Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.

Abstract:

:Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 Å resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS·tRNA CUA Pyl pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Jiang HK,Wang YH,Weng JH,Kurkute P,Li CL,Lee MN,Chen PJ,Tseng HW,Tsai MD,Wang YS

doi

10.1021/acs.biochem.0c00307

subject

Has Abstract

pub_date

2020-06-23 00:00:00

pages

2205-2209

issue

24

eissn

0006-2960

issn

1520-4995

journal_volume

59

pub_type

杂志文章
  • Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene.

    abstract::The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determine the mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarily cis-syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotational and translational settings of...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991771m

    authors: Liu X,Mann DB,Suquet C,Springer DL,Smerdon MJ

    更新日期:2000-01-25 00:00:00

  • 3'-Phosphoadenosine 5'-phosphosulfate binding site of flavonol 3-sulfotransferase studied by affinity chromatography and 31P NMR.

    abstract::The function of Lys-59, Arg-141, and Arg-277 in PAPS binding and catalysis of the flavonol 3-sulfotransferase was investigated. Affinity chromatography of conservative mutants with PAPS analogues allowed us to determine that Lys-59 interacts with the 5' portion of the nucleotide, while Arg-141 interacts with the 3' po...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982239m

    authors: Marsolais F,Laviolette M,Kakuta Y,Negishi M,Pedersen LC,Auger M,Varin L

    更新日期:1999-03-30 00:00:00

  • Interaction of cytochrome c with flavocytochrome b2.

    abstract::Flavocytochrome b2 from Saccharomyces cerevisiae couples L-lactate dehydrogenation to cytochrome c reduction. At 25 degrees C, 0.10 M ionic strength, and saturating L-lactate concentration, the turnover rate is 207 s-1 [per cytochrome c reduced; Miles, C. S., Rouviere, N., Lederer, F., Mathews, F. S., Reid, G. A., Bla...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9522561

    authors: Daff S,Sharp RE,Short DM,Bell C,White P,Manson FD,Reid GA,Chapman SK

    更新日期:1996-05-21 00:00:00

  • The mast cell function-associated antigen and its interactions with the type I Fcepsilon receptor.

    abstract::Rat mucosal-type mast cells of the RBL-2H3 line express a glycoprotein termed the MAst cell Function-associated Antigen (MAFA). When MAFA is clustered by its specific monoclonal antibody G63, secretion normally triggered by aggregating these cells' type I Fcepsilon receptor (FcepsilonRI) is substantially inhibited. Th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi011566i

    authors: Song J,Hagen GM,Roess DA,Pecht I,Barisas BG

    更新日期:2002-01-22 00:00:00

  • Proximity of periplasmic loops in the lactose permease of Escherichia coli determined by site-directed cross-linking.

    abstract::Out of over 60 single-Cys mutants in putative periplasmic loops in lactose permease, three mutants [Tyr101 --> Cys (loop III/IV), Leu313 --> Cys (loop IX/X), and Ser375 --> Cys (loop XI/XII)] spontaneously form disulfide-linked dimers, indicating that these loops are located on the periphery of the 12-helix bundle tha...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971172k

    authors: Sun J,Kaback HR

    更新日期:1997-09-30 00:00:00

  • Mannitol-specific carrier protein from the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system can be extracted as a dimer from the membrane.

    abstract::The association state of the mannitol-specific enzyme II (EIIMtl) has been studied both in the purified form and embedded in the cytoplasmic membrane. Membrane fragments obtained from mannitol-grown Escherichia coli catalyze the phosphoenolpyruvate- (PEP) dependent phosphorylation of both glucose and mannitol; thus th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00319a003

    authors: Roossien FF,Robillard GT

    更新日期:1984-11-20 00:00:00

  • 2D NMR studies and 3D structure of the parallel-stranded duplex oligonucleotide Acrm5-alpha-d(TCTAAACTC)-beta-d(AGATTTGAG) via complete relaxation matrix analysis of the NOE effects and molecular mechanics calculations.

