当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

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 addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

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

doi

10.1016/j.jmb.2005.12.007

keywords:

subject

Has Abstract

pub_date

2006-03-10 00:00:00

pages

1137-51

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(05)01567-6

journal_volume

356

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Preliminary X-ray crystallographic studies on alcohol dehydrogenase from Drosophila.

    abstract：:The alcohol dehydrogenase (ADHase) enzyme catalyses the oxidation of alcohols to aldehydes or ketones using NAD+ as a cofactor. Functional ADHase from Drosophila lebanonensis is a dimer, with a monomeric molecular weight of 27,000 and with 254 residues in each polypeptide chain. Crystals of the protein have been grown...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90705-o

    authors： Gordon EJ,Bury SM,Sawyer L,Atrian S,Gonzalez-Duarte R

    更新日期：1992-09-05 00:00:00

  • Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation.

    abstract：:The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.08.049

    authors： Li AY,Lee J,Borek D,Otwinowski Z,Tibbits GF,Paetzel M

    更新日期：2011-10-28 00:00:00

  • Prediction of functionally important residues based solely on the computed energetics of protein structure.

    abstract：:Catalytic and other functionally important residues in proteins can often be mutated to yield more stable proteins. Many of these residues are charged residues that are located in electrostatically unfavorable environments. Here it is demonstrated that because continuum electrostatics methods can identify these destab...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5009

    authors： Elcock AH

    更新日期：2001-09-28 00:00:00

  • The ATPase cycle of PcrA helicase and its coupling to translocation on DNA.

    abstract：:The superfamily 1 bacterial helicase PcrA has a role in the replication of certain plasmids, acting with the initiator protein (RepD) that binds to and nicks the double-stranded origin of replication. PcrA also translocates single-stranded DNA with discrete steps of one base per ATP hydrolyzed. Individual rate constan...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.07.071

    authors： Toseland CP,Martinez-Senac MM,Slatter AF,Webb MR

    更新日期：2009-10-02 00:00:00

  • Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: the requirements for assembly into the bacteriophage particle.

    abstract：:Filamentous bacteriophage assemble at the host membrane in a non-lytic process; the gene-3 minor coat protein (P3) is required for release from the membrane and subsequently, for recognition and infection of a new host. P3 contains at least three distinct domains: two N-terminal domains that mediate host recognition a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00950-1

    authors： Weiss GA,Roth TA,Baldi PF,Sidhu SS

    更新日期：2003-09-26 00:00:00

  • Phenotypic suppression by incorporation of an alien amino acid.

    abstract：:Azaleucine is a naturally occurring amino acid antibiotic that can be incorporated into proteins by mimicking leucine. In spite of its highly toxic character, the contrast between the hydrophobic side-chain of leucine and the basic side-chain of azaleucine suggested a mechanism for rescuing certain mutants. We constru...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1269

    authors： Lemeignan B,Sonigo P,Marlière P

    更新日期：1993-05-20 00:00:00

  • Characterization of novel proteins based on known protein structures.

    abstract：:The genome sciences face the challenge to characterize structure and function of a vast number of novel genes. Sequence search techniques are used to infer functional and structural information from similarities to experimentally characterized genes or proteins. The persistent goal is to refine these techniques and to...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3501

    authors： Koppensteiner WA,Lackner P,Wiederstein M,Sippl MJ

    更新日期：2000-03-03 00:00:00

  • 3D gene of foot-and-mouth disease virus. Conservation by convergence of average sequences.

    abstract：:The nucleotide sequence of the 3D (polymerase) gene of eight epidemiologically related isolates of foot-and-mouth disease virus of serotype C1 is reported. The genetic heterogeneity of 3D RNA is compared with that of the VP1-coding RNA of the same viruses. Regression lines of substitutions per nucleotide that distingu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90367-1

    authors： Villaverde A,Martínez-Salas E,Domingo E

    更新日期：1988-12-05 00:00:00

  • Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding.

    abstract：:The mom gene of bacteriophage Mu, which codes for a DNA modification function, is regulated in a complex manner at both transcriptional and translational levels. The phage-encoded C protein functions as an activator of mom transcription. The mom promoter has features of an activator-dependent weak promoter, and the C ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0379

    authors： Ramesh V,Nagaraja V

    更新日期：1996-07-05 00:00:00

  • Automatic definition of recurrent local structure motifs in proteins.

    abstract：:An automatic procedure for defining recurrent folding motifs in proteins of known structure is described. These motifs are formed by short polypeptide fragments of equal size containing between four and seven residues. The method applies a classical clustering algorithm that operates on distances between selected back...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(05)80194-9

    authors： Rooman MJ,Rodriguez J,Wodak SJ

    更新日期：1990-05-20 00:00:00

  • Phosphorylation and mutation of phospholamban alter physical interactions with the sarcoplasmic reticulum calcium pump.

