The anticodon loop is a major identity determinant of Saccharomyces cerevisiae tRNA(Leu).

Abstract:

:The recognition of tRNALeu, one of the class II tRNAs having a long variable arm, by leucyl-tRNA synthetase in Saccharomyces cerevisiae was studied using the T7 transcription system. Exchanging the anticodon arm of tRNALeu but not the D- or T psi C-arm to that of tRNASer seriously affected the leucine accepting activity. Two nucleotides in the anticodon loop, A35 and G37, were found to be important for leucylation. It was also found that the discriminator base, A73, is required for leucylation, and G73 of tRNASer functions as a negative identity determinant for leucyl-tRNA synthetase. Introducing a set of three base substitutions at positions 35, 37 and 73 was sufficient to convert tRNASer into an efficient leucine acceptor. These results indicate that the identity elements of tRNALeu lie at the second position of the anticodon and the 3' adjacent to the anticodon as well as the discriminator position. Such a sequence specific recognition manner is significantly different from that of Escherichia coli, in which not the anticodon but the tertiary structural elements play a key role in discriminating from other class II tRNAs. The leucine system is the first example which shows that the requirement of the anticodon sequence is variable among species.

journal_name

J Mol Biol

authors

Soma A,Kumagai R,Nishikawa K,Himeno H

doi

10.1006/jmbi.1996.0610

subject

Has Abstract

pub_date

1996-11-15 00:00:00

pages

707-14

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(96)90610-5

journal_volume

263

pub_type

杂志文章
  • Mia40 combines thiol oxidase and disulfide isomerase activity to efficiently catalyze oxidative folding in mitochondria.

    abstract::Mia40 (a mitochondrial import and assembly protein) catalyzes disulfide bond formation in proteins in the mitochondrial intermembrane space. By using Cox17 (a mitochondrial copper-binding protein) as a natural substrate, we discovered that, in the presence of Mia40, the formation of native disulfides is strongly favor...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.10.022

    authors: Koch JR,Schmid FX

    更新日期:2014-12-12 00:00:00

  • Fluorescence energy transfer distance measurements using site-directed single cysteine mutants. The membrane insertion of colicin A.

    abstract::The ion-channel-forming C-terminal fragment of colicin A binds to negatively charged lipid vesicles and provides an example of insertion of a soluble protein into a lipid bilayer. The soluble structure is known from X-ray crystallography and consists of a ten-helix bundle containing a hydrophobic helical hairpin. In t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90707-d

    authors: Lakey JH,Baty D,Pattus F

    更新日期:1991-04-05 00:00:00

  • Evolution of function in protein superfamilies, from a structural perspective.

    abstract::The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4513

    authors: Todd AE,Orengo CA,Thornton JM

    更新日期:2001-04-06 00:00:00

  • Central domain of the positive control protein NifA and its role in transcriptional activation.

    abstract::The positive control protein NifA of Klebsiella pneumoniae activates transcription by RNA polymerase containing sigma 54 by catalysing open promoter complex formation. We show that the integrity of the putative ATP-binding pocket in the central domain of NifA is necessary for the positive control function of NifA, but...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90921-6

    authors: Cannon W,Buck M

    更新日期:1992-05-20 00:00:00

  • Structure of the vanadate-induced crystals of sarcoplasmic reticulum Ca2+-ATPase.

    abstract::The projected structure of the vanadate-induced crystalline aggregates of Ca2+-ATPase molecules in isolated sarcoplasmic reticulum membranes has been determined. The molecules form tubular crystals with an oblique surface lattice having cell dimensions a = 65.9 A, b = 114.4 A and gamma = 77.9 degrees. The space group ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90372-3

    authors: Taylor K,Dux L,Martonosi A

    更新日期:1984-03-25 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

  • X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 A resolution.

    abstract::Dihydropyrimidinases (hydantoinases) catalyse the reversible hydrolytic ring-opening of cyclic diamides such as dihydropyrimidines in the catabolism of pyrimidines. In biotechnology, these enzymes find application in the enantiospecific production of amino acids from racemic hydantoins. The crystal structure of a D-en...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00422-9

    authors: Abendroth J,Niefind K,Schomburg D

    更新日期:2002-06-28 00:00:00

  • Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding.

    abstract::The mom gene of bacteriophage Mu, which codes for a DNA modification function, is regulated in a complex manner at both transcriptional and translational levels. The phage-encoded C protein functions as an activator of mom transcription. The mom promoter has features of an activator-dependent weak promoter, and the C ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0379

    authors: Ramesh V,Nagaraja V

    更新日期:1996-07-05 00:00:00

  • FLP protein of 2 mu circle plasmid of yeast induces multiple bends in the FLP recognition target site.

    abstract::The FLP recombinase of the 2 mu plasmid of Saccharomyces cerevisiae binds to a target containing three 13 base-pair symmetry elements called a, b and c. The symmetry elements b and c are in direct orientation while the a element is in inverted orientation with respect to b and c on the opposite side of an eight base-p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80320-1

    authors: Schwartz CJ,Sadowski PD

    更新日期:1990-11-20 00:00:00

  • Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.

