RNA-dependent folding and stabilization of C5 protein during assembly of the E. coli RNase P holoenzyme.

Abstract:

:The pre-tRNA processing enzyme ribonuclease P is a ribonucleoprotein. In Escherichia coli assembly of the holoenzyme involves binding of the small (119 amino acid residue) C5 protein to the much larger (377 nucleotide) P RNA subunit. The RNA subunit makes the majority of contacts to the pre-tRNA substrate and contains the active site; however, binding of C5 stabilizes P RNA folding and contributes to high affinity substrate binding. Here, we show that RNase P ribonucleoprotein assembly also influences the folding of C5 protein. Thermal melting studies demonstrate that the free protein population is a mixture of folded and unfolded conformations under conditions where it assembles quantitatively with the RNA subunit. Changes in the intrinsic fluorescence of a unique tryptophan residue located in the folded core of C5 provide further evidence for an RNA-dependent conformational change during RNase P assembly. Comparisons of the CD spectra of the free RNA and protein subunits with that of the holoenzyme provide evidence for changes in P RNA structure in the presence of C5 as indicated by previous studies. Importantly, monitoring the temperature dependence of the CD signal in regions of the holoenzyme spectra that are dominated by protein or RNA structure permitted analysis of the thermal melting of the individual subunits within the ribonucleoprotein. These analyses reveal a significantly higher Tm for C5 when bound to P RNA and show that unfolding of the protein and RNA are coupled. These data provide evidence for a general mechanism in which the favorable free energy for formation of the RNA-protein complex offsets the unfavorable free energy of structural rearrangements in the RNA and protein subunits.

journal_name

J Mol Biol

authors

Guo X,Campbell FE,Sun L,Christian EL,Anderson VE,Harris ME

doi

10.1016/j.jmb.2006.05.001

subject

Has Abstract

pub_date

2006-06-30 00:00:00

pages

190-203

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)00564-X

journal_volume

360

pub_type

杂志文章
  • Assessing the flexibility of intermediate filaments by atomic force microscopy.

    abstract::Eukaryotic cells contain three cytoskeletal filament systems that exhibit very distinct assembly properties, supramolecular architectures, dynamic behaviour and mechanical properties. Microtubules and microfilaments are relatively stiff polar structures whose assembly is modulated by the state of hydrolysis of the bou...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.038

    authors: Mücke N,Kreplak L,Kirmse R,Wedig T,Herrmann H,Aebi U,Langowski J

    更新日期:2004-01-30 00:00:00

  • Isolation and characterization of mutants affecting functional domains of ColE1 RNAI.

    abstract::The control of DNA replication initiation in the plasmid ColE1 is mediated by RNAI, a 108 nucleotide plasmid-encoded RNA that is entirely complementary to the 5'-terminal region of the replication primer RNA. RNAI acts in trans to inhibit primer maturation. Previously, we constructed a plasmid in which the ColE1 RNAI ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90259-1

    authors: Dooley TP,Tamm J,Polisky B

    更新日期:1985-11-05 00:00:00

  • Site-directed mutagenesis on human cystathionine-gamma-lyase reveals insights into the modulation of H2S production.

    abstract::In recent years, increased interest has been directed towards hydrogen sulfide (H2S) as the third gasotransmitter and its role in various diseases. Cystathionine-gamma-lyase (CSE) is one of the enzymes responsible for the endogenous production of H2S in mammals. With the aid of the crystal structures of human CSE and ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.058

    authors: Huang S,Chua JH,Yew WS,Sivaraman J,Moore PK,Tan CH,Deng LW

    更新日期:2010-02-26 00:00:00

  • The 0.93A crystal structure of sphericase: a calcium-loaded serine protease from Bacillus sphaericus.

