当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

Abstract：

:Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Czudnochowski N,Wang AL,Finer-Moore J,Stroud RM

doi

10.1016/j.jmb.2013.05.014

subject

Has Abstract

pub_date

2013-10-23 00:00:00

pages

3875-87

issue

20

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(13)00328-8

journal_volume

425

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structure of the minimal interface between ApoE and LRP.

    abstract：:Clusters of complement-type ligand-binding repeats (CRs) in the low-density lipoprotein receptor (LDLR) family are thought to mediate the interactions with their various ligands. Apolipoprotein E (ApoE), a key ligand for cholesterol homeostasis, has been shown to interact with LDLR-related protein 1 (LRP) through thes...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.03.022

    authors： Guttman M,Prieto JH,Handel TM,Domaille PJ,Komives EA

    更新日期：2010-04-30 00:00:00

  • Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability.

    abstract：:Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein g3p and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. Recently we have shown that the two receptors are contacted in a sequential manner, such that binding of TolA by the N...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2720

    authors： Holliger P,Riechmann L,Williams RL

    更新日期：1999-05-14 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

  • Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation.

    abstract：:Deleted in Split hand/Split foot 1 (DSS1) was previously identified as a novel 12-O-tetradecanoylphorbol-13-acetate (TPA)-inducible gene with possible involvement in early event of mouse skin carcinogenesis. The mechanisms by which human DSS1 (HsDSS1) exerts its biological effects via regulation of the ubiquitin-prote...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.08.044

    authors： Wei SJ,Williams JG,Dang H,Darden TA,Betz BL,Humble MM,Chang FM,Trempus CS,Johnson K,Cannon RE,Tennant RW

    更新日期：2008-11-14 00:00:00

  • Distinctive features of the two classes of eukaryotic peptide deformylases.

    abstract：:Peptide deformylases (PDFs) are essential enzymes of the N-terminal protein processing pathway of eubacteria. The recent discovery of two types of PDFs in higher plants, PDF1A and PDF1B, and the detection of PDF1A in humans, have raised questions concerning the importance of deformylation in eukaryotes. Here, we have ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5175

    authors： Serero A,Giglione C,Meinnel T

    更新日期：2001-12-07 00:00:00

  • Virtual interaction profiles of proteins.

    abstract：:We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of pep...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5035

    authors： Wollacott AM,Desjarlais JR

    更新日期：2001-10-19 00:00:00

  • CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications.

    abstract：:To investigate protective immunity conferred by CTL against viral pathogens, we have analyzed CD8(+) T cell responses to the immunodominant nucleoprotein epitope (NP(366-374)) of influenza A virus in B6 mice during primary and secondary infections in vivo. Unlike the highly biased TCR Vbeta repertoire, the associated ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.057

    authors： Zhong W,Dixit SB,Mallis RJ,Arthanari H,Lugovskoy AA,Beveridge DL,Wagner G,Reinherz EL

    更新日期：2007-09-14 00:00:00

  • Stability of coliphage lambda DNA replication initiator, the lambda O protein.

    abstract：:The initiator of coliphage lambda DNA replication, lambda O protein, may be detected among other 35S-labeled phage and bacterial proteins by a method based on immunoprecipitation. This method makes it possible to study lambda O proteolytic degradation in lambda plasmid-harboring or lambda phage-infected cells; it avoi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90624-s

    authors： Wegrzyn G,Pawlowicz A,Taylor K

    更新日期：1992-08-05 00:00:00

  • In vivo characterization of mutants of the bacteriophage f1 gene V protein isolated by saturation mutagenesis.

    abstract：:The gene V protein of bacteriophage f1 binds to single-stranded nucleic acids and is essential for propagation of phage f1. We tested the function of gene V protein mutants with single amino acid substitutions in two ways: by the ability of the mutant proteins to support phage growth, and by the ability of the mutant ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1165

    authors： Terwilliger TC,Zabin HB,Horvath MP,Sandberg WS,Schlunk PM

    更新日期：1994-02-18 00:00:00

  • 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 activi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0610

    authors： Soma A,Kumagai R,Nishikawa K,Himeno H

    更新日期：1996-11-15 00:00:00

  • Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis.

    abstract：:Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. The...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.03.021

    authors： Guzzo CR,Dunger G,Salinas RK,Farah CS

    更新日期：2013-06-26 00:00:00

  • Crystallization and preliminary X-ray diffraction studies of the spinach-chloroplast thioredoxin f.

