Crystallization and preliminary crystallographic analysis of NADPH:FMN oxidoreductase from Vibrio harveyi.

Abstract:

:Crystals of NADPH:FMN oxidoreductase from Vibrio harveyi have been obtained and characterized by X-ray diffraction. This enzyme plays a role in the generation of light in luminescent bacteria by providing reduced FMN to luciferase. Large, high quality crystals were grown using polyethylene glycol 6000 at pH 7.0. They crystallize in the monoclinic space group P2(1) with cell dimensions a = 51.2 A, b = 85.9 A, c = 58.1 A, beta = 109.3 degrees, and diffract to 1.8 A. We expect two molecules per asymmetric unit. High resolution data sets have been recorded and a search is under way for heavy-atom derivatives.

journal_name

J Mol Biol

authors

Tanner J,Lei B,Liu M,Tu SC,Krause KL

doi

10.1006/jmbi.1994.1501

subject

Has Abstract

pub_date

1994-08-12 00:00:00

pages

283-7

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(84)71501-4

journal_volume

241

pub_type

杂志文章
  • Effects of experimentally achievable improvements in the quality of NMR distance constraints on the accuracy of calculated protein structures.

    abstract::New methods for collecting cross-relaxation data from proteins and nucleic acids make it possible to improve the accuracy and precision of interproton distance measurements used as input for NMR solution structure determinations. It thus is of interest to determine whether such experimentally achievable improvements i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0254

    authors: Hoogstraten CG,Markley JL

    更新日期:1996-05-03 00:00:00

  • Novel alleles of the Escherichia coli dnaA gene.

    abstract::The Escherichia coli dnaA gene is required for replication of the bacterial chromosome. To identify residues critical for its replication activity, a method to select novel mutations was developed that relied on lytic growth of lambda from an inserted pSC101 replication origin. Replication from the lambda origin was i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1209

    authors: Sutton MD,Kaguni JM

    更新日期:1997-09-05 00:00:00

  • DNA looping alters local DNA conformation during transcription.

    abstract::The effect of protein-mediated DNA looping on local DNA conformation during active transcription was studied using the lac repressor-operator system. Our results suggest that lac repressor-mediated DNA looping within a plasmid DNA molecule containing two lac repressor binding sequences in vivo effectively separates pl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90658-s

    authors: Wu HY,Liu LF

    更新日期:1991-06-20 00:00:00

  • Characterization of a Tn5 pre-cleavage synaptic complex.

    abstract::Protein catalyzed DNA rearrangements typically require assembly of complex nucleoprotein structures. In transposition and integration reactions, these structures, termed synaptic complexes, are mandatory for catalysis. We characterize the Tn5 pre-cleavage synaptic complex, the simplest transposition complex described ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4048

    authors: Bhasin A,Goryshin IY,Steiniger-White M,York D,Reznikoff WS

    更新日期:2000-09-08 00:00:00

  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry.

    abstract::We have devised a molecular model building computer program (DEZYMER) which builds new ligand binding sites into a protein of known three-dimensional structure. It alters only the sequence and the side-chain structure of the protein, leaving the protein backbone fold intact by definition. The program searches for a co...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90510-d

    authors: Hellinga HW,Richards FM

    更新日期:1991-12-05 00:00:00

  • The loop sequence plays crucial roles for isomerization of intramolecular DNA triplexes in supercoiled plasmids.

    abstract::The effect of base composition in the central region of polypurine.polypyrimidine (Pur.Pyr) tracts on the formation of intramolecular DNA triplexes in plasmids was examined using chemical probes (diethyl pyrocarbonate and OsO4), and two-dimensional (2-D) agarose gel electrophoresis. Two isomers exist for an intramolec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80025-7

    authors: Shimizu M,Kubo K,Matsumoto U,Shindo H

    更新日期:1994-01-07 00:00:00

  • Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations.

    abstract::Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light ch...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.10.016

    authors: Blancas-Mejía LM,Tischer A,Thompson JR,Tai J,Wang L,Auton M,Ramirez-Alvarado M

    更新日期:2014-01-23 00:00:00

  • Selective Autophagy Receptors in Neuronal Health and Disease.

    abstract::Neurons are electrically excitable, postmitotic cells that perform sensory, relaying, and motor functions. Because of their unique morphological and functional specialization, cells of this type are sensitive to the stress caused by accumulation of misfolded proteins or damaged organelles. Autophagy is the fundamental...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2019.10.013

    authors: Conway O,Akpinar HA,Rogov VV,Kirkin V

    更新日期:2020-04-03 00:00:00

  • Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases.