    abstract::We have previously isolated sphericase (Sph), an extracellular mesophilic serine protease produced by Bacillus sphaericus. The Sph amino acid sequence is highly homologous to two cold-adapted subtilisins from Antarctic bacilli S39 and S41 (76% and 74% identity, respectively). Sph is calcium-dependent, 310 amino acid r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.07.011

    authors: Almog O,González A,Klein D,Greenblatt HM,Braun S,Shoham G

    更新日期:2003-10-03 00:00:00

  • Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.

    abstract::The refined structure of the peripheral light-harvesting complex from Rhodopseudomonas acidophila strain 10050 reveals a membrane protein with protein-protein interactions in the trans-membrane region exclusively of a van der Waals nature. The dominant factors in the formation of the complex appear to be extramembrano...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0966

    authors: Prince SM,Papiz MZ,Freer AA,McDermott G,Hawthornthwaite-Lawless AM,Cogdell RJ,Isaacs NW

    更新日期:1997-05-02 00:00:00

  • Solution structure of a C-terminal coiled-coil domain from bovine IF(1): the inhibitor protein of F(1) ATPase.

    abstract::Bovine IF(1) is a basic, 84 amino acid residue protein that inhibits the hydrolytic action of the F(1)F(0) ATP synthase in mitochondria under anaerobic conditions. Its oligomerization state is dependent on pH. At a pH value below 6.5 it forms an active dimer. At higher pH values, two dimers associate to form an inacti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4570

    authors: Gordon-Smith DJ,Carbajo RJ,Yang JC,Videler H,Runswick MJ,Walker JE,Neuhaus D

    更新日期:2001-04-27 00:00:00

  • Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton.

    abstract::The antibiotic thiostrepton, a thiazole-containing peptide, inhibits translation and ribosomal GTPase activity by binding directly to a limited and highly conserved region of the large subunit ribosomal RNA termed the GTPase center. We have previously used a filter binding assay to examine the binding of ribosomal pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90932-v

    authors: Ryan PC,Lu M,Draper DE

    更新日期:1991-10-20 00:00:00

  • Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release.

    abstract::In honeybee (Apis mellifera) societies, the queen controls the development and the caste status of the members of the hive. Queen bees secrete pheromonal blends comprising 10 or more major and minor components, mainly hydrophobic. The major component, 9-keto-2(E)-decenoic acid (9-ODA), acts on the workers and male bee...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.05.067

    authors: Pesenti ME,Spinelli S,Bezirard V,Briand L,Pernollet JC,Campanacci V,Tegoni M,Cambillau C

    更新日期:2009-07-31 00:00:00

  • Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope.

    abstract::Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.10.014

    authors: Stanfield RL,Julien JP,Pejchal R,Gach JS,Zwick MB,Wilson IA

    更新日期:2011-12-02 00:00:00

  • Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin.

    abstract::The interplay between metal binding, carbohydrate binding activity, stability and structure of the lectin from Pterocarpus angolensis was investigated. Removal of the metals leads to a more flexible form of the protein with significantly less conformational stability. Crystal structures of this metal-free form show si...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.006

    authors: Garcia-Pino A,Buts L,Wyns L,Loris R

    更新日期:2006-08-04 00:00:00

  • Expression and structural analysis of 14-3-3 proteins.

    abstract::The 14-3-3 family of proteins plays a role in a wide variety of cellular functions including regulation of protein kinase C and exocytosis. Using antisera specific for the N termini of 14-3-3 isoforms described previously and an additional antiserum specific for the C terminus of epsilon isoform, protease digestion of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.0031

    authors: Jones DH,Martin H,Madrazo J,Robinson KA,Nielsen P,Roseboom PH,Patel Y,Howell SA,Aitken A

    更新日期:1995-01-27 00:00:00

  • Hemoglobin allostery: new views on old players.

    abstract::Proteins are dynamic molecular machines whose structure and function are modulated by environmental perturbations and natural selection. Allosteric regulation, discovered in 1963 as a novel molecular mechanism of enzymatic adaptation [Monod, Changeux & Jacob (1963). J. Mol. Biol.6, 306-329], seems to be the leit motiv...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.12.018

    authors: Miele AE,Bellelli A,Brunori M

    更新日期:2013-05-13 00:00:00

  • The Role of RNA in Biological Phase Separations.

