DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction.


:The ligation of a decadeoxynucleotide containing the EcoRI recognition site forms a series of multimers which appear to be curved based on observed anomalous gel migration in polyacrylamide gels. The degree of DNA curvature present in the recognition sequence, based upon the observed migration anomaly, can be altered by modifications to the purine functional groups at the 2- and 6-positions. Deletion of the guanine 2-amino group, occurring in the minor groove of the B-DNA helix, is most effective in increasing the observed DNA curvature. Conversely, the displacement of an amino group from the major groove to the minor groove eliminates curvature. DNA curvature is also modulated by the exocyclic group at the purine 6-position with decreasing curvature observed when changing the amino group to a carbonyl or proton substituent. Differences in the kinetic parameters characterizing the cleavage reaction by the endonuclease for many of the modified sequences are the result of modifications of functional groups in the major groove, which are likely to contact the endonuclease during catalysis. However, with two examples, significant decreases in the observed specificity constant (kcat/Km), characterizing the protein-nucleic acid interaction, cannot be easily explained in terms of such functional group contacts. It is more likely in these cases that the functional group modifications affect the efficiency of the endonuclease-DNA interaction by modulation of the structure of the double-stranded DNA helix. With both examples, modifications have been made to minor groove substituents. The extent of DNA curvature is increased significantly for one and decreased for the other, compared with that observed for the native recognition site. The results suggest that curvature of the DNA helix axis is an intrinsic property of the d(GAATTC) sequence which helps to optimize the protein-nucleic acid interactions observed for the EcoRI restriction endonuclease.


J Mol Biol


Diekmann S,McLaughlin LW




Has Abstract


1988-08-20 00:00:00














  • S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region.

    abstract::The region of the Escherichia coli 16 S ribosomal RNA recognized by the ribosomal protein S4 has been defined by assaying a set of 13 16 S rRNA fragments for S4 binding. The fragments were prepared by transcription in vitro, and binding constants were measured in three ways: retention of labeled RNA fragments on nitro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Vartikar JV,Draper DE

    更新日期:1989-09-20 00:00:00

  • Structure of short thick filaments from Limulus muscle.

    abstract::Shortened Limulus thick filaments, isolated from stimulated muscle, are structurally similar to long filaments, isolated from unstimulated muscle, except for length. Both have 3-fold screw symmetry with a helical repeat at approximately 43 nm, axial spacing of 14.5 nm between successive crowns of crossbridges and 4-fo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Levine RJ,Kensler RW

    更新日期:1985-03-20 00:00:00

  • Transcription of the xyl operon is controlled in Bacillus subtilis by tandem overlapping operators spaced by four base-pairs.

    abstract::The expression of xylose utilization in Bacillus subtilis is regulated at the level of transcription by xylose dependent Xyl repressor-xyl operator interaction. We have structurally and functionally characterized the binding sites of Xyl repressor in the xyl regulatory region. Methylation and hydroxyl radical protecti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Dahl MK,Degenkolb J,Hillen W

    更新日期:1994-10-28 00:00:00

  • Molecular evolution of the HBII-52 snoRNA cluster.

    abstract::HBII-52 is a human brain-specific C/D box snoRNA that potentially regulates the editing and/or alternative splicing of the serotonin receptor. Forty-two nearly identical copies of the HBII-52 gene are located immediately downstream of the SNRPN protein-coding gene in an imprinted locus associated with Prader-Willi syn...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Nahkuri S,Taft RJ,Korbie DJ,Mattick JS

    更新日期:2008-09-12 00:00:00

  • Conformational properties of the iso-1-cytochrome C denatured state: dependence on guanidine hydrochloride concentration.

    abstract::Production of seven single surface histidine variants of yeast iso-1-cytochrome c allowed measurement of the apparent pK(a), pK(a)(obs), for histidine-heme loop formation for loops of nine to 83 amino acid residues under varying denaturing conditions (2 M to 6 M guanidine hydrochloride, gdnHCl). A linear correlation b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wandschneider E,Bowler BE

    更新日期:2004-05-21 00:00:00

  • The 1.9 A resolution structure of phospho-serine 46 HPr from Enterococcus faecalis.

    abstract::The histidine-containing phosphocarrier protein HPr is a central component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species. In Gram-positive bacteria, phosphorylation of HPr at conserved serine 46 (P-Ser-HPr) p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Audette GF,Engelmann R,Hengstenberg W,Deutscher J,Hayakawa K,Quail JW,Delbaere LT

    更新日期:2000-11-03 00:00:00

  • Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthetase required for sporulation in Bacillus subtilis.

    abstract::Dipicolinic acid (DPA) is a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. Previous work has shown that mutations in the spoVF locus of Bacillus subtilis prevent the formation of DPA, a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Daniel RA,Errington J

    更新日期:1993-07-20 00:00:00

  • Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor.

