P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor.

Abstract:

:Type IV pili are bacterial extracellular filaments that can be retracted to create force and motility. Retraction is accomplished by the motor protein PilT. Crystal structures of Pseudomonas aeruginosa PilT with and without bound beta,gamma-methyleneadenosine-5'-triphosphate have been solved at 2.6 A and 3.1 A resolution, respectively, revealing an interlocking hexamer formed by the action of a crystallographic 2-fold symmetry operator on three subunits in the asymmetric unit and held together by extensive ionic interactions. The roles of two invariant carboxylates, Asp Box motif Glu163 and Walker B motif Glu204, have been assigned to Mg(2+) binding and catalysis, respectively. The nucleotide ligands in each of the subunits in the asymmetric unit of the beta,gamma-methyleneadenosine-5'-triphosphate-bound PilT are not equally well ordered. Similarly, the three subunits in the asymmetric unit of both structures exhibit differing relative conformations of the two domains. The 12 degrees and 20 degrees domain rotations indicate motions that occur during the ATP-coupled mechanism of the disassembly of pili into membrane-localized pilin monomers. Integrating these observations, we propose a three-state "Ready, Active, Release" model for the action of PilT.

journal_name

J Mol Biol

authors

Misic AM,Satyshur KA,Forest KT

doi

10.1016/j.jmb.2010.05.066

subject

Has Abstract

pub_date

2010-07-30 00:00:00

pages

1011-21

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(10)00570-X

journal_volume

400

pub_type

杂志文章
  • A specific hydrophobic core in the alpha-lactalbumin molten globule.

    abstract::Molten globules are partially structured protein folding intermediates that adopt a native-like overall backbone topology in the absence of extensive detectable tertiary interactions. It is important to determine the extent of specific tertiary structure present in molten globules and to understand the role of specifi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1825

    authors: Wu LC,Kim PS

    更新日期:1998-07-03 00:00:00

  • Double-strand break repair machinery is sensitive to UV radiation.

    abstract::The precision of the repair of linearized plasmid DNA was analyzed using a nonsense mutation inactivated beta-glucuronidase (uidA) marker gene delivered to Nicotiana plumbaginifolia protoplasts and Nicotiana tabacum leaves. The reversions at the stop-codon allowed the reactivation of the marker gene. Here we report th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.001

    authors: Ilnytskyy Y,Yao Y,Kovalchuk I

    更新日期:2005-01-28 00:00:00

  • X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution.

    abstract::The crystal structure of the ferredoxin:NADP+ reductase (FNR) from the cyanobacterium Anabaena PCC 7119 has been determined at 2.6 A resolution by multiple isomorphous replacement and refined using 15.0 A to 1.8 A data, collected at 4 degrees C, to an R-factor of 0.172. The model includes 303 residues, the flavin aden...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0553

    authors: Serre L,Vellieux FM,Medina M,Gomez-Moreno C,Fontecilla-Camps JC,Frey M

    更新日期:1996-10-18 00:00:00

  • Titin organisation and the 3D architecture of the vertebrate-striated muscle I-band.

    abstract::The giant muscle protein titin (connectin) is known to serve as a cytoskeletal element in muscle sarcomeres. It elastically restrains lengthening sarcomeres, it aids the integrity and central positioning of the A-band in the sarcomere and it may act as a template upon which some sarcomeric components are laid down dur...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00819-7

    authors: Knupp C,Luther PK,Squire JM

    更新日期:2002-09-27 00:00:00

  • The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence.

    abstract::alpha-Chemokines comprise a family of cytokines that are chemotactic for neutrophils and have a structure similar to platelet factor 4 (PF4), in which the first two cysteine residues are separated by one residue (Cys-X-Cys). The two alpha-chemokines, connective tissue activating peptide-III (CTAP-III) and neutrophil a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0796

    authors: Malkowski MG,Lazar JB,Johnson PH,Edwards BF

    更新日期:1997-02-21 00:00:00

  • Developmental regulation of the aldolase A muscle-specific promoter during in vivo muscle maturation is controlled by a nuclear receptor binding element.

    abstract::During the post-natal period, skeletal muscles undergo important modifications leading to the appearance of different types of myofibers which exhibit distinct contractile and metabolic properties. This maturation process results from the activation of the expression of different sets of contractile proteins and metab...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2821

    authors: Spitz F,Demignon J,Kahn A,Daegelen D,Maire P

    更新日期:1999-06-18 00:00:00

  • Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.

    abstract::Starting from the glycophorin A dimer structure determined by NMR, we performed simulations of both dimer and monomer forms in explicit lipid bilayers with constant normal pressure, lateral area, and temperature using the CHARMM potential. Analysis of the trajectories in four different lipids reveals how lipid chain l...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4072

    authors: Petrache HI,Grossfield A,MacKenzie KR,Engelman DM,Woolf TB

    更新日期:2000-09-22 00:00:00

  • The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

    abstract::Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.11.032

    authors: van Zundert GC,Trellet M,Schaarschmidt J,Kurkcuoglu Z,David M,Verlato M,Rosato A,Bonvin AM