    abstract::The crystal structure of a construct consisting of the FERM and SH2-like domains of the human Janus kinase 1 (JAK1) bound to a fragment of the intracellular domain of the interferon-λ receptor 1 (IFNLR1) has been determined at the nominal resolution of 2.1Å. In this structure, the receptor peptide forms an 85-Å-long e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.10.005

    authors: Zhang D,Wlodawer A,Lubkowski J

    更新日期:2016-11-20 00:00:00

  • Crystallization and subunit structure of canine myeloperoxidase.

    abstract::Three crystal forms of canine myeloperoxidase are described. An orthorhombic form in space group P2(1)2(1)2(1) has unit cell dimensions: a = 108.3 A (1 A = 0.1 nm) b = 205.9 A and c = 139.9 A. A trigonal form in space group P3(1)21 or P3(2)21 has unit cell dimensions: a = b = 138.9 A and c = 145.2 A. A monoclinic form...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90413-x

    authors: Fenna RE

    更新日期:1987-08-20 00:00:00

  • Crystal structure of the molecular chaperone HscA substrate binding domain complexed with the IscU recognition peptide ELPPVKIHC.

    abstract::HscA, a specialized bacterial Hsp70-class molecular chaperone, interacts with the iron-sulfur cluster assembly protein IscU by recognizing a conserved LPPVK sequence motif. We report the crystal structure of the substrate-binding domain of HscA (SBD, residues 389-616) from Escherichia coli bound to an IscU-derived pep...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.025

    authors: Cupp-Vickery JR,Peterson JC,Ta DT,Vickery LE

    更新日期:2004-09-24 00:00:00

  • Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

    abstract::Conformationally constrained environment-dependent amino acid residue substitution tables have been constructed from a database comprising 33 homologous families of protein sequences aligned on the basis of their three-dimensional structures. Residues are allotted to one of 216 (or 54) classes of combinations of struc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1018

    authors: Topham CM,McLeod A,Eisenmenger F,Overington JP,Johnson MS,Blundell TL

    更新日期:1993-01-05 00:00:00

  • Capsids and Portals Influence Each Other's Conformation During Assembly and Maturation.

    abstract::The portal proteins of tailed bacteriophage and Herpesvirus capsids form dodecameric rings that occupy one capsid vertex and are incorporated during the assembly of capsid precursors called procapsids or proheads. Portals are essential and serve as the pore for DNA transit and the site of tail attachment; however, bac...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.01.022

    authors: Maurer JB,Oh B,Moyer CL,Duda RL

    更新日期:2020-03-27 00:00:00

  • Quality control in eukaryotic membrane protein overproduction.

    abstract::The overexpression of authentically folded eukaryotic membrane proteins in milligramme quantities is a fundamental prerequisite for structural studies. One of the most commonly used expression systems for the production of mammalian membrane proteins is the baculovirus expression system in insect cells. However, a det...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.10.012

    authors: Thomas JA,Tate CG

    更新日期:2014-12-12 00:00:00

  • Co-optimization of ribozyme substrate stacking and L-arginine binding.

    abstract::A model of the Tetrahymena catalytic site predicts that nucleotide 262 (nt262) caps an RNA pocket in which nucleoside substrates and arginine-like competitive inhibitors reside. Here we show that substituted RNAs behave as if nt262 stacks on nucleoside substrates, supporting the model. The more frequent an nt262 is in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90095-2

    authors: Yarus M,Majerfeld I

    更新日期:1992-06-20 00:00:00

  • Programming microbes using pulse width modulation of optical signals.

    abstract::Cells transmit and receive information via signalling pathways. A number of studies have revealed that information is encoded in the temporal dynamics of these pathways and has highlighted how pathway architecture can influence the propagation of signals in time and space. The functional properties of pathway architec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.07.036

    authors: Davidson EA,Basu AS,Bayer TS

    更新日期:2013-11-15 00:00:00

  • Growth-rate-dependent accumulation of twelve tRNA species in Escherichia coli.

    abstract::We have previously shown that in Escherichia coli the accumulation of five leucine and three methionine tRNA species is regulated so that those tRNA species that translate major codons increase while those that translate minor codons decrease as the growth rate increases. Here, we have analyzed the growth-rate-depende...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1165

    authors: Emilsson V,Näslund AK,Kurland CG

    更新日期:1993-03-20 00:00:00

  • A calorimetric study of the folding-unfolding of an alpha-helix with covalently closed N and C-terminal loops.

    abstract::The thermal melting of a dicyclic 29-residue peptide, having helix-stabilizing side-chain to side-chain covalent links at each terminal, has been studied by circular dichroism spectropolarimetry (CD) and differential scanning calorimetry (DSC). The CD spectra for this dicyclic peptide indicate that it is monomeric, al...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3025

    authors: Taylor JW,Greenfield NJ,Wu B,Privalov PL

    更新日期:1999-08-27 00:00:00

  • Cystoviral polymerase complex protein P7 uses its acidic C-terminal tail to regulate the RNA-directed RNA polymerase P2.

