Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.

Abstract:

:L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.

journal_name

J Mol Biol

authors

Agrawal RK,Linde J,Sengupta J,Nierhaus KH,Frank J

doi

10.1006/jmbi.2001.4907

keywords:

subject

Has Abstract

pub_date

2001-08-24 00:00:00

pages

777-87

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)94907-1

journal_volume

311

pub_type

杂志文章
  • Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA.

    abstract::The roll-twist-slide correlation in the DNA crystal structures that are collected in the Nucleic Acid Data Base is analyzed in order to obtain a general understanding of the effects of the nucleotide sequence on the 3D structure of a dinucleotide step. It is concluded that the differences between the pyrimidine bases ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1406

    authors: Suzuki M,Amano N,Kakinuma J,Tateno M

    更新日期:1997-12-05 00:00:00

  • Dielectric constant of sickle cell hemoglobin. Dielectric properties of sickle cell hemoglobin in solution and gel.

    abstract::The dielectric constants of sickle cell hemoglobin were determined before and after gelation. The dielectric properties of oxy and deoxy sickle cell hemoglobin in solution are nearly identical to those of oxy and deoxy hemoglobin A. Only in the gel state did deoxy sickle cell hemoglobin display dielectric behavior dif...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80307-6

    authors: Delalic Z,Takashima S,Adachi K,Asakura T

    更新日期:1983-08-15 00:00:00

  • Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins.

    abstract::The bacterial immunity proteins Im7 and Im9 fold with mechanisms of different kinetic complexity. Whilst Im9 folds in a two-state transition at pH 7.0 and 10 degrees C, Im7 populates an on-pathway intermediate under these conditions. In order to assess the role of sequence versus topology in the folding of these prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01249-4

    authors: Friel CT,Capaldi AP,Radford SE

    更新日期:2003-02-07 00:00:00

  • Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

    abstract::What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2. We find that residue...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01434-1

    authors: Kaya H,Chan HS

    更新日期:2003-02-21 00:00:00

  • On the mechanism of leftward frameshifting at several hungry codons.

    abstract::We have used lacZ reporter genes to assess leftward ribosome frameshifting on sequences containing the quadruplet U UUC followed by several different triplets coding for lysine, isoleucine, or leucine. Limitation for lysine-tRNA provokes leftward frameshifting when the slippery quadruplet is followed by either lysine ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0117

    authors: Barak Z,Lindsley D,Gallant J

    更新日期:1996-03-08 00:00:00

  • Reconstitution of selenocysteine incorporation reveals intrinsic regulation by SECIS elements.

    abstract::Selenoproteins are present in all three domains of life and are responsible for a major part of a cell's antioxidant defense against reactive oxygen species. Synthesis of selenoproteins requires the decoding of a UGA codon as selenocysteine (Sec) instead of translation termination. Sec is incorporated into the growing...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.04.016

    authors: Gupta N,DeMong LW,Banda S,Copeland PR

    更新日期:2013-07-24 00:00:00

  • The foldon universe: a survey of structural similarity and self-recognition of independently folding units.

    abstract::We have identified independently folding units, so called "foldons", from non-homologous proteins representing different folds. We applied simple statistical arguments in order to estimate the size of the foldon universe required to construct all foldable proteins. Various alignment procedures yield about 2600 foldons...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1205

    authors: Panchenko AR,Luthey-Schulten Z,Cole R,Wolynes PG

    更新日期:1997-09-12 00:00:00

  • Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme.

    abstract::We have investigated the effects of Co(NH3)6(3+), an analog of hexahydrated Mg2+, on folding and catalysis of the Neurospora VS ribozyme. Most of the metal ion-induced changes detected by chemical modification structure probing in either metal ion are similar, but occur at approximately 33-fold lower concentrations of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4625

    authors: Maguire JL,Collins RA

    更新日期:2001-05-25 00:00:00

  • Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7.

    abstract::Reverse transcription of HIV-1 genomic RNA to double-stranded DNA by reverse transcriptase (RT) is a critical step in HIV-1 replication. This process relies on two viral proteins, the RT enzyme and nucleocapsid protein NCp7 that has well documented nucleic acid chaperone properties. At the beginning of the linear DNA ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00244-4

    authors: Beltz H,Azoulay J,Bernacchi S,Clamme JP,Ficheux D,Roques B,Darlix JL,Mély Y

    更新日期:2003-04-18 00:00:00

  • Mutations that alter initiation codon discrimination by Escherichia coli initiation factor IF3.

    abstract::This work describes the isolation of mutations in infC, the structural gene for IF3, using different genetic screens. Among 21 mutants characterised, seven were shown to produce stable variant IF3 proteins unable to fully complement a strain carrying a chromosomal deletion of the infC gene. The mutants were also shown...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2737

    authors: Sacerdot C,de Cock E,Engst K,Graffe M,Dardel F,Springer M

    更新日期:1999-05-21 00:00:00

  • RecA protein assisted selection reveals a low fidelity of recognition of homology in a duplex DNA by an oligonucleotide.