    abstract::The prokaryotic transcription factors GreA and GreB are involved in the regulation of transcript elongation by RNA polymerase (RNAP). Their known activities include suppression of transcription arrest, enhancement of transcription fidelity, and facilitation of the transition from abortive initiation to productive elon...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Koulich D,Nikiforov V,Borukhov S

    更新日期:1998-02-20 00:00:00

  • Reconstituted and native iron-cores of bacterioferritin and ferritin.

    abstract::The structural and magnetic properties of the iron-cores of reconstituted horse spleen ferritin and Azotobacter vinelandii bacterioferritin have been investigated by high-resolution transmission electron microscopy, electron diffraction and Mossbauer spectroscopy. The structural properties of native horse spleen ferri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mann S,Williams JM,Treffry A,Harrison PM

    更新日期:1987-12-05 00:00:00

  • Two-dimensional crystallization of the light-harvesting complex from Rhodospirillum rubrum.

    abstract::Homogeneous detergent-solubilized B873 light-harvesting complexes from a carotenoid-less mutant of the purple non-sulfur bacterium, Rhodospirillum rubrum G9, were reassembled spontaneously into two-dimensional (2D) hexagonal arrays during extensive and controlled dialysis. As the complexes contain only 1 to 2 mol phos...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ghosh R,Hoenger A,Hardmeyer A,Mihailescu D,Bachofen R,Engel A,Rosenbusch JP

    更新日期:1993-05-20 00:00:00

  • Innate immune response to arenaviral infection: a focus on the highly pathogenic New World hemorrhagic arenaviruses.

    abstract::Arenaviruses are enveloped, negative-stranded RNA viruses that belong to the family Arenaviridae. This diverse family can be further classified into OW (Old World) and NW (New World) arenaviruses based on their antigenicity, phylogeny, and geographical distribution. Many of the NW arenaviruses are highly pathogenic vi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Koma T,Huang C,Kolokoltsova OA,Brasier AR,Paessler S

    更新日期:2013-12-13 00:00:00

  • STRA13 interacts with STAT3 and modulates transcription of STAT3-dependent targets.

    abstract::STRA13 is a pVHL-dependent bHLH transcription factor up-regulated on the mRNA level in multiple cancer cell lines and implicated recently in the regulation of immune cell homeostasis and autoimmunity. In searching for STRA13-interacting proteins with oncogenic potential by the yeast two-hybrid screening, we identified...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ivanova AV,Ivanov SV,Zhang X,Ivanov VN,Timofeeva OA,Lerman MI

    更新日期:2004-07-16 00:00:00

  • The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

    abstract::The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Baird-Titus JM,Clark-Baldwin K,Dave V,Caperelli CA,Ma J,Rance M

    更新日期:2006-03-10 00:00:00

  • Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.

    abstract::Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four memb...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kreusch A,Spraggon G,Lee CC,Klock H,McMullan D,Ng K,Shin T,Vincent J,Warner I,Ericson C,Lesley SA

    更新日期:2003-07-04 00:00:00

  • Site-directed mutants of RTP of Bacillus subtilis and the mechanism of replication fork arrest.

    abstract::DNA replication fork arrest during the termination phase of chromosome replication in Bacillus subtilis is brought about by the replication terminator protein (RTP) bound to specific DNA terminator sequences (Ter sites) distributed throughout the terminus region. An attractive suggestion by others was that crucial to ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Duggin IG,Andersen PA,Smith MT,Wilce JA,King GF,Wake RG

    更新日期:1999-03-12 00:00:00

  • Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain.

    abstract::An extensive computational analysis of available sequence and crystal structure data was used to identify functionally important residue interactions within the motor domain of the kinesin molecular motor. Principal component analysis revealed that all current kinesin crystal structures reside in one of two main confo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Grant BJ,McCammon JA,Caves LS,Cross RA

    更新日期:2007-05-18 00:00:00

  • Active-site properties of the oxidized and reduced C-terminal domain of DsbD obtained by NMR spectroscopy.

    abstract::The periplasmic C-terminal domain of the Escherichia coli DsbD protein (cDsbD) has a thioredoxin fold. The two cysteine residues in the CXXC motif serve as the reductant for the disulfide bond of the N-terminal domain which can in turn act as a reductant for various periplasmic partners. The resulting disulfide bond i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mavridou DA,Stevens JM,Ferguson SJ,Redfield C

    更新日期:2007-07-20 00:00:00

  • Human T cell cyclophilin18 binds to thiol-specific antioxidant protein Aop1 and stimulates its activity.

    abstract::Cyclophilins (CyPs) define a family of proteins binding to the immunosuppressive drug cyclosporin A (CsA). They are evolutionary highly conserved proteins being present in both pro- and eukaryotes and in different subcellular locations. CyPs possess enzymatic activity, namely peptidyl-prolyl cis-trans isomerase (PPIas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Jäschke A,Mi H,Tropschug M

    更新日期:1998-04-10 00:00:00

  • Transcriptional control of IS1 transposition in Escherichia coli.