    abstract::The three-dimensional structure of the duplex formed by the association of the unnatural oligonucleotide alpha-d(TCTAAACTC) covalently linked to an acridine derivative (m5Acr) with its natural and parallel complementary sequence beta-d(AGATTTGAG) was investigated by nuclear magnetic resonance spectroscopy and constrai...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00472a031

    authors: Guesnet JL,Vovelle F,Thuong NT,Lancelot G

    更新日期:1990-05-22 00:00:00

  • Adenosine 5'-triphosphate analogues as structural probes for Escherichia coli glutamine synthetase.

    abstract::Introduction of specific structural probes into substrate binding sites of Escherichia coli glutamine synthetase is now possible. Various analogues of ATP substituted with an amino or sulfhydryl moiety at the 6- or 8-position of the purine ring have been found to substitute for ATP in the autoinactivation reaction of ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00349a020

    authors: Maurizi MR,Ginsburg A

    更新日期:1986-01-14 00:00:00

  • Structure and stability of protein H and the M1 protein from Streptococcus pyogenes. Implications for other surface proteins of gram-positive bacteria.

    abstract::M proteins and other members of the M protein family, expressed on the surface of Streptococcus pyogenes, bind host proteins such as immunoglobulins, albumin, and fibrinogen. Protein H and the M1 protein are expressed by adjacent genes and both belong to the M protein family. In this work, the structure and stability ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00041a051

    authors: Nilson BH,Frick IM,Akesson P,Forsén S,Björck L,Akerström B,Wikström M

    更新日期:1995-10-17 00:00:00

  • Biochemical properties of phosphatidylcholine-binding proteins that share common antigenic determinants with Fc gamma 2b receptor.

    abstract::Biochemical and immunological properties of biosynthetically radiolabeled phosphatidylcholine-(PC-) binding proteins were investigated. The PC-binding proteins were extracted from the detergent lysate of biosynthetically radiolabeled P388D1 cells by affinity chromatography on PC-Sepharose and filtered through a Sephad...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00329a014

    authors: Fernandez-Botran R,Suzuki T

    更新日期:1985-04-09 00:00:00

  • Dynamin is membrane-active: lipid insertion is induced by phosphoinositides and phosphatidic acid.

    abstract::Dynamin is a large GTPase involved in the regulation of membrane constriction and fission during receptor-mediated endocytosis. Dynamin contains a pleckstrin-homology domain which is essential for endocytosis and which binds to anionic phospholipids. Here, we show for the first time that dynamin is a membrane-active m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000971r

    authors: Burger KN,Demel RA,Schmid SL,de Kruijff B

    更新日期:2000-10-10 00:00:00

  • Effect of the Met344His mutation on the conformational dynamics of bovine beta-1,4-galactosyltransferase: crystal structure of the Met344His mutant in complex with chitobiose.

    abstract::Beta-1,4-galactosyltransferase (beta4Gal-T1) in the presence of manganese ion transfers galactose from UDP-galactose (UDP-Gal) to N-acetylglucosamine (GlcNAc) that is either free or linked to an oligosaccharide. Crystallographic studies on bovine beta4Gal-T1 have shown that the primary metal binding site is located in...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049007+

    authors: Ramakrishnan B,Boeggeman E,Qasba PK

    更新日期:2004-10-05 00:00:00

  • Catalytic mechanism of enzymes: preorganization, short strong hydrogen bond, and charge buffering.

    abstract::During the past decade, there has been much debate about the enormous catalytic rate enhancement observed in enzymatic reactions involving carbanion intermediates. Our recent theoretical study has demonstrated the importance of the short strong hydrogen bond (SSHB) in the enzymatic reactions. Nevertheless, other recen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0255118

    authors: Kim KS,Kim D,Lee JY,Tarakeshwar P,Oh KS

    更新日期:2002-04-23 00:00:00

  • 1H nuclear magnetic resonance double resonance study of oxytocin in aqueous solution.

    abstract::Peptide NH resonances in the 250 MHZ 1H nuclear magnetic resonance (NMR) spectrum of oxytocin in H2O were assigned to specific amino acid residues by the "underwater decoupling" technique (i.e., decoupling from corresponding CalphaH resonances, which are buried beneath the intense water peak). These experiments confir...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00650a025

    authors: Glickson JD,Rowan R,Pitner TP,Dadok J,Bothner-By AA,Walter R

    更新日期:1976-03-09 00:00:00

  • Modeling the three-dimensional structures of bacterial aminotransferases.