    abstract::Intramembrane enzymes are often difficult for biochemical characterization. Human vitamin K epoxide reductase (VKOR) is the target of warfarin. However, this intramembrane enzyme becomes insensitive to warfarin inhibition in vitro, preventing the characterization of inhibition kinetics for decades. Here we employ stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.05.009

    authors: Li S,Liu S,Yang Y,Li W

    更新日期:2020-08-21 00:00:00

  • Nuclear magnetic resonance studies of the internal dynamics in Apo, (Cd2+)1 and (Ca2+)2 calbindin D9k. The rates of amide proton exchange with solvent.

    abstract::The backbone dynamics of the EF-hand Ca(2+)-binding protein, calbindin D9k, has been investigated in the apo, (Cd2+)1 and (Ca2+)2 states by measuring the rate constants for amide proton exchange with solvent. 15N-1H correlation spectroscopy was utilized to follow direct 1H-->2H exchange of the slowly exchanging amide ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90524-n

    authors: Skelton NJ,Kördel J,Akke M,Chazin WJ

    更新日期:1992-10-20 00:00:00

  • Protein structure comparison by alignment of distance matrices.

    abstract::With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1489

    authors: Holm L,Sander C

    更新日期:1993-09-05 00:00:00

  • Molecular Insights into the Architecture of the Human SMC5/6 Complex.

    abstract::A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share a common SMC-kleisin architecture allowing them to embrace DNA. In SMC5/6, the NSE1 and NSE3 KITE and NSE4 kleisin subunits form a stable subcomple...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.04.024

    authors: Adamus M,Lelkes E,Potesil D,Ganji SR,Kolesar P,Zabrady K,Zdrahal Z,Palecek JJ

    更新日期:2020-06-12 00:00:00

  • The rate of polyQ-mediated aggregation is dramatically affected by the number and location of surrounding domains.

    abstract::The nine polyglutamine (polyQ) neurodegenerative diseases are caused in part by a gain-of-function mechanism involving protein misfolding, the deposition of β-sheet-rich aggregates and neuronal toxicity. While previous experimental evidence suggests that the polyQ-induced misfolding mechanism is context dependent, the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.09.014

    authors: Robertson AL,Bate MA,Buckle AM,Bottomley SP

    更新日期:2011-11-04 00:00:00

  • Oxygen transport by fetal bovine hemoglobin.

    abstract::The functional properties of fetal bovine hemoglobin have been studied as a function of temperature, chloride and 2,3-diphosphoglycerate (DPG) concentration. The fetal bovine erythrocyte has six times the concentration of the allosteric modulator DPG compared with the adult cell, and yet the oxygen affinity of the fet...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0019

    authors: Clementi ME,Scatena R,Mordente A,Condò SG,Castagnola M,Giardina B

    更新日期:1996-01-12 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

    doi:10.1016/0022-2836(85)90351-1

    authors: Levine RJ,Kensler RW

    更新日期:1985-03-20 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

  • Active-site determination of a pyrimidine dimer glycosylase.

    abstract::One mechanism for the repair of UV-induced DNA damage is the base excision repair pathway. The initial step in this pathway and the specificity for the type of damage that is to be repaired reside in DNA glycosylase/abasic (AP) lyases. Cleavage of the glycosyl bond of the 5' pyrimidine of a cyclobutane pyrimidine dime...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3369

    authors: Garvish JF,Lloyd RS

    更新日期:2000-01-21 00:00:00

  • Crystal structure of metastasis-associated protein S100A4 in the active calcium-bound form.

    abstract::S100A4 (metastasin) is a member of the S100 family of calcium-binding proteins that is directly involved in tumorigenesis. Until recently, the only structural information available was the solution NMR structure of the inactive calcium-free form of the protein. Here we report the crystal structure of human S100A4 in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.04.076

    authors: Pathuri P,Vogeley L,Luecke H

    更新日期:2008-10-31 00:00:00

  • Primate evolution of the alpha-globin gene cluster and its Alu-like repeats.

    abstract::The arrangement of alpha-globin genes in Old World and New World monkeys and a prosimian, galago, has been determined by restriction mapping. Recombinant DNAs containing galago and Old World monkey alpha-globin genes have been isolated and subjected to a partial sequence determination for comparison to alpha-globin ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90022-7

    authors: Sawada I,Schmid CW

    更新日期:1986-12-20 00:00:00

  • A novel method to detect functional microRNA targets.

    abstract::MicroRNA (miRNA) molecules are non-coding RNAs, 19 to 24 nt in length that have been identified recently as important regulators of gene expression. Several computational methods have been developed to describe the target recognition mechanism by miRNA. We propose here a novel method to detect miRNA-mRNA complexes in ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.02.063

    authors: Vatolin S,Navaratne K,Weil RJ

    更新日期:2006-05-12 00:00:00

  • An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs.

