当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.

Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.

Abstract：

:In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ability to form the regular Watson-Crick pairing with a thymine residue. Therefore, a DNA dodecamer with the sequence d(CGCGmo(6)AATTCGCG) has been synthesized and its crystal structure determined. The methoxylation has no significant effect on the overall DNA conformation, which is that of a standard B-form duplex. The methoxylated adenine moieties adopt the amino tautomer with an anti conformation around the C(6)-N(6) bond to the N(1) atom, and they form a Watson-Crick base-pair with thymine residues on the opposite strand, similar to an unmodified adenine residue. It is concluded that methoxylated adenine can present two alternate faces for base-pairing, thanks to the amino<-->imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Chatake T,Hikima T,Ono A,Ueno Y,Matsuda A,Takénaka A

doi

10.1006/jmbi.1999.3304

keywords:

subject

Has Abstract

pub_date

1999-12-17 00:00:00

pages

1223-30

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(99)93304-1

journal_volume

294

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.

    abstract：:HtrA (high-temperature requirement A) family proteins play important roles in protein-quality control processes in the bacterial periplasm. A common feature of all members of this family is their modular organization comprising a chymotrypsin-like protease domain and at least one PDZ (postsynaptic density of 95 kDa, d...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.06.023

    authors： Schubert A,Wrase R,Hilgenfeld R,Hansen G

    更新日期：2015-08-28 00:00:00

  • Crystal structure of human cyclin K, a positive regulator of cyclin-dependent kinase 9.

    abstract：:Cyclin K and the closely related cyclins T1, T2a, and T2b interact with cyclin-dependent kinase 9 (CDK9) forming multiple nuclear complexes, referred to collectively as positive transcription elongation factor b (P-TEFb). Through phosphorylation of the C-terminal domain of the RNA polymerase II largest subunit, distin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.057

    authors： Baek K,Brown RS,Birrane G,Ladias JA

    更新日期：2007-02-16 00:00:00

  • Crystal structure of the dog lipocalin allergen Can f 2: implications for cross-reactivity to the cat allergen Fel d 4.

    abstract：:The dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. Here, the first crystal structure of recombinant rCan f 2 at 1.45 A resolution displays a classical lipocalin fold with a conserved Gly-Xaa-Trp motif, in which Trp19 stabilizes the overall topology of the monomeric ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.05.043

    authors： Madhurantakam C,Nilsson OB,Uchtenhagen H,Konradsen J,Saarne T,Högbom E,Sandalova T,Grönlund H,Achour A

    更新日期：2010-08-06 00:00:00

  • Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site.

    abstract：:The grass Lolium perenne produces an ice-binding protein (LpIBP) that helps this perennial tolerate freezing by inhibiting the recrystallization of ice. Ice-binding proteins (IBPs) are also produced by freeze-avoiding organisms to halt the growth of ice and are better known as antifreeze proteins (AFPs). To examine th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.01.032

    authors： Middleton AJ,Marshall CB,Faucher F,Bar-Dolev M,Braslavsky I,Campbell RL,Walker VK,Davies PL

    更新日期：2012-03-09 00:00:00

  • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model.

    abstract：:In order to systematically analyze functionally relevant dynamical correlations within macromolecular complexes, we have developed computational methods based on the normal mode analysis of an elastic network model. First, we define two types of dynamical correlations (fluctuation-based and density-based), which are c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.12.020

    authors： Zheng W,Brooks B

    更新日期：2005-02-25 00:00:00

  • Effects of rifampicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli.

    abstract：:Rifampicin resistant (Rifr mutations map in the rpoB gene encoding the beta subunit of Escherichia coli RNA polymerase. We have used our collection of 17 sequenced Rifr mutations to investigate the involvement of E. coli RNA polymerase in the antitermination systems enhancing expression of delayed early lambda genes o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90573-6

    authors： Jin DJ,Cashel M,Friedman DI,Nakamura Y,Walter WA,Gross CA

    更新日期：1988-11-20 00:00:00

  • Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex.

    abstract：:The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding do...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.05.048

    authors： Sue SC,Cervantes C,Komives EA,Dyson HJ

    更新日期：2008-07-25 00:00:00

  • Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.

    abstract：:The X-ray crystal structure of a catalytic-site mutant EQ208 [Glu208-->Gln] of alpha-amylase from Bacillus subtilis cocrystallized with maltopentaose (G5) and acarbose has been determined by multiple isomorphous replacement at 2.5 A resolution. Restrained crystallographic refinement has resulted in an R-factor of 19.8...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1599

    authors： Fujimoto Z,Takase K,Doui N,Momma M,Matsumoto T,Mizuno H

    更新日期：1998-03-27 00:00:00

  • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein.

    abstract：:A simple continuum model of a de novo designed model of a four-helix bundle is presented. The thermodynamics and kinetics of the model are studied using Langevin simulations. We use a three-letter minimal off-lattice representation of a de novo designed four-helix bundle protein. The native state of the model, which c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0578

    authors： Guo Z,Thirumalai D

    更新日期：1996-10-25 00:00:00

  • Structure of a foreign peptide displayed on the surface of bacteriophage M13.