    abstract：:Thioredoxins are low-molecular-mass proteins that function as hydrogen carriers in DNA synthesis and in the transformation of sulfur metabolites. They also act as regulatory proteins in the light-dependent enzyme activation during photosynthesis. F-type thioredoxin from spinach chloroplasts, a monomeric protein of 113...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90488-r

    authors： Génovésio-Taverne JC,Jetzer Y,Sauder U,Hohenester E,Hughet C,Jansonius JN,Gardet-Salvi L,Schürmann P

    更新日期：1991-12-05 00:00:00

  • Multimodal and Polymorphic Interactions between Anillin and Actin: Their Implications for Cytokinesis.

    abstract：:Cytokinesis of animal cells requires the assembly of a contractile ring, which promotes daughter cell splitting. Anillin is a conserved scaffold protein involved in organizing the structural components of the contractile ring including filamentous actin (F-actin), myosin, and septins and in forming the subsequent midb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.01.020

    authors： Jananji S,Risi C,Lindamulage IKS,Picard LP,Van Sciver R,Laflamme G,Albaghjati A,Hickson GRX,Kwok BH,Galkin VE

    更新日期：2017-03-10 00:00:00

  • Multiple roles of prolyl residues in structure and folding.

    abstract：:To explore the ways that proline residues may influence the conformational options of a polypeptide backbone, we have characterized Pro-->Ala mutants of cellular retinoic acid-binding protein I (CRABP I). While all three Xaa-Pro bonds are in the trans conformation in the native protein and the equilibrium stability of...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4002

    authors： Eyles SJ,Gierasch LM

    更新日期：2000-08-18 00:00:00

  • Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy.

    abstract：:Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.01.004

    authors： von Appen A,Beck M

    更新日期：2016-05-22 00:00:00

  • The salt-dependence of a protein-ligand interaction: ion-protein binding energetics.

    abstract：:Using the binding of a nucleotide inhibitor (guanosine-3'-monophosphate) to a ribonuclease (ribonuclease Sa) as a model system, we show that the salt-dependence of the interaction arises due to specific ion binding at the site of nucleotide binding. The presence of specific ion-protein binding is concluded from a comb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.12.018

    authors： Waldron TT,Schrift GL,Murphy KP

    更新日期：2005-02-25 00:00:00

  • RecA protein dynamics in the interior of RecA nucleoprotein filaments.

    abstract：:We characterize aspects of the conformation and dynamic state of RecA filaments when bound to dsDNA that are specifically linked to the presence of the second of the two bound DNA strands. Filaments bound to dsDNA exhibit a facile exchange between free and bound RecA monomers or oligomers in the filament interior that...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0200

    authors： Shan Q,Cox MM

    更新日期：1996-04-12 00:00:00

  • The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.

    abstract：:The E. coli RecBCD enzyme facilitates the loading of RecA onto single-stranded DNA produced by the combined helicase/nuclease activity of RecBCD. The nuclease domain of RecB protein, RecB(nuc), has been previously shown to bind RecA. Surprisingly, RecB(nuc) also binds to phage and eukaryotic homologs of RecA, leading ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.042

    authors： Lucarelli D,Wang YA,Galkin VE,Yu X,Wigley DB,Egelman EH

    更新日期：2009-08-14 00:00:00

  • Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.

    abstract：:The substrate-binding H-site of human glutathione transferase (GST) M2-2 was subjected to iterative saturation mutagenesis in order to obtain an efficient enzyme with the novel epoxide substrate indene 1,2-oxide. Residues 10, 116, and 210 were targeted, and the activities with the alternative substrates, benzyl isothi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.07.039

    authors： Norrgård MA,Mannervik B

    更新日期：2011-09-09 00:00:00

  • Distinct modes of recognition of the lipoyl domain as substrate by the E1 and E3 components of the pyruvate dehydrogenase multienzyme complex.

    abstract：:Two-dimensional (15)N-heteronuclear single-quantum coherence (HSQC) NMR studies with a di-domain (lipoyl domain+ linker+ peripheral subunit-binding domain) of the dihydrolipoyl acetyltransferase (E2) component of the pyruvate dehydrogenase complex of Bacillus stearothermophilus allowed a molecular comparison of the ne...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.018

    authors： Fries M,Stott KM,Reynolds S,Perham RN

    更新日期：2007-02-09 00:00:00

  • Temporal regulation and overlap organization of two Caulobacter flagellar genes.