    abstract::We have developed an in vitro selection procedure to elucidate the specificity of RecA assisted oligonucleotide recognition of double stranded DNA. The procedure was based on formation of a synaptic complex between an oligonucleotide-RecA filament and a supercoiled plasmid bearing a homologous partially degenerate reg...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1164

    authors: Malkov VA,Sastry L,Camerini-Otero RD

    更新日期:1997-08-15 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

  • Crystal structure of the pertussis toxin-ATP complex: a molecular sensor.

    abstract::Pertussis toxin is a major virulence factor of Bordetella pertussis, the causative agent of whooping cough. The protein is a hexamer containing a catalytic subunit (S1) that is tightly associated with a pentameric cell-binding component (B-oligomer). In vitro experiments have shown that ATP and a number of detergents ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0277

    authors: Hazes B,Boodhoo A,Cockle SA,Read RJ

    更新日期:1996-05-17 00:00:00

  • Characterization of human cytomegalovirus uracil DNA glycosylase (UL114) and its interaction with polymerase processivity factor (UL44).

    abstract::Here, we report the molecular characterization of the human cytomegalovirus uracil DNA glycosylase (UNG) UL114. Purified UL114 was shown to be a DNA glycosylase, which removes uracil from double-stranded and single-stranded DNA. However, kinetic analysis has shown that viral UNG removed uracil more slowly compared wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.028

    authors: Ranneberg-Nilsen T,Dale HA,Luna L,Slettebakk R,Sundheim O,Rollag H,Bjørås M

    更新日期:2008-08-29 00:00:00

  • Correlation between conformational and binding properties of nebulin repeats.

    abstract::Nebulin, a large protein (600 to 800 kDa) located in the thin filament of striated vertebrate muscle, is assumed to bind and stabilise F-actin. Complete sequence determination of human nebulin has only recently been accomplished showing a uniform modular structure along the whole length of the molecule. Up to 97% of t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0169

    authors: Pfuhl M,Winder SJ,Castiglione Morelli MA,Labeit S,Pastore A

    更新日期:1996-03-29 00:00:00

  • Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein.

    abstract::The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein domains, and is found in many proteins involved in recognition of a wide variety of RNAs. Two structures of RNA complexes of human U1A protein have revealed important aspects of RNP-RNA recognition, but have also raised intriguing question...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3311

    authors: Mittermaier A,Varani L,Muhandiram DR,Kay LE,Varani G

    更新日期:1999-12-10 00:00:00

  • Trypanosoma brucei variant-specific glycoprotein gene chromatin is sensitive to single-strand-specific endonuclease digestion.

    abstract::Active variant surface glycoprotein (VSG) gene chromatin is preferentially digested by the restriction enzyme HinfI in nuclei of bloodstream variants of Trypanosoma brucei. HinfI sensitivity of VSG gene chromatin is not observed in nuclei of relapse variants in which the VSG gene has been inactivated in situ. Active V...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90559-6

    authors: Greaves DR,Borst P

    更新日期:1987-10-05 00:00:00

  • Proteasome Structure and Assembly.

    abstract::The eukaryotic 26S proteasome is a large multisubunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle and the 20S core particle. Most substrates are first covalently modified by ubiquitin, which the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2017.05.027

    authors: Budenholzer L,Cheng CL,Li Y,Hochstrasser M

    更新日期:2017-11-10 00:00:00

  • Regulation of the Caenorhabditis elegans gut cysteine protease gene cpr-1: requirement for GATA motifs.

    abstract::Expression of the Caenorhabditis elegans cysteine protease gene cpr-1 is regulated both spatially and temporally. In situ hybridisation and Northern blot analysis have shown that this gene is expressed exclusively in gut cells of all developmental stages except the embryo. We now show by transgenic transformation with...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2093

    authors: Britton C,McKerrow JH,Johnstone IL

    更新日期:1998-01-01 00:00:00

  • Nucleosome core particle stability and conformational change. Effect of temperature, particle and NaCl concentrations, and crosslinking of histone H3 sulfhydryl groups.

    abstract::We have studied the reversible dissociation of core size DNA from chicken erythrocyte nucleosome core particles in solutions containing 0 X 1 M to 0 X 6 M-NaCl. Dissociation increases with increasing NaCl concentration, increasing temperature and decreasing particle concentration. At high particle concentrations, no f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90383-8

    authors: Ausio J,Seger D,Eisenberg H

    更新日期:1984-06-15 00:00:00

  • Mutational analysis of the pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA. Aminoacylation efficiency and RNA pseudoknot stability.