    abstract：:The use of filamentous bacteriophage M13 as a vehicle for display of foreign peptides and proteins provides a means for the construction of therapeutic, diagnostic and technological tools of broad utility. The usefulness of this technology is dependent on the ability of an inserted peptide to act as a ligand when fuse...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1489

    authors： Kishchenko G,Batliwala H,Makowski L

    更新日期：1994-08-12 00:00:00

  • Noncoding RNAs: Regulators of the Mammalian Transcription Machinery.

    abstract：:Transcription by RNA polymerase II (Pol II) is required to produce mRNAs and some noncoding RNAs (ncRNAs) within mammalian cells. This coordinated process is precisely regulated by multiple factors, including many recently discovered ncRNAs. In this perspective, we will discuss newly identified ncRNAs that facilitate ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.02.019

    authors： Eidem TM,Kugel JF,Goodrich JA

    更新日期：2016-06-19 00:00:00

  • Domain closure mechanism in transferrins: new viewpoints about the hinge structure and motion as deduced from high resolution crystal structures of ovotransferrin N-lobe.

    abstract：:The crystal structure of holo hen ovotransferrin N-lobe refined at 1.65 A resolution has been obtained. The final model gave an R-factor of 0.173 in the resolution range between 10.0 and 1.65 A. The comparison of the structure with previous high-resolution apo and Fe(3+)-loaded, domain-opened intermediate structures p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4719

    authors： Mizutani K,Mikami B,Hirose M

    更新日期：2001-06-15 00:00:00

  • Tests of the single-hit DNA damage model.

    abstract：:The algebra of target theory for damage by radiation was laid out by Atwood and Norman in 1949. Their equations provide a widely embraced framework for distinguishing single-hit and multi-hit mechanisms of damage. The present work asks whether in vitro damage to DNA duplexes by different agents affects amplification b...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.07.012

    authors： Spangler R,Goddard NL,Spangler DN,Thaler DS

    更新日期：2009-09-18 00:00:00

  • Integration host factor binds specifically to sites in the ilvGMEDA operon in Escherichia coli.

    abstract：:Integration host factor (IHF) of Escherichia coli is a histone-like protein that is involved both in site-specific recombination and in regulating the expression of a number of phage and bacterial genes. We have shown previously that transcription of the ilvGMEDA operon in E. coli is greatly reduced in IHF mutants. We...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90212-4

    authors： Tsui P,Freundlich M

    更新日期：1988-10-05 00:00:00

  • Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation.

    abstract：:Escherichia coli RecBCD is a DNA helicase/nuclease that functions in double-stranded DNA break repair. RecBCD possesses two motors (RecB, a 3' to 5' translocase, and RecD, a 5' to 3' translocase). Current DNA unwinding models propose that motor translocation is tightly coupled to base pair melting. However, some bioch...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.07.002

    authors： Simon MJ,Sokoloski JE,Hao L,Weiland E,Lohman TM

    更新日期：2016-07-31 00:00:00

  • Crystallization of a DNA duplex 15-mer containing unpaired bases: d(CGCGAAATTTACGCG).

    abstract：:Crystals of an almost self-complementary DNA 15-mer d(CGCGAAATTTACGCG) have been grown by the vapor diffusion technique at 4 degrees C. The space group is I222 with a = 37.3 A, b = 54.6 A and c = 104.8 A. Solution studies showed that the 15-mer forms a duplex with the extra adenine residue unpaired: (sequence; see tex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90503-1

    authors： Miller M,Wlodawer A,Appella E,Sussman JL

    更新日期：1987-06-20 00:00:00

  • Organization and evolution of a higher plant alphoid-like satellite DNA sequence.

    abstract：:Two recombinant plasmids containing, respectively, three and eight tandem repeats of a 177 base-pair (bp) element from radish nuclear DNA have been isolated. These plasmids were used as probes to investigate the organization and the copy number of this element within the genome. This sequence is present in congruent t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90329-3

    authors： Grellet F,Delcasso D,Panabieres F,Delseny M

    更新日期：1986-02-20 00:00:00

  • Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease.

    abstract：:Chagasin is a protein produced by Trypanosoma cruzi, the parasite that causes Chagas' disease. This small protein belongs to a recently defined family of cysteine protease inhibitors. Although resembling well-known inhibitors like the cystatins in size (110 amino acid residues) and function (they all inhibit papain-li...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.005

    authors： Ljunggren A,Redzynia I,Alvarez-Fernandez M,Abrahamson M,Mort JS,Krupa JC,Jaskolski M,Bujacz G

    更新日期：2007-08-03 00:00:00

  • Functional interplay between CBP and PCAF in acetylation and regulation of transcription factor KLF13 activity.

    abstract：:The transcriptional co-activators CBP/p300 and PCAF participate in transcriptional activation by many factors. We have shown that both CBP/p300 and PCAF stimulate the transcriptional activation by KLF13, a member of the KLF/Sp1 family, either individually or cooperatively. Here we further investigated how CBP and PCAF...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00429-7

    authors： Song CZ,Keller K,Chen Y,Stamatoyannopoulos G

    更新日期：2003-05-30 00:00:00

  • A continuum model for protein-protein interactions: application to the docking problem.