    abstract::The refined crystallographic structure of the "closed" conformation of chicken mitochondrial aspartate aminotransferase has been used as a template for the construction of models of the two Escherichia coli aminotransferases encoded by the tyrB and aspC genes. The main results are as follows: (1) Only minor changes ar...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00422a009

    authors: Seville M,Vincent MG,Hahn K

    更新日期:1988-11-01 00:00:00

  • Normal cellular Ha ras p21 protein causes local disruption of bilayer phospholipid.

    abstract::We have investigated the interactions of the p21 protein of c-Ha ras with its phospholipid environment. Gel filtration of detergent-"solubilized" p21 revealed that this preparation consisted of a mixture of multimolecular aggregates of protein and phospholipid and also a population of individual p21 molecules. Additio...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00412a028

    authors: Montgomery GW,Jagger BA,Bailey PD

    更新日期:1988-06-14 00:00:00

  • Molecular functions of conserved aspects of the GHMP kinase family.

    abstract::The sequences and three-dimensional structures of the galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase (GHMP) family were compared to identify highly conserved surface residues. The functions of these solvent-accessible residues were assessed by determining the effects of their substit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048963o

    authors: Andreassi JL 2nd,Leyh TS

    更新日期:2004-11-23 00:00:00

  • A fluorescent hydrophobic probe used for monitoring the kinetics of exocytosis phenomena.

    abstract::A fluorescence method is presented for quantitatively analyzing exocytosis phenomena and monitoring their kinetics. The method is based on the particular properties of a hydrophobic fluorescent probe, 1-[4-(trimethylammonio)phenyl]-6-phenylhexa-1,3,5-triene (TMA-DPH) [Prendergast, F.G., Haugland, R.P., & Callahan, P.J...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00356a045

    authors: Bronner C,Landry Y,Fonteneau P,Kuhry JG

    更新日期:1986-04-22 00:00:00

  • Tropomyosin stabilizes the pointed end of actin filaments by slowing depolymerization.

    abstract::Tropomyosin is postulated to confer stability to actin filaments in nonmuscle cells. We have found that a nonmuscle tropomyosin isolated from the intestinal epithelium can directly stabilize actin filaments by slowing depolymerization from the pointed, or slow-growing, filament end. Kinetics of elongation and depolyme...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00447a035

    authors: Broschat KO,Weber A,Burgess DR

    更新日期:1989-10-17 00:00:00

  • Catalytic reaction profile for alcohol oxidation by galactose oxidase.

    abstract::Galactose oxidase is a remarkable enzyme containing a metalloradical redox cofactor capable of oxidizing a variety of primary alcohols during enzyme turnover. Recent studies using 1-O-methyl alpha-D-galactopyranoside have revealed an unusually large kinetic isotope effect (KIE) for oxidation of the alpha-deuterated al...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010303l

    authors: Whittaker MM,Whittaker JW

    更新日期:2001-06-19 00:00:00

  • Physical and functional interactions of Caenorhabditis elegans WRN-1 helicase with RPA-1.

    abstract::The Caenorhabditis elegans Werner syndrome protein, WRN-1, a member of the RecQ helicase family, has a 3'-5' DNA helicase activity. Worms with defective wrn-1 exhibit premature aging phenotypes and an increased level of genome instability. In response to DNA damage, WRN-1 participates in the initial stages of checkpoi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200791p

    authors: Hyun M,Park S,Kim E,Kim DH,Lee SJ,Koo HS,Seo YS,Ahn B

    更新日期:2012-02-21 00:00:00

  • Conformationally restricted thrombin inhibitors resistant to proteolytic digestion.

    abstract::A new type of thrombin exo-site inhibitor has been designed with enhanced inhibitory potency and increased metabolic stability. With the aid of the model of the structure of the thrombin-hirudin fragment complex [Yue, S.-Y., DiMaio, J., Szewczuk, Z., Purisima, E. O., Ni, F., & Konishi, Y. (1992) Protein Eng. 5, 77-85]...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00153a004

    authors: Szewczuk Z,Gibbs BF,Yue SY,Purisima EO,Konishi Y

    更新日期:1992-09-29 00:00:00

  • Effect of AMP on mRNA binding by yeast NAD+-specific isocitrate dehydrogenase.

