当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > 1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins.

1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins.

Abstract：

:We have solved the crystal structure of FRase I, the major NAD(P)H:FMN oxidoreductase of Vibrio fischeri, by the multiple isomorphous replacement method (MIR) at 1.8 A resolution with the conventional R factor of 0.187. The crystal structure of FRase I complexed with its competitive inhibitor, dicoumarol, has also been solved at 2.2 A resolution with the conventional R factor of 0.161. FRase I is a homodimer, having one FMN cofactor per subunit, which is situated at the interface of two subunits. The overall fold can be divided into two domains; 80% of the residues form a rigid core and the remaining, a small flexible domain. The overall core folding is similar to those of an NADPH-dependent flavin reductase of Vibrio harveyi (FRP) and the NADH oxidase of Thermus thermophilus (NOX) in spite of the very low identity in amino acid sequences (10% with FRP and 21% with NOX). 56% of alpha-carbons of FRase I core residues could be superposed onto NOX counterparts with an r.m.s. distance of 1.2 A. The remaining residues have relatively high B-values and may be essential for defining the substrate specificity. Indeed, one of them, Phe124, was found to participate in the binding of dicoumarol through stacking to one of the rings of dicoumarol. Upon binding of dicoumarol, most of the exposed re-face of the FMN cofactor is buried, which is consistent with the ping pong bi bi catalytic mechanism.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Koike H,Sasaki H,Kobori T,Zenno S,Saigo K,Murphy ME,Adman ET,Tanokura M

doi

10.1006/jmbi.1998.1871

subject

Has Abstract

pub_date

1998-07-10 00:00:00

pages

259-73

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(98)91871-X

journal_volume

280

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • A pentavalent single-domain antibody approach to tumor antigen discovery and the development of novel proteomics reagents.

    abstract：:Proteomics research has delivered many novel tumor targets. However, due to key limitations, it does not specifically identify targets that are most accessible for drug delivery, such as cell-surface antigens. A novel tumor antigen discovery platform based on screening a single domain antibody (sdAb) library against t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.05.069

    authors： Zhang J,Li Q,Nguyen TD,Tremblay TL,Stone E,To R,Kelly J,Roger MacKenzie C

    更新日期：2004-07-30 00:00:00

  • Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis.

    abstract：:4-alpha-Glucanotransferase (GTase) is an essential enzyme in alpha-1,4-glucan metabolism in bacteria and plants. It catalyses the transfer of maltooligosaccharides from an 1,4-alpha-D-glucan molecule to the 4-hydroxyl group of an acceptor sugar molecule. The crystal structures of Thermotoga maritima GTase and its comp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00570-3

    authors： Roujeinikova A,Raasch C,Sedelnikova S,Liebl W,Rice DW

    更新日期：2002-08-02 00:00:00

  • Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs.

    abstract：:Interactions of transmembrane helices play a crucial role in the folding and oligomerisation of integral membrane proteins. In order to uncover novel sequence motifs mediating these interactions, we randomised one face of a transmembrane helix with a set of non-polar or moderately polar amino acids. Those sequences ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.09.056

    authors： Unterreitmeier S,Fuchs A,Schäffler T,Heym RG,Frishman D,Langosch D

    更新日期：2007-11-30 00:00:00

  • Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

    abstract：:Proteins with ultra-fast folding/unfolding kinetics are excellent candidates for study by molecular dynamics. Here, we describe such simulations of a three helix bundle protein, the engrailed homeodomain (En-HD), which folds via the diffusion-collision model. The unfolding pathway of En-HD was characterized by seven s...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.06.074

    authors： DeMarco ML,Alonso DO,Daggett V

    更新日期：2004-08-20 00:00:00

  • Membrane structure of CtrA3, a copper-transporting P-type-ATPase from Aquifex aeolicus.

    abstract：:We have produced and characterized two new copper-transporting ATPases, CtrA2 and CtrA3 from Aquifex aeolicus, that belong to the family of heavy metal ion-transporting P(IB)-type ATPases. CtrA2 has a CPC metal-binding sequence in TM6 and a CxxC metal-binding N-terminal domain, while CtrA3 has a CPH metal-binding moti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.01.094

    authors： Chintalapati S,Al Kurdi R,van Scheltinga AC,Kühlbrandt W

    更新日期：2008-05-02 00:00:00

  • Three-dimensional solid-state NMR study of a seven-helical integral membrane proton pump--structural insights.

    abstract：:Proteorhodopsin (PR) is a recently discovered ubiquitous eubacterial retinal-binding light-driven proton pump. Almost 1000 PR variants are widely distributed in species of marine and freshwater bacteria, suggesting PR's important photobiological role. PR is a typical seven-transmembrane alpha-helical membrane protein ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.01.011

    authors： Shi L,Ahmed MA,Zhang W,Whited G,Brown LS,Ladizhansky V

    更新日期：2009-03-06 00:00:00

  • Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility.