    abstract：:The biogenesis of the bacterial flagellum and chemotaxis apparatus in both Escherichia coli and Caulobacter crescentus requires the ordered expression of over 40 genes whose expression is controlled by a trans-acting regulatory hierarchy. In C. crescentus, additional control mechanisms ensure that the transcription of...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90365-3

    authors： Kaplan JB,Dingwall A,Bryan R,Champer R,Shapiro L

    更新日期：1989-01-05 00:00:00

  • Automatic definition of recurrent local structure motifs in proteins.

    abstract：:An automatic procedure for defining recurrent folding motifs in proteins of known structure is described. These motifs are formed by short polypeptide fragments of equal size containing between four and seven residues. The method applies a classical clustering algorithm that operates on distances between selected back...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/S0022-2836(05)80194-9

    authors： Rooman MJ,Rodriguez J,Wodak SJ

    更新日期：1990-05-20 00:00:00

  • A dimer is the minimal proton-conducting unit of the influenza a virus M2 channel.

    abstract：:When influenza A virus infects host cells, its integral matrix protein M2 forms a proton-selective channel in the viral envelope. Although X-ray crystallography and NMR studies using fragment peptides have suggested that M2 stably forms a tetrameric channel irrespective of pH, the oligomeric states of the full-length ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.05.002

    authors： Kawano K,Yano Y,Matsuzaki K

    更新日期：2014-07-15 00:00:00

  • Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases.

    abstract：:Colicin endonucleases (DNases) are bound and inactivated by immunity (Im) proteins. Im proteins are broadly cross-reactive yet specific inhibitors binding cognate and non-cognate DNases with K(d) values that vary between 10(-4) and 10(-14) M, characteristics that are explained by a 'dual-recognition' mechanism. In thi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.03.055

    authors： Keeble AH,Joachimiak LA,Maté MJ,Meenan N,Kirkpatrick N,Baker D,Kleanthous C

    更新日期：2008-06-13 00:00:00

  • Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin.

    abstract：:To study mechanisms of nucleosome positioning, small circular plasmids were constructed, assembled into chromatin in vivo in Saccharomyces cerevisiae, and their chromatin structures were analysed with respect to positions of nucleosomes and nuclease-sensitive regions. Plasmids used include insertions of the URA3 gene ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90291-3

    authors： Thoma F

    更新日期：1986-07-20 00:00:00

  • Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction.

    abstract：:beta-Barrel membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Little is known about how residues in membrane beta-barrels interact preferentially with other residues on adjacent strands. We have developed probabilistic models to quantify propensities of residu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.09.094

    authors： Jackups R Jr,Liang J

    更新日期：2005-12-09 00:00:00

  • Enhancing the contrast of ApoB to locate the surface components in the 3D density map of human LDL.

    abstract：:A 26 Å resolution map of the structure of human low-density lipoprotein (LDL) was obtained from electron cryomicroscopy and single-particle image reconstruction. The structure showed a discoidal-shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.10.034

    authors： Liu Y,Atkinson D

    更新日期：2011-01-07 00:00:00

  • Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.

    abstract：:Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule move together. Previous work has shown that this domain closure involves two hinges. Using the newly refined structure of the open form, the structural mechanism underlying this motion is analyzed here i...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1592

    authors： Gerstein M,Anderson BF,Norris GE,Baker EN,Lesk AM,Chothia C

    更新日期：1993-11-20 00:00:00

  • Missense mutations in the Bacillus subtilis gnt repressor that diminish operator binding ability.

    abstract：:The Bacillus subtilis gnt operon is negatively regulated by the gnt repressor (GntR, 243 amino acids), which is antagonized by gluconate. The GntR protein belongs to a new family of bacterial regulatory proteins (GntR family). To locate the DNA-binding domain of the GntR protein, we obtained mutations of this protein,...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1270

    authors： Yoshida K,Fujita Y,Sarai A

    更新日期：1993-05-20 00:00:00

  • Structure and function of the hairpin ribozyme.

    abstract：:The hairpin ribozyme belongs to the family of small catalytic RNAs that cleave RNA substrates in a reversible reaction that generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. The hairpin catalytic motif was discovered in the negative strand of the tobacco ringspot virus satellite RNA, where hairpin ribozyme-med...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1006/jmbi.2000.3560

    authors： Fedor MJ

    更新日期：2000-03-24 00:00:00