    abstract::Yeast mitochondrial NAD+-specific isocitrate dehydrogenase (IDH) has previously been shown to bind specifically to 5'-untranslated regions of yeast mitochondrial mRNAs, and transcripts containing these regions have been found to allosterically inhibit activity of the enzyme. This inhibition is relieved by AMP, an allo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0200662

    authors: Anderson SL,Schirf V,McAlister-Henn L

    更新日期:2002-06-04 00:00:00

  • Properties of overlapping EREs: synergistic activation of transcription and cooperative binding of ER.

    abstract::We have designed a novel estrogen-responsive unit, overERE, which consists of two overlapping ERE separated by 5 bp (center-to-center). In gel retardation assays, this sequence forms a low-mobility complex that migrates like an estrogen receptor tetramer. The receptor-overERE complex was specific and was supershifted ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972445e

    authors: Massaad C,Coumoul X,Sabbah M,Garlatti M,Redeuilh G,Barouki R

    更新日期:1998-04-28 00:00:00

  • A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile.

    abstract::ArsR (or ArsR/SmtB) family metalloregulatory homodimeric repressors collectively respond to a wide range of metal ion inducers in regulating homeostasis and resistance of essential and nonessential metal ions in bacteria. BxmR from the cyanobacterium Osciliatoria brevis is the first characterized ArsR protein that sen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801313y

    authors: Liu T,Chen X,Ma Z,Shokes J,Hemmingsen L,Scott RA,Giedroc DP

    更新日期:2008-10-07 00:00:00

  • Functional characterization of the secondary actin binding site of myosin II.

    abstract::The role of the interaction between actin and the secondary actin binding site of myosin (segment 565-579 of rabbit skeletal muscle myosin, referred to as loop 3 in this work) has been studied with proteolytically generated smooth and skeletal muscle myosin subfragment 1 and recombinant Dictyostelium discoideum myosin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991595h

    authors: Van Dijk J,Furch M,Lafont C,Manstein DJ,Chaussepied P

    更新日期:1999-11-16 00:00:00

  • The C-terminus of tissue factor pathway inhibitor is essential to its anticoagulant activity.

    abstract::Tissue factor pathway inhibitor (TFPI) from different cell lines shows up to 15-fold differences in the ratio of anticoagulant to chromogenic activity. The anticoagulant activity was dependent on the purification procedure used and it was possible to isolate two fractions of recombinant TFPI. Only one of these fractio...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00107a002

    authors: Nordfang O,Bjørn SE,Valentin S,Nielsen LS,Wildgoose P,Beck TC,Hedner U

    更新日期:1991-10-29 00:00:00

  • The role of methionine-192 of the chymotrypsin active site in the binding and catalysis of mono(amino acid) and peptide substrates.

    abstract::We find that specific oxidation for the Met-192 residue in delta-chymotrypsin to methionine sulfoxide results in a twofold increase in Km(app) and unchanged kcat in the hydrolysis of N-acetyl mono(amino acid) amide substrates. However, the catalyzed hydrolyses of N-acetyl dipeptide amide substrates by (methionine sulf...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00664a006

    authors: Treadway WJ Jr,Schultz RM

    更新日期:1976-09-21 00:00:00

  • Ligand migration and binding in nonsymbiotic hemoglobins of Arabidopsis thaliana.

    abstract::We have studied carbon monoxide (CO) migration and binding in the nonsymbiotic hemoglobins AHb1 and AHb2 of Arabidopsis thaliana using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures. Both proteins have similar amino acid sequences but di...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi100768g

    authors: Nienhaus K,Dominici P,Astegno A,Abbruzzetti S,Viappiani C,Nienhaus GU

    更新日期:2010-09-07 00:00:00

  • Stoichiometry and specificity of lipid-protein interaction with myelin proteolipid protein studied by spin-label electron spin resonance.

    abstract::The interaction of spin-labeled lipids with the myelin proteolipid apoprotein in complexes with dimyristoylphosphatidylcholine of varying lipid/protein ratios has been studied with electron spin resonance spectroscopy. A first shell of approximately 10 lipids per 25 000-dalton protein is found to be motionally restric...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00300a011

    authors: Brophy PJ,Horváth LI,Marsh D

    更新日期:1984-02-28 00:00:00