP...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi050019k

    authors： Mukasa T,Lee Y,Knowles AF

    更新日期：2005-08-23 00:00:00

  • Sequence-selective topoisomerase II inhibition by anthracycline derivatives in SV40 DNA: relationship with DNA binding affinity and cytotoxicity.

    abstract：:Topoisomerase II mediated double-strand breaks produced by anthracycline analogues were studied in SV40 DNA. The compounds included doxorubicin, daunorubicin, two doxorubicin stereoisomers (4'-epimer and beta-anomer), and five chromophore-modified derivatives, with a wide range of cytotoxic activity and DNA binding af...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00454a033

    authors： Capranico G,Zunino F,Kohn KW,Pommier Y

    更新日期：1990-01-16 00:00:00

  • Identification of unfolding domains in large proteins by their unfolding rates.

    abstract：:Three unfolding domains in rabbit muscle aldolase destabilized in 3 M urea have been identified from their unfolding rate constants (0.10, 0.036, and 0.0064 min-1). The populations of folded and various, partially unfolded forms were determined by amide hydrogen exchange and mass spectrometry. Results of this study sh...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi972711o

    authors： Deng Y,Smith DL

    更新日期：1998-05-05 00:00:00

  • Metal ion activator effects on intrinsic isotope effects for hydride transfer from decarboxylation in the reaction catalyzed by the NAD-malic enzyme from Ascaris suum.

    abstract：:The mechanism of the oxidative decarboxylation reaction catalyzed by the NAD-malic enzyme from Ascaris suum has been examined with several different divalent metal ion activators and dinucleotide substrates. Primary deuterium and tritium isotope effects have been obtained and, in combination with the partitioning rati...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00010a015

    authors： Karsten WE,Gavva SR,Park SH,Cook PF

    更新日期：1995-03-14 00:00:00

  • Nativelike intermediate on the unfolding pathway of pig kidney fructose-1,6-bisphosphatase.

    abstract：:The unfolding and dissociation of the tetrameric enzyme fructose-1,6-bisphosphatase from pig kidney by guanidine hydrochloride have been investigated at equilibrium by monitoring enzyme activity, ANS binding, intrinsic (tyrosine) protein fluorescence, exposure of thiol groups, fluorescence of extrinsic probes (AEDANS,...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi034203m

    authors： Reyes AM,Ludwig HC,Yañez AJ,Rodríguez PH,Slebe JC

    更新日期：2003-06-17 00:00:00

  • Vicinal dithiol-disulfide distribution in the Escherichia coli mannitol specific carrier enzyme IImtl.

    abstract：:Escherichia coli mannitol specific EII in membrane vesicles can be inhibited by the action of the oxidizable substrate-reduced phenazine methosulfate (PMS) in a manner similar to E. coli enzyme IIGlc [Robillard, G. T., & Konings, W. (1981) Biochemistry 20, 5025-5032]. The fact that reduced PMS and various oxidizing ag...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00297a006

    authors： Roossien FF,Robillard GT

    更新日期：1984-01-17 00:00:00