    abstract：:Phospholamban physically interacts with the sarcoplasmic reticulum calcium pump (SERCA) and regulates contractility of the heart in response to adrenergic stimuli. We studied this interaction using electron microscopy of 2D crystals of SERCA in complex with phospholamban. In earlier studies, phospholamban oligomers we...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.11.014

    authors： Glaves JP,Trieber CA,Ceholski DK,Stokes DL,Young HS

    更新日期：2011-01-21 00:00:00

  • Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

    abstract：:RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-bi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.005

    authors： Ma WK,Paudel BP,Xing Z,Sabath IG,Rueda D,Tran EJ

    更新日期：2016-03-27 00:00:00

  • Non-receptor tyrosine kinases c-Abl and Arg regulate the activity of C/EBPbeta.

    abstract：:The CCAAT/enhancer-binding protein beta (C/EBPbeta) is a critical transcription factor that regulates gene expression during numerous biological processes, including differentiation, metabolism, homeostasis, proliferation, tumorigenesis, inflammation, and apoptosis. In this study, interactions between C/EBPbeta and ei...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.055

    authors： Li X,Liu X,Wang G,Zhu X,Qu X,Li X,Yang Y,Peng L,Li C,Li P,Huang W,Ma Q,Cao C

    更新日期：2009-08-28 00:00:00

  • Low resolution crystal structure of muconolactone isomerase. A decamer with a 5-fold symmetry axis.

    abstract：:Muconolactone isomerase from Pseudomonas putida crystallizes from sodium sulfate solution in space group P2(1) (a = 65.84 A, b = 105.70 A, c = 77.20 A, beta = 90.5 degrees) with ten 11,000 Mr subunits per asymmetric unit. The 7 A resolution crystal structure was solved by single isomorphous replacement followed by 10-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90382-1

    authors： Katz BA,Ollis D,Wyckoff HW

    更新日期：1985-07-20 00:00:00

  • Invertebrate myosin filament: subfilament arrangement in the wall of tubular filaments of insect flight muscles.

    abstract：:Transverse sections (100 to 140 nm thick) of the flight muscles of the fleshfly Phormia terrae-novae and the housefly Musca domestica were studied. The images of 56 tubular myosin filaments of the fleshfly and 62 filaments of the housefly were digitized and computer processed by rotational averaging. The rotational po...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90637-7

    authors： Beinbrech G,Ashton FT,Pepe FA

    更新日期：1988-06-05 00:00:00

  • Alpha-synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils.

    abstract：:Two mutations in the alpha-synuclein gene (A30P and A53T) have been linked to autosomal dominant early-onset Parkinson's disease (PD). Both mutations promote the formation of transient protofibrils (prefibrillar oligomers), suggesting that protofibrils are linked to cytotoxicity. In this work, the effect of these muta...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00735-0

    authors： Lashuel HA,Petre BM,Wall J,Simon M,Nowak RJ,Walz T,Lansbury PT Jr

    更新日期：2002-10-04 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

  • Involvement of C-terminal structural elements of equine infectious anemia virus reverse transcriptase in DNA polymerase and ribonuclease H activities.

    abstract：:In order to investigate the modes of DNA synthesis supported by the 66 and 51 kDa subunits of equine infectious anemia virus reverse transcriptase (EIAV RT), recombinant p66 polypeptides containing a modified ribonuclease H (RNase H) domain were purified and evaluated. Defined heteropolymeric template-primer combinati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0181

    authors： Rausch JW,Arts EJ,Wöhrl BM,Le Grice SF

    更新日期：1996-04-05 00:00:00

  • Oligomerization of the SPP1 scaffolding protein.

    abstract：:Viral scaffolding proteins direct polymerization of major capsid protein subunits into icosahedral procapsid structures. The scaffolding protein of bacteriophage SPP1 was engineered with a C-terminal hexahistidine tag (gp11-His(6)) and purified. The protein is an alpha-helical-rich molecule with a very elongated shape...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.02.028

    authors： Poh SL,el Khadali F,Berrier C,Lurz R,Melki R,Tavares P

    更新日期：2008-05-02 00:00:00

  • Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases.

    abstract：:As regulators of ubiquitous biological processes, serine proteases can cause disease states when inappropriately expressed or regulated, and are thus rational targets for inhibition by drugs. Recently we described a new inhibition mechanism applicable for the development of potent, selective small molecule serine prot...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3071

    authors： Katz BA,Luong C

    更新日期：1999-09-24 00:00:00

  • Sequence information within proteasomal prosequences mediates efficient integration of beta-subunits into the 20 S proteasome complex.