    更新日期:2017-02-03 00:00:00

  • Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the Pdu microcompartment.

    abstract::Bacterial microcompartments (MCPs) are the simplest organelles known. They function to enhance metabolic pathways by confining several related enzymes inside an all-protein envelope called the shell. In this study, we investigated the factors that govern MCP assembly by performing scanning mutagenesis on the surface r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.04.012

    authors: Sinha S,Cheng S,Sung YW,McNamara DE,Sawaya MR,Yeates TO,Bobik TA

    更新日期:2014-06-12 00:00:00

  • NMR studies of the interactions of SpoIIAA with its partner proteins that regulate sporulation in Bacillus subtilis.

    abstract::SpoIIAA is a key component in the network of interactions that regulate the first sporulation-specific transcription factor, sigma(F), in Bacillus subtilis. In its unphosphorylated form SpoIIAA is either phosphorylated by or forms a non-covalent complex with SpoIIAB, whereas in its phosphorylated form it is dephosphor...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5142

    authors: Clarkson J,Campbell ID,Yudkin MD

    更新日期:2001-11-30 00:00:00

  • Crystal structure of tryptophanase.

    abstract::The X-ray structure of tryptophanase (Tnase) reveals the interactions responsible for binding of the pyridoxal 5'-phosphate (PLP) and atomic details of the K+ binding site essential for catalysis. The structure of holo Tnase from Proteus vulgaris (space group P2(1)2(1)2(1) with a = 115.0 A, b = 118.2 A, c = 153.7 A) h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1561

    authors: Isupov MN,Antson AA,Dodson EJ,Dodson GG,Dementieva IS,Zakomirdina LN,Wilson KS,Dauter Z,Lebedev AA,Harutyunyan EH

    更新日期:1998-02-27 00:00:00

  • Conformation of BCL-XL upon Membrane Integration.

    abstract::BCL-XL is an anti-apoptotic BCL-2 family protein found both in the cytosol and bound to intracellular membranes. Structural studies of BCL-XL have advanced by deleting its hydrophobic C-terminus and adding detergents to enhance solubility. However, since the C-terminus is essential for function and detergents strongly...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.02.019

    authors: Yao Y,Fujimoto LM,Hirshman N,Bobkov AA,Antignani A,Youle RJ,Marassi FM

    更新日期:2015-07-03 00:00:00

  • Purification and secondary structure determination of simian immunodeficiency virus p27.

    abstract::We have developed a novel method for the expression and purification of p27, the major core protein of simian immunodeficiency virus. Circular dichroism measurements of purified p27 were used to determine the relative amounts of alpha-helix, beta-sheet and unordered secondary structural elements. These empirically det...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80308-0

    authors: Burns NR,Craig S,Lee SR,Richardsons MH,Stenner N,Adams SE,Kingsman SM,Kingsman AJ

    更新日期:1990-11-20 00:00:00

  • Crystallization and preliminary X-ray analysis of phenylalanine hydroxylase from rat liver.

    abstract::Phenylalanine hydroxylase from rat liver has been crystallized from polyethylene glycol 4500 with sodium formate. The crystals are tetragonal rods and belong to space group P4(1)22 or P4(3)22 with unit cell dimensions a = b = 57.6 A and c = 304.1 A. They diffract to at least 2.4 A resolution and have one molecule per ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90694-2

    authors: Celikel R,Davis MD,Dai XP,Kaufman S,Xuong NH

    更新日期:1991-04-05 00:00:00

  • In vitro protein-primed initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3' nucleotide of the linear template: a stepwise sliding-back mechanism.

    abstract::Phage Cp-1 from Streptoccocus pneumoniae makes use of a protein-priming mechanism to start replication of its linear DNA: the first reaction consists of the addition of 5' dAMP to a molecule of the primer protein, an initiation event occurring at both DNA ends. After elongation of the initiation complex, the primer pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0407

    authors: Martín AC,Blanco L,García P,Salas M,Méndez J

    更新日期:1996-07-19 00:00:00

  • Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

    abstract::Epistasis is a key factor in evolution since it determines which combinations of mutations provide adaptive solutions and which mutational pathways toward these solutions are accessible by natural selection. There is growing evidence for the pervasiveness of sign epistasis--a complete reversion of mutational effects, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.05.011

    authors: Dellus-Gur E,Elias M,Caselli E,Prati F,Salverda ML,de Visser JA,Fraser JS,Tawfik DS

    更新日期:2015-07-17 00:00:00

  • Refinement of the influenza virus hemagglutinin by simulated annealing.

    abstract::We have applied the method of simulated annealing to the refinement of the 3 A resolution crystal structure of the influenza virus hemagglutinin glycoprotein, using the program X-PLOR. Two different methods were introduced into X-PLOR to treat the non-crystallographic symmetry present in this and in other crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90234-D

    authors: Weis WI,Brünger AT,Skehel JJ,Wiley DC

    更新日期:1990-04-20 00:00:00

  • Modular structure of the trigger factor required for high activity in protein folding.