    abstract::In bacteriophages of the cystovirus family, the polymerase complex (PX) encodes a 75-kDa RNA-directed RNA polymerase (P2) that transcribes the double-stranded RNA genome. Also a constituent of the PX is the essential protein P7 that, in addition to accelerating PX assembly and facilitating genome packaging, plays a re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.04.028

    authors: Alphonse S,Arnold JJ,Bhattacharya S,Wang H,Kloss B,Cameron CE,Ghose R

    更新日期:2014-07-15 00:00:00

  • Aurora Kinase B Phosphorylates Histone H3.3 at Serine 31 during Mitosis in Mammalian Cells.

    abstract::Serine 31 of histone H3.3 is phosphorylated during mitosis in mammalian cells and has been shown to influence chromosome segregation. We established a screening system to identify candidate kinase(s) phosphorylating H3.3S31 by using siRNA library targeting 720 human kinases, and we confirmed the results with an indepe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.01.016

    authors: Li M,Dong Q,Zhu B

    更新日期:2017-06-30 00:00:00

  • Sequence and membrane determinants of the random coil-helix transition of α-synuclein.

    abstract::A random coil-helix transition underlies the association of the presynaptic protein α-synuclein (αS) with curved vesicle membranes to fold Asp2-Ala89 into a continuous helix. To clarify this transition, we examined αS folding cooperativity, helix nucleation and propagation in relation to membrane stabilization and lea...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.02.024

    authors: Lokappa SB,Suk JE,Balasubramanian A,Samanta S,Situ AJ,Ulmer TS

    更新日期:2014-05-15 00:00:00

  • Slowing bacterial translation speed enhances eukaryotic protein folding efficiency.

    abstract::The mechanisms for de novo protein folding differ significantly between bacteria and eukaryotes, as evidenced by the often observed poor yields of native eukaryotic proteins upon recombinant production in bacterial systems. Polypeptide synthesis rates are faster in bacteria than in eukaryotes, but the effects of gener...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.12.042

    authors: Siller E,DeZwaan DC,Anderson JF,Freeman BC,Barral JM

    更新日期:2010-03-12 00:00:00

  • Recycling of ribosomal complexes stalled at the step of elongation in Escherichia coli.

    abstract::Translating ribosomes often stall during elongation. The stalled ribosomes are known to be recycled by tmRNA (SsrA)-mediated trans-translation. Another process that recycles the stalled ribosomes is characterized by peptidyl-tRNA release. However, the mechanism of peptidyl-tRNA release from the stalled ribosomes is no...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.033

    authors: Singh NS,Ahmad R,Sangeetha R,Varshney U

    更新日期:2008-07-11 00:00:00

  • X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution.

    abstract::Escherichia coli pyridoxine 5'-phosphate oxidase catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate by the FMN oxidation of pyridoxine 5'-phosphate forming FMNH(2) and H(2)O(2). Recent studies have shown that in addition to the active site, pyridoxine 5'-phosphate oxidase contains a non-catalyti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4734

    authors: Safo MK,Musayev FN,di Salvo ML,Schirch V

    更新日期:2001-07-20 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

  • Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism.

    abstract::A new inhibitor, H-Ala-Ile-pyrrolidin-2-yl boronic acid, was developed as an inhibitor against prolyl tripeptidyl aminopeptidase with a K(i) value of 88.1 nM. The structure of the prolyl tripeptidyl aminopeptidase complexed with the inhibitor (enzyme-inhibitor complex) was determined at 2.2 A resolution. The inhibitor...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.09.077

    authors: Xu Y,Nakajima Y,Ito K,Zheng H,Oyama H,Heiser U,Hoffmann T,Gärtner UT,Demuth HU,Yoshimoto T

    更新日期:2008-01-18 00:00:00

  • Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase.

    abstract::The enzyme mercuric ion reductase MerA is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess metallochaperone-like N-terminal domains (NmerA) that can transfer Hg(2+) to the catalytic core domain (Core) for reduction to Hg(0). These domains are tethered to the h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.08.042

    authors: Johs A,Harwood IM,Parks JM,Nauss RE,Smith JC,Liang L,Miller SM

    更新日期:2011-10-28 00:00:00

  • Transphosphorylation of the TorR response regulator requires the three phosphorylation sites of the TorS unorthodox sensor in Escherichia coli.

    abstract::Two-component regulatory systems allow cells to adapt to environmental changes. In Escherichia coli, the TorS/TorR two-component system induces the expression of the tor structural operon encoding the trimethylamine N-oxide reductase respiratory system in response to substrate availability. TorS belongs to a sensor su...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0919

    authors: Jourlin C,Ansaldi M,Méjean V

    更新日期:1997-04-11 00:00:00

  • Characterization of the heterogeneity and specificity of interpolypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics.

    abstract::The aggregation of proteins often results in highly ordered fibrillar structures. While significant insights have been obtained on structural aspects of amyloid fibrils, little is known about the structures of protofibrils, which are presumed to be the precursors of fibrils. An understanding of the molecular mechanism...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.08.053

    authors: Jha A,Udgaonkar JB,Krishnamoorthy G

    更新日期:2009-10-30 00:00:00