Modulator of drug activity B from Escherichia coli: crystal structure of a prokaryotic homologue of DT-diaphorase.

Abstract:

:Modulator of drug activity B (MdaB) is a putative member of the DT-diaphorase family of NAD(P)H:oxidoreductases that afford cellular protection against quinonoid compounds. While there have been extensive investigations of mammalian homologues, putative prokaryotic members of this enzyme family have received little attention. The three-dimensional crystal structure of apo-MdaB reported herein exhibits significant structural similarity to a number of flavoproteins, including the mammalian DT-diaphorases. We have shown by mass spectrometry that the endogenously associated cofactor is flavin adenine dinucleotide and we present here the structure of MdaB in complex with this compound. Growth of Escherichia coli carrying null mutations in the genes encoding MdaB or quinol monooxygenase, the gene for which shares the mdaB promoter, were not affected by the presence of menadione. However, over-expression of recombinant quinol monooxygenase conferred a state of resistance against both tetracycline and adriamycin. This work suggests that the redox cycle formed by these proteins protects E. coli from the toxic effects of polyketide compounds rather than the oxidative stress of menadione alone.

journal_name

J Mol Biol

authors

Adams MA,Jia Z

doi

10.1016/j.jmb.2006.03.053

subject

Has Abstract

pub_date

2006-06-02 00:00:00

pages

455-65

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)00403-7

journal_volume

359

pub_type

杂志文章
  • Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein.

    abstract::The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurem...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.12.021

    authors: Bayro MJ,Chen B,Yau WM,Tycko R

    更新日期:2014-03-06 00:00:00

  • Functional determinants of the Epstein-Barr virus protease.

    abstract::Herpesvirus proteases are essential for the production of progeny virus. They cleave the assembly protein that fills the immature capsid in order to make place for the viral DNA. The recombinant protease of the human gamma-herpesvirus Epstein-Barr virus (EBV) was expressed in Escherichia coli and purified. Circular di...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4854

    authors: Buisson M,Valette E,Hernandez JF,Baudin F,Ebel C,Morand P,Seigneurin JM,Arlaud GJ,Ruigrok RW

    更新日期:2001-08-03 00:00:00

  • Identification of the receptor-recognition surface of bombyxin-II, an insulin-like peptide of the silkmoth Bombyx mori: critical importance of the B-chain central part.

    abstract::Bombyxin-II, a brain-secretory peptide of the silkmoth Bombyx mori, shares 40% sequence identify and the characteristics core structure with human insulin. In spite of the structural similarity, no cross-activity is observed between them. To localize the active region of bombyxin-II, we have synthesized chimeric molec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0589

    authors: Nagata K,Hatanaka H,Kohda D,Kataoka H,Nagasawa H,Isogai A,Ishizaki H,Suzuki A,Inagaki F

    更新日期:1995-11-10 00:00:00

  • Molecular dynamics of native protein. I. Computer simulation of trajectories.

    abstract::The motion of the atoms in the small protein bovine pancreatic trypsin inhibitor has been simulated for about 60 picoseconds using two different potential energy functions. In one known as HHL the hydrogen bond is purely electrostatic, in the other, known as L79, the hydrogen bond is a directional O . . . H interactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80304-0

    authors: Levitt M

    更新日期:1983-08-15 00:00:00

  • Ligand-induced assembling of the type I interferon receptor on supported lipid bilayers.

    abstract::Type I interferons (IFNs) elicit antiviral, antiproliferative and immuno-modulatory responses through binding to a shared receptor consisting of the transmembrane proteins ifnar1 and ifnar2. Differential signaling by different interferons, in particular IFNalphas and IFNbeta, suggests different modes of receptor engag...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.059

    authors: Lamken P,Lata S,Gavutis M,Piehler J

    更新日期:2004-07-30 00:00:00

  • What drives proteins into the major or minor grooves of DNA?

    abstract::The energetic profiles of a significant number of protein-DNA systems at 20 degrees C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy-driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by fa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2006.09.059

    authors: Privalov PL,Dragan AI,Crane-Robinson C,Breslauer KJ,Remeta DP,Minetti CA

    更新日期:2007-01-05 00:00:00

  • The alternatively folded state of the antibody C(H)3 domain.

    abstract::The C(H)3 domain of antibodies is characterized by two antiparallel beta-sheets forming a disulfide-linked sandwich-like structure. At acidic pH values and low ionic strength, C(H)3 becomes completely unfolded. The addition of salt transforms the acid-unfolded protein into an alternatively folded state exhibiting a ch...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4707

    authors: Thies MJ,Kammermeier R,Richter K,Buchner J

    更新日期:2001-06-22 00:00:00

  • Local rather than global folding enables the lead-dependent activity of the 8-17 deoxyribozyme: evidence from contact photo-crosslinking.