    abstract::The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic d...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1206

    authors: Zarnt T,Tradler T,Stoller G,Scholz C,Schmid FX,Fischer G

    更新日期:1997-09-05 00:00:00

  • Cell Heterogeneity in Staphylococcal Communities.

    abstract::The human pathogen Staphylococcus aureus is a gram-positive bacterium that causes difficult-to-treat infections. One of the reasons why S. aureus is such as successful pathogen is due to the cell-to-cell physiological variability that exists within microbial communities. Many laboratories around the world study the ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2019.06.011

    authors: García-Betancur JC,Lopez D

    更新日期:2019-11-22 00:00:00

  • The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex.

    abstract::In Saccharomyces cerevisiae, the SIF2 gene product is an integral component of the Set3 complex (SET3C), an assembly of proteins with some homology to the human SMRT and N-CoR corepressor complexes. SET3C has histone deacetylase activity that is responsible for repressing a set of meiotic genes. We have determined the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.025

    authors: Cerna D,Wilson DK

    更新日期:2005-08-26 00:00:00

  • Peroxisome proliferator-activated receptor alpha controls hepatic heme biosynthesis through ALAS1.

    abstract::Heme is an essential prosthetic group of proteins involved in oxygen transport, energy metabolism and nitric oxide production. ALAS1 (5-aminolevulinate synthase) is the rate-limiting enzyme in heme synthesis in the liver and is highly regulated to adapt to the metabolic demand of the hepatocyte. In the present study, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,收录出版

    doi:10.1016/j.jmb.2009.03.024

    authors: Degenhardt T,Väisänen S,Rakhshandehroo M,Kersten S,Carlberg C

    更新日期:2009-05-01 00:00:00

  • Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

    abstract::Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mediator of angiogenesis and vasculogenesis. VEGF is involved pathologically in cancer, proliferative retinopathy and rheumatoid arthritis, and as such represents an important therapeutic target. Three classes of disulfide-constrained pept...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5370

    authors: Pan B,Li B,Russell SJ,Tom JY,Cochran AG,Fairbrother WJ

    更新日期:2002-02-22 00:00:00

  • Regulation of Microtubule Assembly by Tau and not by Pin1.

    abstract::The molecular mechanism by which the microtubule-associated protein (MAP) tau regulates the formation of microtubules (MTs) is poorly understood. The activity of tau is controlled via phosphorylation at specific Ser/Thr sites. Of those phosphorylation sites, 17 precede a proline, making them potential recognition site...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.03.010

    authors: Kutter S,Eichner T,Deaconescu AM,Kern D

    更新日期:2016-05-08 00:00:00

  • DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites.

    abstract::At low ionic strength, the SfiI restriction enzyme cleaved at similar rates both supercoiled and linear DNA with two SfiI sites and linear DNA with one SfiI site. For the substrates with two sites, the majority of the DNA was converted directly to products cut at both sites; the enzyme appears to bind to two sites bef...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0506

    authors: Nobbs TJ,Halford SE

    更新日期:1995-09-29 00:00:00

  • Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants.

    abstract::Plasmid pBR322 prepared from Escherichia coli strains carrying deletion of the DNA topoisomerase I gene (delta topA) with a compensatory mutation of the DNA gyrase gene (gyrA or gyrB) and from their TopA+ transductants was analyzed by agarose gel electrophoresis followed by electron microscopy, and compared with that ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90338-x

    authors: Shishido K,Komiyama N,Ikawa S

    更新日期:1987-05-05 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

  • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain.

    abstract::Riboswitches are cis-acting genetic regulatory elements found commonly in bacterial mRNAs that consist of a metabolite-responsive aptamer domain coupled to a regulatory switch. Purine riboswitches respond to intracellular concentrations of either adenine or guanine/hypoxanthine to control gene expression. The aptamer ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.04.003

    authors: Gilbert SD,Stoddard CD,Wise SJ,Batey RT

    更新日期:2006-06-09 00:00:00

  • Parallel and antiparallel Holliday junctions differ in structure and stability.

    abstract::Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy differe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90942-y

    authors: Lu M,Guo Q,Seeman NC,Kallenbach NR

    更新日期:1991-10-20 00:00:00

  • Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA.

    abstract::Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.01.058

    authors: Krishna R,Prabu JR,Manjunath GP,Datta S,Chandra NR,Muniyappa K,Vijayan M

    更新日期:2007-04-06 00:00:00

  • The Role of RNA Interference in Stem Cell Biology: Beyond the Mutant Phenotypes.

    abstract::Complex gene regulation systems ensure the maintenance of cellular identity during early development in mammals. Eukaryotic small RNAs have emerged as critical players in RNA interference (RNAi) by mediating gene silencing during embryonic stem cell self-renewal. Most of the proteins involved in the biogenesis of smal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2017.01.014

    authors: Bodak M,Cirera-Salinas D,Luitz J,Ciaudo C

    更新日期:2017-05-19 00:00:00