    abstract::The coat protein of positive-stranded RNA viruses often contains a positively charged tail that extends toward the center of the capsid and interacts with the viral genome. Electrostatic interaction between the tail and the RNA has been postulated as a major force in virus assembly and stabilization. The goal of this ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.03.023

    authors: Ni P,Wang Z,Ma X,Das NC,Sokol P,Chiu W,Dragnea B,Hagan M,Kao CC

    更新日期:2012-06-22 00:00:00

  • Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

    abstract::EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds af...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.01.025

    authors: Defeu Soufo HJ,Reimold C,Breddermann H,Mannherz HG,Graumann PL

    更新日期:2015-04-24 00:00:00

  • Angular disorder in actin: is it consistent with general principles of protein structure?

    abstract::Harold Erickson has recently provided a useful analysis of helical structures having one class versus two classes of intersubunit bonds. His analysis is based upon an assumption that the subunits themselves are essentially unchanged upon bond formation (polymerization). He shows that such a structure having two classe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90743-p

    authors: Egelman EH,DeRosier DJ

    更新日期:1991-02-05 00:00:00

  • Growth rate-dependent control, feedback regulation and steady-state mRNA levels of the threonyl-tRNA synthetase gene of Escherichia coli.

    abstract::The expression of the gene thrS encoding threonyl-tRNA synthetase is under the control of two apparently different regulatory loops: translational feedback regulation and growth rate-dependent control. The translational feedback regulation is due to the binding of threonyl-tRNA synthetase to a site located in the lead...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0445

    authors: Comer MM,Dondon J,Graffe M,Yarchuk O,Springer M

    更新日期:1996-08-16 00:00:00

  • Crystal structure of human carboxypeptidase M, a membrane-bound enzyme that regulates peptide hormone activity.

    abstract::Carboxypeptidase M (CPM), an extracellular glycosylphosphatidyl-inositol(GPI)-anchored membrane glycoprotein belonging to the CPN/E subfamily of "regulatory" metallo-carboxypeptidases, specifically removes C-terminal basic residues from peptides and proteins. Due to its wide distribution in human tissues, CPM is belie...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.02.058

    authors: Reverter D,Maskos K,Tan F,Skidgel RA,Bode W

    更新日期:2004-04-23 00:00:00

  • Crystallization and preliminary X-ray analysis of Gc, the vitamin D-binding protein in serum.

    abstract::The vitamin D-binding protein, Gc, was purified from human serum and crystallized using the hanging-drop method. The best crystals were grown from 28% polyethylene glycol 400 in 50 mM-sodium acetate at pH 4.8. These crystals diffract to 3.4 A and the observed diffraction is consistent with orthorhombic space groups P4...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90097-p

    authors: Vogelaar NJ,Lindberg U,Schutt CE

    更新日期:1991-08-05 00:00:00

  • One protein, two enzymes revisited: a structural entropy switch interconverts the two isoforms of acireductone dioxygenase.

    abstract::Acireductone dioxygenase (ARD) catalyzes different reactions between O2 and 1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene (acireductone) depending upon the metal bound in the active site. Ni2+ -ARD cleaves acireductone to formate, CO and methylthiopropionate. If Fe2+ is bound (ARD'), the same substrates yield methylthi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.08.060

    authors: Ju T,Goldsmith RB,Chai SC,Maroney MJ,Pochapsky SS,Pochapsky TC

    更新日期:2006-11-03 00:00:00

  • Functional regions and structural features of the gB glycoprotein of herpes simplex virus type 1. An analysis of linker insertion mutants.

    abstract::Glycoprotein B (gB) of Herpes simplex virus type 1 (HSV-1) plays an essential role in viral entry. A set of more than 100 HpaI (GTTAAC) linker insertion mutations and their derivatives were isolated in plasmids specifying the gB coding and flanking sequences. Mutations including addition, deletion and nonsense mutatio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90639-0

    authors: Cai WZ,Person S,DebRoy C,Gu BH

    更新日期:1988-06-05 00:00:00

  • Evolutionary stabilization of the gene-3-protein of phage fd reveals the principles that govern the thermodynamic stability of two-domain proteins.

    abstract::The gene-3-protein (G3P) of filamentous phage is essential for their propagation. It consists of three domains. The CT domain anchors G3P in the phage coat, the N2 domain binds to the F pilus of Escherichia coli and thus initiates infection, and the N1 domain continues by interacting with the TolA receptor. Phage are ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00359-0

    authors: Martin A,Schmid FX

    更新日期:2003-05-09 00:00:00

  • Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.

    abstract::We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.10.086

    authors: Liu L,Baase WA,Matthews BW

    更新日期:2009-01-16 00:00:00