    abstract::The 8-17 deoxyribozyme is an in vitro selected enzyme capable of sequence-specific cleavage of RNA. While selected to be a magnesium and zinc-utilizing enzyme, the 8-17 DNAzyme has been shown to utilize lead for its catalysis. Fluorescence-based experiments have indicated that the magnesium- and zinc-utilizing version...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.028

    authors: Liu Y,Sen D

    更新日期:2010-01-15 00:00:00

  • APOBEC3B and AID have similar nuclear import mechanisms.

    abstract::Members of the APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) protein family catalyze DNA cytosine deamination and underpin a variety of immune defenses. For instance, several family members, including APOBEC3B (A3B), elicit strong retrotransposon and retrovirus restriction activities. Howev...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.03.011

    authors: Lackey L,Demorest ZL,Land AM,Hultquist JF,Brown WL,Harris RS

    更新日期:2012-06-22 00:00:00

  • Consensus protein design without phylogenetic bias.

    abstract::Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.04.039

    authors: Jäckel C,Bloom JD,Kast P,Arnold FH,Hilvert D

    更新日期:2010-06-18 00:00:00

  • Active transcription is required for maintenance of epigenetic memory in the malaria parasite Plasmodium falciparum.

    abstract::The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. The primary antigenic and virulence determinant expressed on the surface of infected red blood cells is PfEMP1 (P. falciparum erythrocyte membrane protein 1), a protein that mediates adhesion and sequestration of the paras...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.015

    authors: Dzikowski R,Deitsch KW

    更新日期:2008-10-03 00:00:00

  • Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK.

    abstract::RepA protein of plasmid P1 binds to arrays of 19 bp repeat sequences (iterons) and mediates initiation of replication and its control. Escherichia coli heat shock proteins DnaJ and DnaK can stimulate iteron binding activity of RepA in an ATP-dependent fashion. It has been proposed that RepA binds to DNA as monomers an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1367

    authors: DasGupta S,Mukhopadhyay G,Papp PP,Lewis MS,Chattoraj DK

    更新日期:1993-07-05 00:00:00

  • On the relative ability of centromeric GNA triplets to form hairpins versus self-paired duplexes.

    abstract::While tandem repeats of the human centromere DNA pentamer sequence TGRAA form stable "self-complementary" [TGRAATGRAA]2 duplexes (R = G or A) containing the GA-bracketed unpaired purine stack motif, their phase-shifted variants NAATGNAATG (N = A, G, C, T) were found to exist in solution as an equilibrium mixture of a ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0331

    authors: Chou SH,Zhu L,Reid BR

    更新日期:1996-06-14 00:00:00

  • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI.

    abstract::The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.053

    authors: Wood KM,Daniels LE,Halford SE

    更新日期:2005-07-08 00:00:00

  • Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities.

    abstract::The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both encoding proteins of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.03.013

    authors: Guo Y,Kragelund BB,White MF,Peng X

    更新日期:2015-06-19 00:00:00

  • Substitution of Asp114 or Arg116 in the fingers domain of moloney murine leukemia virus reverse transcriptase affects interactions with the template-primer resulting in decreased processivity.

    abstract::Reverse transcriptase, an essential retroviral DNA polymerase, replicates the single-stranded RNA genome of the retrovirus, producing a double-stranded DNA copy, which is subsequently integrated into the host's genome. Substitution of Ala for either Asp114 or Arg116, two highly conserved residues in the fingers domain...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4281

    authors: Gu J,Villanueva RA,Snyder CS,Roth MJ,Georgiadis MM

    更新日期:2001-01-12 00:00:00

  • Determination of the cleavage site of the phage T4 prohead protease in gene product 68. Influence of protein secondary structure on cleavage specificity.

    abstract::The cleavage site of the T4 prohead protease in gene product 68 of bacteriophage T4 has been determined by direct protein sequencing. It is located close to the carboxy-terminal end of a predicted alpha-helix in the sequence Asn-Val-Glu-Ala between the Glu and Ala residues. Secondary structure seems to be more importa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90138-x

    authors: Keller B,Kellenberger E,Bickle TA,Tsugita A

    更新日期:1985-12-05 00:00:00

  • Ancylostoma ceylanicum excretory-secretory protein 2 adopts a netrin-like fold and defines a novel family of nematode proteins.

    abstract::Hookworms are human parasites that have devastating effects on global health, particularly in underdeveloped countries. Ancylostoma ceylanicum infects humans and animals, making it a useful model organism to study disease pathogenesis. A. ceylanicum excretory-secretory protein 2 (AceES-2), a highly immunoreactive mole...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.02.033

    authors: Kucera K,Harrison LM,Cappello M,Modis Y

    更新日期:2011-04-22 00:00:00

  • Transferrin, is a mixed chelate-protein ternary complex involved in the mechanism of iron uptake by serum-transferrin in vitro?

    abstract::Iron uptake by transferrin from triacetohydroxamatoFe(III) (Fe(AHA)3) in the presence of bicarbonate has been investigated between pH 7 and 8.2. The protein transits from the opened apo- to the closed holoform by several steps with the accumulation of at least three kinetic intermediates. All these steps are accompani...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3238

    authors: Pakdaman R,Abdallah FB,El Hage Chahine JM

    更新日期:1999-11-12 00:00:00

  • Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites.