    abstract::Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase sep...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.05.003

    authors: Fay MM,Anderson PJ

    更新日期:2018-11-02 00:00:00

  • A miniprotein scaffold used to assemble the polyproline II binding epitope recognized by SH3 domains.

    abstract::SH3 domains are molecular-recognition modules that function by interacting with proteins containing sequences in polyproline II (PPII) conformation. The main limitation in designing short-ligand peptides to interact with these domains is the preservation of this helical arrangement, for which a high content of proline...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.06.078

    authors: Cobos ES,Pisabarro MT,Vega MC,Lacroix E,Serrano L,Ruiz-Sanz J,Martinez JC

    更新日期:2004-09-03 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

  • Regulation of mating-type information in yeast. Negative control requiring sequences both 5' and 3' to the regulated region.

    abstract::The genome of the yeast Saccharomyces cerevisiae contains three complete copies of the genetic information governing cell mating type. Normally, only the information in one of the copies (the MAT locus) is expressed; the other two copies (HML and HMR) are repressed and serve as donors of mating-type sequences that can...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90492-3

    authors: Abraham J,Nasmyth KA,Strathern JN,Klar AJ,Hicks JB

    更新日期:1984-07-05 00:00:00

  • Force-induced conformational change of bacteriorhodopsin.

    abstract::The cytoplasmic surface topography of purple membranes imaged by the atomic force microscope depends mainly on the force applied to the stylus. Imaged at forces of 300 pN, individual bacteriorhodopsin molecules reveal two domains. The resulting donut-shaped trimers reversibly transform into structures exhibiting three...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0292

    authors: Müller DJ,Büldt G,Engel A

    更新日期:1995-06-02 00:00:00

  • The crystal structures of trout Hb I in the deoxy and carbonmonoxy forms.

    abstract::We have determined the X-ray crystallographic structure of trout Hb I in both the deoxy and carbonmonoxy forms to resolution limits of 2.3 angstroms and 2.5 angstroms, respectively. The overall fold of the molecule is highly similar to that of human HbA despite the low level of sequence identity between these proteins...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0355

    authors: Tame JR,Wilson JC,Weber RE

    更新日期:1996-06-21 00:00:00

  • Human liver cathepsin D. Purification, crystallization and preliminary X-ray diffraction analysis of a lysosomal enzyme.

    abstract::The two-chain form of active cathepsin D, a glycosylated, lysosomal aspartic proteinase, has been isolated from human liver. Isoelectric focusing revealed two major species of enzyme that differed by approximately 0.2 pI unit. Crystals suitable for X-ray diffraction analysis were prepared from acidic solutions using p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90696-h

    authors: Gulnik S,Baldwin ET,Tarasova N,Erickson J

    更新日期:1992-09-05 00:00:00

  • Both binding sites of the starch-binding domain of Aspergillus niger glucoamylase are essential for inducing a conformational change in amylose.

    abstract::The interaction of the two binding sites of the starch-binding domain (SBD) of Aspergillus niger glucoamylase 1 (GA-I) with substrate has been investigated by using atomic force microscopy (AFM) and UV difference spectroscopy in combination with site-specific mutants of both SBD and GA-I. The SBD possesses two binding...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5097

    authors: Giardina T,Gunning AP,Juge N,Faulds CB,Furniss CS,Svensson B,Morris VJ,Williamson G

    更新日期:2001-11-09 00:00:00

  • A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction.

    abstract::Several RNA-cleaving deoxyribozymes (DNAzymes) have been reported for efficient cleavage of purine-containing junctions, but none is able to efficiently cleave pyrimidine-pyrimidine (Pyr-Pyr) junctions. We hypothesize that a stronger Pyr-Pyr cleavage activity requires larger DNAzymes with complex structures that are d...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.047

    authors: Lam JC,Withers JB,Li Y

    更新日期:2010-07-23 00:00:00

  • Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3'-terminal intron alterations on cleavage at the 5' and 3' splice site.