    abstract：:The parA partitioning system of plasmid R1 consists of three different components: the cis-acting centromere-like parC site, and the two trans-acting proteins ParM and ParR. These three components are contained within a region of 1.6 kb. The parC site is located upstream of the two genes, parM and parR, which are expr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(94)90058-2

    authors： Dam M,Gerdes K

    更新日期：1994-03-11 00:00:00

  • Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods.

    abstract：:The secondary structure of porin, maltoporin and OmpA protein reconstituted in lipid membranes is determined by Raman spectroscopy. The three proteins have similar structures consisting of 50 to 60% beta-strand, about 20% beta-turn, and less than 15% alpha-helix. Employing a method for structural prediction that accou...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90292-5

    authors： Vogel H,Jähnig F

    更新日期：1986-07-20 00:00:00

  • The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1.

    abstract：:Reverse transcriptases (RTs) encoded by a wide range of mobile retroelements have had a major impact on the structure and function of genomes. Among the most abundant elements in eukaryotes are the non long terminal repeat (LTR) retrotransposons. Here we compare the dNTP concentration requirements and error rates of t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.02.015

    authors： Jamburuthugoda VK,Eickbush TH

    更新日期：2011-04-15 00:00:00

  • Understanding the Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 1 (MMDS1)-Impact of a Disease-Causing Gly208Cys Substitution on Structure and Activity of NFU1 in the Fe/S Cluster Biosynthetic Pathway.

    abstract：:Iron-sulfur (Fe/S)-cluster-containing proteins constitute one of the largest protein classes, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, and radical generation. Consequently, the biosynthetic machinery for Fe/S clusters is evolutionarily cons...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.01.021

    authors： Wachnowsky C,Wesley NA,Fidai I,Cowan JA

    更新日期：2017-03-24 00:00:00

  • Use of site-specific recombination as a probe of DNA structure and metabolism in vivo.

    abstract：:We used site-specific recombination catalyzed by the bacteriophage lambda Int system to probe DNA structure and metabolism in vivo. In vitro, the complexity of catenated products was linearly proportional to substrate supercoil density. A system was developed that gave efficient, controlled Int recombination in Escher...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90369-x

    authors： Bliska JB,Cozzarelli NR

    更新日期：1987-03-20 00:00:00

  • Genome-wide survey of prokaryotic O-protein phosphatases.

    abstract：:Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.07.004

    authors： Bhaduri A,Sowdhamini R

    更新日期：2005-09-23 00:00:00

  • Equilibrium DNA-binding of AraC protein. Compensation for displaced ions.

    abstract：:Experiments on the AraC regulatory protein of Escherichia coli suggest a mechanism that DNA-binding proteins can use to reduce potentially drastic alterations in their affinity for DNA resulting from changes in salt concentration. Measurement of the net number of ions apparently displaced as AraC protein binds DNA and...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90193-8

    authors： Martin KJ,Schleif RF

    更新日期：1987-06-05 00:00:00

  • Solution structure of an EGF module pair from the Plasmodium falciparum merozoite surface protein 1.

    abstract：:The solution structure of the 96-residue C-terminal fragment of the merozoite surface protein 1 (MSP-1) from Plasmodium falciparum has been determined using nuclear magnetic resonance (NMR) spectroscopic measurements on uniformly13C/15N-labelled protein, efficiently expressed in the methylotrophic yeast Komagataella (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2753

    authors： Morgan WD,Birdsall B,Frenkiel TA,Gradwell MG,Burghaus PA,Syed SE,Uthaipibull C,Holder AA,Feeney J

    更新日期：1999-05-28 00:00:00

  • Jab1 mediates protein degradation of the Rad9-Rad1-Hus1 checkpoint complex.

    abstract：:The Rad1-Rad9-Hus1 (9-1-1) complex serves a dual role as a DNA-damage sensor in checkpoint signaling and as a mediator in the DNA repair pathway. However, the intercellular mechanisms that regulate the 9-1-1 complex are poorly understood. Jab1, the fifth component of the COP9 signalosome complex, has a central role in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.095

    authors： Huang J,Yuan H,Lu C,Liu X,Cao X,Wan M

    更新日期：2007-08-10 00:00:00

  • A novel allosteric mechanism in haemoglobin. Structure of bovine deoxyhaemoglobin, absence of specific chloride-binding sites and origin of the chloride-linked Bohr effect in bovine and human haemoglobin.

    abstract：:The structure of bovine deoxyhaemoglobin has been determined at 2.2 A resolution and refined to an R-factor of 0.193 for all 32,583 reflections, and a free R-factor of 0.249 for 1527 reflections excluded from the refinement. The structure shows no significant differences between the alpha-carbon positions of bovine an...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1530

    authors： Perutz MF,Fermi G,Poyart C,Pagnier J,Kister J

    更新日期：1993-10-05 00:00:00

  • A flexible loop in tyrosine hydroxylase controls coupling of amino acid hydroxylation to tetrahydropterin oxidation.