    abstract：:The maturation of proteases is governed by prosequences. During the biogenesis of the highly oligomeric eukaryotic 20 S proteasome five different prosequence-containing subunits have to be integrated and processed either by autocatalysis or by neighbouring subunits. To analyse the functional impact of proteasomal pros...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2660

    authors： Schmidt M,Zantopf D,Kraft R,Kostka S,Preissner R,Kloetzel PM

    更新日期：1999-04-23 00:00:00

  • Cooperativity in the thermosome.

    abstract：:The thermosome from Thermoplasma acidophilum is a type II chaperonin composed of eight alpha and eight beta subunits. The genes encoding the two types of subunit were co-expressed in Escherichia coli and the alpha8/beta8 complex purified from the cell extract. The isolated complex showed steady-state ATPase properties...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.01.066

    authors： Bigotti MG,Clarke AR

    更新日期：2005-04-22 00:00:00

  • The three-dimensional structure at 2.4 A resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae.

    abstract：:The crystal structures of glycosylated native proteinase A, an aspartic proteinase found in the vacuole of Saccharomyces cerevisiae, and its complex with a difluorostatone-containing tripeptide have been determined by molecular replacement to 3.5 A and 2.4 A resolutions, respectively. Superposition of the bound and na...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0880

    authors： Aguilar CF,Cronin NB,Badasso M,Dreyer T,Newman MP,Cooper JB,Hoover DJ,Wood SP,Johnson MS,Blundell TL

    更新日期：1997-04-11 00:00:00

  • Crystallization of porcine liver ribonuclease inhibitor a member of the family of proteins containing leucine-rich repeats.

    abstract：:Single crystals of the RNase inhibitor from porcine liver have been obtained from 30 to 34% saturated ammonium sulphate solutions at pH 6.0 to 7.2, containing 20 mM dithiothreitol, at room temperature over a period of two to three weeks. Because the inhibitor contains 30 1/2-cystinyl residues, all of which occur in th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1299

    authors： Neumann U,Hofsteenge J,Arkema AH,Dijkstra BW

    更新日期：1993-05-20 00:00:00

  • Control of expression of the Tn10-encoded tetracycline resistance operon. II. Interaction of RNA polymerase and TET repressor with the tet operon regulatory region.

    abstract：:The promoter and operator sequences of the Tn10-encoded tetracycline resistance operon are determined in vitro by transcription studies of purified DNA restriction fragments, protection of guanosine from methylation by dimethylsulphate, and DNase I footprinting employing the purified TET repressor protein. In vitro tr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(84)80037-6

    authors： Hillen W,Schollmeier K,Gatz C

    更新日期：1984-01-15 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

    doi：10.1016/j.jmb.2004.05.025

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

    更新日期：2004-07-16 00:00:00

  • Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase.

    abstract：:An understanding of the structural basis for protein-protein interactions, and molecular recognition in general, requires complete characterization of binding energetics. Not only does this include quantification of the changes that occur in all of the thermodynamic parameters upon binding, including the enthalpy, ent...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.0977

    authors： Baker BM,Murphy KP

    更新日期：1997-05-02 00:00:00

  • Neuronal BC1 RNA: microtubule-dependent dendritic delivery.

    abstract：:RNA localization is an important means of post-transcriptional regulation of gene expression in many eukaryotic cell types. In neurons, select RNAs are delivered to postsynaptic dendritic microdomains, a mechanism that is considered a key underpinning in the administration of long-term synaptic plasticity. BC1 RNA is ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.11.090

    authors： Cristofanilli M,Iacoangeli A,Muslimov IA,Tiedge H

    更新日期：2006-03-10 00:00:00

  • Three-dimensional structure of NADH-dehydrogenase from Neurospora crassa by electron microscopy and conical tilt reconstruction.

    abstract：:NADH-dehydrogenase (Complex I) is the first complex of the mitochondrial respiratory chain. It is an amphipatic molecule located in the inner mitochondrial membrane and is composed of at least 35 unique subunits encoded by both mitochondrial and nuclear DNA. The whole complex was isolated in detergent from the fungus ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0753

    authors： Guénebaut V,Vincentelli R,Mills D,Weiss H,Leonard KR

    更新日期：1997-01-31 00:00:00

  • Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

    abstract：:The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90391-4

    authors： Namba K,Pattanayek R,Stubbs G

    更新日期：1989-07-20 00:00:00