    abstract::The movement of the bacterial insertion sequence IS1 often generates cointegrate structures in which donor and target replicons are connected by direct repeats of IS1. The experiments reported here were designed to understand how IS1 transposition is controlled. Our physical characterization of the structures of coint...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Biel SW,Adelt G,Berg DE

    更新日期:1984-04-05 00:00:00

  • The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity.

    abstract::Maltosyltransferase (MTase) from the hyperthermophile Thermotoga maritima represents a novel maltodextrin glycosyltransferase acting on starch and malto-oligosaccharides. It catalyzes the transfer of maltosyl units from alpha-1,4-linked glucans or malto-oligosaccharides to other alpha-1,4-linked glucans, malto-oligosa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Roujeinikova A,Raasch C,Burke J,Baker PJ,Liebl W,Rice DW

    更新日期:2001-09-07 00:00:00

  • Multiple sequence threading: an analysis of alignment quality and stability.

    abstract::Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Taylor WR

    更新日期:1997-06-27 00:00:00

  • High-resolution structure of the major periplasmic domain from the cell shape-determining filament MreC.

    abstract::Bacterial cell shape is dictated by the cell wall, a plastic structure that must adapt to growth and division whilst retaining its function as a selectively permeable barrier. The modulation of cell wall structure is achieved by a variety of enzymatic functions, all of which must be spatially regulated in a precise ma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lovering AL,Strynadka NCJ

    更新日期:2007-09-28 00:00:00

  • Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance.

    abstract::Two-dimensional nuclear Overhauser enhancement spectra are presented of the complex of lac repressor headpiece with a 14 base-pair lac operator fragment. Analysis of nuclear Overhauser enhancements observed between protein and DNA shows that the second helix of the headpiece ("the recognition helix") binds in the majo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Boelens R,Scheek RM,van Boom JH,Kaptein R

    更新日期:1987-01-05 00:00:00

  • MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca2+ Ion Bound at the Constriction Zone.

    abstract::The Gram-negative organism Campylobacter jejuni is the major cause of food poisoning. Unlike Escherichia coli, which has two major porins, OmpC and OmpF, C. jejuni has one, termed major outer membrane protein (MOMP) through which nutrients and antibiotics transit. We report the 2.1-Å crystal structure of C. jejuni MOM...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ferrara LGM,Wallat GD,Moynié L,Dhanasekar NN,Aliouane S,Acosta-Gutiérrez S,Pagès JM,Bolla JM,Winterhalter M,Ceccarelli M,Naismith JH

    更新日期:2016-11-06 00:00:00

  • Calcium supports loop closure but not catalysis in Rubisco.

    abstract::Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses CO(2) assimilation in biology. A prerequisite for catalysis is an activation process, whereby an active site lysine is selectively carbamylated. The carbamyl group is then stablised by a metal ion, which in vivo is Mg(2+). Other divalent metal ions ca...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Karkehabadi S,Taylor TC,Andersson I

    更新日期:2003-11-14 00:00:00

  • Evolution of protein binding modes in homooligomers.

    abstract::The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Dayhoff JE,Shoemaker BA,Bryant SH,Panchenko AR

    更新日期:2010-01-29 00:00:00

  • Crystal structure of the molecular chaperone HscA substrate binding domain complexed with the IscU recognition peptide ELPPVKIHC.

    abstract::HscA, a specialized bacterial Hsp70-class molecular chaperone, interacts with the iron-sulfur cluster assembly protein IscU by recognizing a conserved LPPVK sequence motif. We report the crystal structure of the substrate-binding domain of HscA (SBD, residues 389-616) from Escherichia coli bound to an IscU-derived pep...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cupp-Vickery JR,Peterson JC,Ta DT,Vickery LE

    更新日期:2004-09-24 00:00:00

  • E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase.

    abstract::NusG is an essential transcription factor in Escherichia coli that is capable of increasing the overall rate of transcription. Transcript elongation by RNA polymerase (RNAP) is frequently interrupted by pauses of varying durations, and NusG is known to decrease the occupancy of at least some paused states. However, it...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Herbert KM,Zhou J,Mooney RA,Porta AL,Landick R,Block SM

    更新日期:2010-05-28 00:00:00

  • Structural characterisation and comparison of the native and A-states of equine lysozyme.

    abstract::Native state 1H NMR resonance assignments for 125 of the 129 residues of equine lysozyme have enabled measurement of the hydrogen exchange kinetics for over 60 backbone amide and three tryptophan indole hydrogen atoms in the native state. Native holo equine lysozyme hydrogen exchange protection factors are as large as...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Morozova-Roche LA,Arico-Muendel CC,Haynie DT,Emelyanenko VI,Van Dael H,Dobson CM

    更新日期:1997-05-23 00:00:00

  • TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

    abstract::The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 fro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Dermoun Z,Foulon A,Miller MD,Harrington DJ,Deacon AM,Sebban-Kreuzer C,Roche P,Lafitte D,Bornet O,Wilson IA,Dolla A

    更新日期:2010-07-16 00:00:00