    abstract：:The prediction of protein-protein interactions in solution is a major goal of theoretical structural biology. Here, we implement a continuum description of the thermodynamic processes involved. The model differs considerably from previous models in its use of "molecular surface" area to describe the hydrophobic compon...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0375

    authors： Jackson RM,Sternberg MJ

    更新日期：1995-07-07 00:00:00

  • Crystallization and preliminary X-ray analysis of human alpha-galactosidase A complex.

    abstract：:Human alpha-galactosidase A (alpha-D-galactoside galactohydrolase; EC 3.2.1.22), the glycosylated lysosomal enzyme deficient in Fabry disease, has been crystallized as a complex with the inhibitor N-6-aminohexanoyl-alpha-D-galactopyranosylamine. The "hanging drop" method of vapor diffusion was used to grow crystals fr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1397

    authors： Murali R,Ioannou YA,Desnick RJ,Burnett RM

    更新日期：1994-06-17 00:00:00

  • Recognition and cleavage of the bacteriophage P1 packaging site (pac). II. Functional limits of pac and location of pac cleavage termini.

    abstract：:Bacteriophage P1 initiates the processive packaging of its DNA at a unique site called pac. We show that a functional pac site is contained within a 161 base-pair segment of P1 EcoRI fragment 20. It extends from a position 71 base-pairs to a position 232 base-pairs from the EcoRI-22 proximal side of that fragment. The...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90675-9

    authors： Sternberg N,Coulby J

    更新日期：1987-04-05 00:00:00

  • Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution.

    abstract：:Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution using MIR phases in combination with density modification (s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0526

    authors： Momany C,Ernst S,Ghosh R,Chang NL,Hackert ML

    更新日期：1995-10-06 00:00:00

  • Properties of chemically modified Ni(II)-Fe(II) hybrid hemoglobins. Ni(II) protoporphyrin IX as a model for a permanent deoxy-heme.

    abstract：:Chemical modifications, NES-Cys(beta 93), des-Arg(alpha 141), and both modifications on the same molecule, were made to Ni-Fe hybrid hemoglobins, and their effect on individual subunits was investigated by measuring oxygen equilibrium curves, the Fe(II)-N epsilon (His F8) stretching Raman lines, and light-absorption s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90368-2

    authors： Shibayama N,Morimoto H,Kitagawa T

    更新日期：1986-11-20 00:00:00

  • Structural changes common to catalysis in the Tpx peroxiredoxin subfamily.

    abstract：:Thiol peroxidases (Tpxs) are dimeric 2-Cys peroxiredoxins from bacteria that preferentially reduce alkyl hydroperoxides. Catalysis requires two conserved residues, the peroxidatic cysteine and the resolving cysteine, which are located in helix alpha(2) and helix alpha(3), respectively. The partial unraveling of helice...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.08.040

    authors： Hall A,Sankaran B,Poole LB,Karplus PA

    更新日期：2009-11-06 00:00:00

  • Specific heteromeric association of four transmembrane peptides derived from platelet glycoprotein Ib-IX complex.

    abstract：:As the receptor on the platelet surface for von Willebrand factor, glycoprotein (GP) Ib-IX complex is critically involved in hemostasis and thrombosis. How the complex is assembled from GP Ibalpha, GP Ib beta and GP IX subunits, all of which are type I transmembrane proteins, is not entirely clear. Genetic and mutatio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.07.037

    authors： Luo SZ,Li R

    更新日期：2008-10-03 00:00:00

  • Purification and secondary structure determination of simian immunodeficiency virus p27.

    abstract：:We have developed a novel method for the expression and purification of p27, the major core protein of simian immunodeficiency virus. Circular dichroism measurements of purified p27 were used to determine the relative amounts of alpha-helix, beta-sheet and unordered secondary structural elements. These empirically det...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80308-0

    authors： Burns NR,Craig S,Lee SR,Richardsons MH,Stenner N,Adams SE,Kingsman SM,Kingsman AJ

    更新日期：1990-11-20 00:00:00

  • Structurally similar but functionally diverse ZU5 domains in human erythrocyte ankyrin.

    abstract：:The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.01.041

    authors： Yasunaga M,Ipsaro JJ,Mondragón A

    更新日期：2012-04-06 00:00:00

  • Structural basis of interaction between urokinase-type plasminogen activator and its receptor.

    abstract：:Recent studies indicate that binding of the urokinase-type plasminogen activator (uPA) to its high-affinity receptor (uPAR) orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes, including wound healing, angiogenesis, inflammation, and cancer ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.08.063

    authors： Barinka C,Parry G,Callahan J,Shaw DE,Kuo A,Bdeir K,Cines DB,Mazar A,Lubkowski J

    更新日期：2006-10-20 00:00:00

  • The MCM Helicase Motor of the Eukaryotic Replisome.

    abstract：:The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.01.024

    authors： Abid Ali F,Costa A

    更新日期：2016-05-08 00:00:00