    abstract：:The role of a polypeptide loop in tyrosine hydroxylase (TyrH) whose homolog in phenylalanine hydroxylase (PheH) takes on a different conformation when substrates are bound has been studied using site-directed mutagenesis. The loop spans positions 177 to 191; alanine was introduced into those positions, introducing one...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.03.016

    authors： Daubner SC,McGinnis JT,Gardner M,Kroboth SL,Morris AR,Fitzpatrick PF

    更新日期：2006-06-02 00:00:00

  • A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding.

    abstract：:The hydroxyl radical footprint of the TATA-binding protein (TBP) bound to the high-affinity sequence TATAAAAG of the adenovirus 2 major late promoter has been quantitatively compared to a 2 ns molecular dynamics simulation of the complex in aqueous solution at room temperature using the CHARMM23 potential. The nucleot...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4173

    authors： Pastor N,Weinstein H,Jamison E,Brenowitz M

    更新日期：2000-11-17 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

  • Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22.

    abstract：:Packaging of viral genomes inside empty procapsids is driven by a powerful ATP-hydrolyzing motor, formed in many double-stranded DNA viruses by a complex of a small terminase (S-terminase) subunit and a large terminase (L-terminase) subunit, transiently docked at the portal vertex during genome packaging. Despite rece...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.08.013

    authors： McNulty R,Lokareddy RK,Roy A,Yang Y,Lander GC,Heck AJR,Johnson JE,Cingolani G

    更新日期：2015-10-09 00:00:00

  • Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure.

    abstract：:Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.01.036

    authors： Qualley DF,Cooper SE,Ross JL,Olson ED,Cantara WA,Musier-Forsyth K

    更新日期：2019-03-15 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

  • Nascent β Structure in the Elongated Hydrophobic Region of a Gerstmann-Sträussler-Scheinker PrP Allele.

    abstract：:Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrPC). Gerstmann-Sträussler-Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human Pr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.04.027

    authors： Fu ZL,Holmes PC,Westaway D,Sykes BD

    更新日期：2019-06-28 00:00:00

  • An algorithm for the prediction of proteasomal cleavages.

    abstract：:Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3683

    authors： Kuttler C,Nussbaum AK,Dick TP,Rammensee HG,Schild H,Hadeler KP

    更新日期：2000-05-05 00:00:00

  • pH-dependent interactions and the stability and folding kinetics of the N-terminal domain of L9. Electrostatic interactions are only weakly formed in the transition state for folding.

    abstract：:The role of electrostatic interactions in the stability and the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) was investigated by determining the effects of varying the pH conditions. Urea denaturations and thermal unfolding experiments were used to measure the free energy of folding, DeltaG degr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3752

    authors： Luisi DL,Raleigh DP

    更新日期：2000-06-16 00:00:00

  • Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.

    abstract：:The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.06.028

    authors： Chan S,Segelke B,Lekin T,Krupka H,Cho US,Kim MY,So M,Kim CY,Naranjo CM,Rogers YC,Park MS,Waldo GS,Pashkov I,Cascio D,Perry JL,Sawaya MR

    更新日期：2004-08-06 00:00:00

  • Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution.

    abstract：:The free form of ribonuclease T1 (RNase T1) has been crystallized at neutral pH, and the three-dimensional structure of the enzyme has been determined at 1.5 A nominal resolution. Restrained least-squares refinement yielded an R value of 14.3% for 12,623 structure amplitudes. The high resolution of the structure analy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90215-r

    authors： Martinez-Oyanedel J,Choe HW,Heinemann U,Saenger W

    更新日期：1991-11-20 00:00:00

  • Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.

    abstract：:We have applied a search strategy for determining the optimal packing of protein secondary structure elements to the rotational positioning of the seven transmembrane helices of bacteriorhodopsin. The search is based on the assumption that the relative orientations of the helices within the bundle are conditioned prin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(94)90015-9

    authors： Tuffery P,Etchebest C,Popot JL,Lavery R

    更新日期：1994-03-04 00:00:00

  • Translocation of histone proteins across lipid bilayers and Mycoplasma membranes.

    abstract：:We show that the three core histones H2A, H3 and H4 can transverse lipid bilayers of large unilamellar vesicles (LUVs) and multilamellar vesicles (MLVs). In contrast, the histone H2B, although able to bind to the liposomes, fails to penetrate the unilamellar and the multilamellar vesicles. Translocation across the lip...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.046

    authors： Rosenbluh J,Hariton-Gazal E,Dagan A,Rottem S,Graessmann A,Loyter A

    更新日期：2005-01-14 00:00:00

  • The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.

    abstract：:Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its prophage expresses the oac gene that alters the antigenic properties of the surface O-antigen polysaccharide of its host bacterium. We have determined the complete sequence of its 39,044 bp genome. The sequence shows that Sf6 is a member ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.03.068

    authors： Casjens S,Winn-Stapley DA,Gilcrease EB,Morona R,Kühlewein C,Chua JE,Manning PA,Inwood W,Clark AJ

    更新日期：2004-05-28 00:00:00