    abstract::A shortened derivative of the group IIA intron from the mitochondrial cytochrome-c-oxidase subunit I gene (COI I1) of the ascomycete Podospora anserina can undergo self-splicing in vitro. When compared to self-splicing group IIB introns from yeast mitochondria (aI5c, bI1) the autocatalytic reaction shows a lower effic...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1309

    authors: Schmidt U,Sägebarth R,Schmelzer C,Stahl U

    更新日期:1993-06-05 00:00:00

  • Modeling a minimal ribosome based on comparative sequence analysis.

    abstract::We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00568-5

    authors: Mears JA,Cannone JJ,Stagg SM,Gutell RR,Agrawal RK,Harvey SC

    更新日期:2002-08-09 00:00:00

  • Molecular evolution of antibody affinity for sensitive detection of botulinum neurotoxin type A.

    abstract::Botulism is caused by botulinum neurotoxin (BoNT), the most poisonous substance known. Potential use of BoNT as a biothreat agent has made development of sensitive assays for toxin detection and potent antitoxin for treatment of intoxication a high priority. To improve detection and treatment of botulism, molecular ev...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.003

    authors: Razai A,Garcia-Rodriguez C,Lou J,Geren IN,Forsyth CM,Robles Y,Tsai R,Smith TJ,Smith LA,Siegel RW,Feldhaus M,Marks JD

    更新日期:2005-08-05 00:00:00

  • Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration.

    abstract::The enthalpy of hydration of polar and non-polar groups upon protein unfolding has been estimated for four globular proteins in the temperature range 5 to 125 degrees C, using structural information on the groups in these proteins exposed to water in the native and unfolded states and volume-corrected calorimetric inf...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1416

    authors: Makhatadze GI,Privalov PL

    更新日期:1993-07-20 00:00:00

  • Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle.

    abstract::Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the ph...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00903-3

    authors: Onufriev A,Smondyrev A,Bashford D

    更新日期:2003-10-03 00:00:00

  • Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA.

    abstract::Complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. The dominating components in ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a single modified nucleoside at position 2501 in 23S rRNA-has previously...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.06.036

    authors: Havelund JF,Giessing AM,Hansen T,Rasmussen A,Scott LG,Kirpekar F

    更新日期:2011-08-19 00:00:00

  • Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression.

    abstract::The enantioselectivity of lipase from Burkhorderia cepacia KWI-56 has been inverted using a novel in vitro technique for construction and screening of a protein library by single-molecule DNA amplification by PCR followed by in vitro coupled transcription/translation system termed single-molecule-PCR-linked in vitro e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00782-4

    authors: Koga Y,Kato K,Nakano H,Yamane T

    更新日期:2003-08-15 00:00:00

  • Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity.

    abstract::The structures of three crystal forms of the class mu human glutathione transferase GSTM2-2 have been determined. X-ray phase information was obtained independently from molecular replacement and from anomalous scattering by a single isomorphous derivative. One crystal form contains a single monomer in the asymmetric ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1336

    authors: Raghunathan S,Chandross RJ,Kretsinger RH,Allison TJ,Penington CJ,Rule GS

    更新日期:1994-05-20 00:00:00

  • Mapping the stability determinants of bacterial tyrosyl transfer RNA synthetases by an experimental evolutionary approach.

    abstract::The tyrosyl-tRNA synthetases from Bacillus stearothermophilus (Bst-TyrTS) and Escherichia coli (Eco-TyrTS) are 56% identical in amino acid sequence. To map and characterize the set of interactions that makes Bst-TyrTS more stable than Eco-TyrTS, a family of nine hybrid proteins was constructed between the two enzymes....

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1575

    authors: Guez-Ivanier V,Hermann M,Baldwin D,Bedouelle H

    更新日期:1993-11-05 00:00:00