    abstract::The interaction of trp repressor with its DNA targets is unusual in that specific recognition in this system does not rely exclusively on direct hydrogen bonds to the DNA bases that are crucial for sequence-specific recognition. It has been suggested that trp operators are mainly recognized by water-mediated interacti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0826

    authors: Bareket-Samish A,Cohen I,Haran TE

    更新日期:1997-03-21 00:00:00

  • Preliminary crystallographic analysis of the breakage-reunion domain of the Escherichia coli DNA gyrase A protein.

    abstract::The 64 x 10(3) Mr N-terminal breakage-reunion domain of the Escherichia coli DNA gyrase A protein was purified from an over-expressing strain. When complexed with the gyrase B protein, this truncated A protein has all of the enzymic properties of the full-length counterpart, although with reduced efficiency in some ca...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80162-7

    authors: Reece RJ,Dauter Z,Wilson KS,Maxwell A,Wigley DB

    更新日期:1990-10-20 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

  • The entropy cost of protein association.

    abstract::The temperature induced unfolding/dissociation of the dimeric subtilisin inhibitor from Streptomyces and its mutant D83C having an S-S crosslink between the subunits has been studied calorimetrically. Comparison of the entropies measured at different concentrations of dimer showed that the entropy cost of crosslinking...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1368

    authors: Tamura A,Privalov PL

    更新日期:1997-11-14 00:00:00

  • Manganese water-soluble porphyrin senses DNA conformation.

    abstract::We have determined the sites that are preferentially cleaved by Mn(T4MPyP) (where T4MPyP is the dianion of 5, 10, 15, 20, tetrakis (4-N-methylpyridine)porphyrin) on synthetic DNAs and on both intrinsically curved and average-shaped natural DNA sequences. On the basis of cleavage selectivity and of DNase I footprinting...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1969

    authors: Di Mauro E,Saladino R,Tagliatesta P,De Sanctis V,Negri R

    更新日期:1998-09-11 00:00:00

  • The Isoniazid Paradigm of Killing, Resistance, and Persistence in Mycobacterium tuberculosis.

    abstract::Isoniazid (INH) was the first synthesized drug that mediated bactericidal killing of the bacterium Mycobacterium tuberculosis, a major clinical breakthrough. To this day, INH remains a cornerstone of modern tuberculosis (TB) chemotherapy. This review describes the serendipitous discovery of INH, its effectiveness on T...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2019.02.016

    authors: Vilchèze C,Jacobs WR Jr

    更新日期:2019-08-23 00:00:00

  • Identity elements required for enzymatic formation of N2,N2-dimethylguanosine from N2-monomethylated derivative and its possible role in avoiding alternative conformations in archaeal tRNA.

    abstract::Here, we have investigated the specificity of purified recombinant tRNA:m(2)(2)G10 methyltransferase of Pyrococcus abyssi ((Pab)Trm-m(2)(2)G10 enzyme). This archaeal enzyme catalyses mono- and dimethylation of the N(2)-exocyclic amino group of guanine at position 10 of several tRNA species. Our results indicate that o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.12.087

    authors: Urbonavicius J,Armengaud J,Grosjean H

    更新日期:2006-03-24 00:00:00

  • The crystal structure of DehI reveals a new alpha-haloacid dehalogenase fold and active-site mechanism.

    abstract::Haloacid dehalogenases catalyse the removal of halides from organic haloacids and are of interest for bioremediation and for their potential use in the synthesis of industrial chemicals. We present the crystal structure of the homodimer DehI from Pseudomonas putida strain PP3, the first structure of a group I alpha-ha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.02.035

    authors: Schmidberger JW,Wilce JA,Weightman AJ,Whisstock JC,Wilce MC

    更新日期:2008-04-18 00:00:00

  • Structural assembly of the active site in an aldo-keto reductase by NADPH cofactor.

    abstract::A 1.9 A resolution X-ray structure of the apo-form of Corynebacterium 2,5-diketo-d-gluconic acid reductase A (2,5-DKGR A), a member of the aldo-keto reductase superfamily, has been determined by molecular replacement using the NADPH-bound form of the same enzyme as the search model. 2,5-DKGR A catalyzes the NADPH-depe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4739

    authors: Sanli G,Blaber M

    更新日期:2001-06-22 00:00:00

  • The EGF-like protein dlk1 inhibits notch signaling and potentiates adipogenesis of mesenchymal cells.

    abstract::The EGF-like homeotic gene Dlk1 appears to function as an inhibitor of adipogenesis. Overexpression of Dlk1 prevents adipogenesis of 3T3-L1 cells. Dlk1-deficient mice are obese; however, adipose tissue still develops in Fc-dlk1 transgenic mice, suggesting that Dlk1 is not a strict inhibitor of adipogenesis. To clarify...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.043

    authors: Nueda ML,Baladrón V,Sánchez-Solana B,Ballesteros MA,Laborda J

    更新日期:2007-04-13 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