    abstract::Site-directed mutations were introduced in the connecting loops and one of the two stem regions of the RNA pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA. The kinetic parameters of valylation for each mutated RNA were determined in a cell-free extract from wheat germ. Structure mapping was per...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90727-2

    authors: Mans RM,Van Steeg MH,Verlaan PW,Pleij CW,Bosch L

    更新日期:1992-01-05 00:00:00

  • Folding transitions during assembly of the eukaryotic mRNA cap-binding complex.

    abstract::The cap-binding protein eIF4E is the first in a chain of translation initiation factors that recruit 40S ribosomal subunits to the 5' end of eukaryotic mRNA. During cap-dependent translation, this protein binds to the 5'-terminal m(7)Gppp cap of the mRNA, as well as to the adaptor protein eIF4G. The latter then intera...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.12.034

    authors: von der Haar T,Oku Y,Ptushkina M,Moerke N,Wagner G,Gross JD,McCarthy JE

    更新日期:2006-03-03 00:00:00

  • Reconstituted and native iron-cores of bacterioferritin and ferritin.

    abstract::The structural and magnetic properties of the iron-cores of reconstituted horse spleen ferritin and Azotobacter vinelandii bacterioferritin have been investigated by high-resolution transmission electron microscopy, electron diffraction and Mossbauer spectroscopy. The structural properties of native horse spleen ferri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90290-7

    authors: Mann S,Williams JM,Treffry A,Harrison PM

    更新日期:1987-12-05 00:00:00

  • Intriguing conformation changes associated with the trans/cis isomerization of a prolyl residue in the active site of the DsbA C33A mutant.

    abstract::Escherichia coli DsbA belongs to the thioredoxin family and catalyzes the formation of disulfide bonds during the folding of proteins in the bacterial periplasm. It active site (C30-P31-H32-C33) consists of a disulfide bridge that is transferred to newly translocated proteins. The work reported here refers to the DsbA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.01.049

    authors: Ondo-Mbele E,Vivès C,Koné A,Serre L

    更新日期:2005-04-01 00:00:00

  • Fourteen protomers compose the oligomer III of the proton-rotor in spinach chloroplast ATP synthase.

    abstract::Three fundamentally different chloroplast ATP synthase samples of increasing complexity were visualized by atomic force microscopy. The samples are distinguishable in respect to the isolation technique, the detergent employed, and the final subunit composition. The homo-oligomer III was isolated following SDS treatmen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.08.046

    authors: Seelert H,Dencher NA,Müller DJ

    更新日期:2003-10-17 00:00:00

  • Structural determinants of natriuretic peptide receptor specificity and degeneracy.

    abstract::Cardiovascular homeostasis and blood pressure regulation are reliant, in part, on interactions between natriuretic peptide (NP) hormones and natriuretic peptide receptors (NPR). The C-type NPR (NPR-C) is responsible for clearance of NP hormones from the circulation, and displays a cross-reactivity for all NP hormones ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.060

    authors: He XL,Dukkipati A,Garcia KC

    更新日期:2006-08-25 00:00:00

  • Segregation of type I collagen homo- and heterotrimers in fibrils.

    abstract::Normal type I collagen is a heterotrimer of two alpha1(I) and one alpha2(I) chains, but various genetic and environmental factors result in synthesis of homotrimers that consist of three alpha1(I) chains. The homotrimers completely replace the heterotrimers only in rare recessive disorders. In the general population, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.08.008

    authors: Han S,McBride DJ,Losert W,Leikin S

    更新日期:2008-10-31 00:00:00

  • Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH.

    abstract::The crystal structure of the homodimer of quinone oxidoreductase from Escherichia coli has been determined using the multiple isomorphous replacement method at 2.2 A resolution and refined to an R-factor of 14.1% The crystallographic asymmetric unit contains one functional dimer with the two subunits being related by ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0337

    authors: Thorn JM,Barton JD,Dixon NE,Ollis DL,Edwards KJ

    更新日期:1995-06-16 00:00:00

  • Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

    abstract::The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90134-6

    authors: Kostrewa D,Granzin J,Stock D,Choe HW,Labahn J,Saenger W

    更新日期:1992-07-05 00:00:00

  • Premature stop codons inactivate the RT6 genes of the human and chimpanzee species.

    abstract::RT6 is a glycosyl phosphatidylinositol-anchored cell membrane protein, whose expression is restricted to peripheral T cells and intraepithelial lymphocytes. It has attracted interest as a T cell differentiation marker and activation antigen in rats. The only known protein to which RT6 shows significant homology is a r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1680

    authors: Haag F,Koch-Nolte F,Kühl M,Lorenzen S,Thiele HG

    更新日期:1994-10-28 00:00:00