Stable substructures of eightfold beta alpha-barrel proteins: fragment complementation of phosphoribosylanthranilate isomerase.

Abstract:

:The (beta alpha)8 (or "TIM")-barrel protein phosphoribosylanthranilate isomerase from Saccharomyces cerevisiae was cleaved between the sixth and seventh beta alpha module to test the capacity of the resulting fragments to adopt native format autonomously. The fragments, which were expressed from separate coding sequences, were soluble and monomeric. The amino-terminal fragment p1 was compact, possessed an almost nativelike far-UV but a strongly reduced near-UV CD spectrum, and unfolded cooperativity with guanidinium chloride. In contrast, the carboxyl-terminal fragment p2 was less compact than fragment p1, possessed only a weak far-UV and no detectable near-UV CD spectrum, and unfolded noncooperatively. The fragments assembled stoichiometrically to a complex with Kd = 0.2 microM, which was enzymically almost fully active. The rate of assembly was limited by a first-order process, probably the isomerization of the carboxyl-terminal fragment p2 to an assembly-competent structure. These results support a folding mechanism that comprises an intermediate with the first six beta alpha units folded in roughly native format and the last two beta alpha units partially unfolded. The similar behavior of the analogous fragments of the alpha subunit of tryptophan synthease supports the hypothesis that these two (beta alpha)8-barrel proteins have evolved from a common ancestor.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Eder J,Kirschner K

doi

10.1021/bi00129a010

subject

Has Abstract

pub_date

1992-04-14 00:00:00

pages

3617-25

issue

14

eissn

0006-2960

issn

1520-4995

journal_volume

31

pub_type

杂志文章
  • An inhibitor of ribosomal peptidyl transferase using transition-state analogy.

    abstract::The phosphoramidate of CCdAp and puromycin (CCdApPuro) is a potent inhibitor of ribosomal peptidyl transferase, as assayed by the fragment reaction. Inhibition is competitive at the ribosomal A-site. CCdApPuro protects P-site-associated bases in the peptidyl transferase loop region of 23S rRNA from carbodiimide modifi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00002a001

    authors: Welch M,Chastang J,Yarus M

    更新日期:1995-01-17 00:00:00

  • Purification, characterization, and investigation of the mechanism of aminoglycoside 3'-phosphotransferase type Ia.

    abstract::Aminoglycoside 3'-phosphotransferases [APH(3')s] are the most common cause of bacterial high-level resistance to aminoglycoside antibiotics in clinical isolates. A one-step affinity chromatography was used to purify APH(3') type Ia. The kinetic parameters for turnover of seven aminoglycosides and the corresponding min...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00039a026

    authors: Siregar JJ,Miroshnikov K,Mobashery S

    更新日期:1995-10-03 00:00:00

  • Characterization of the reaction of L-serine and indole with Escherichia coli tryptophan synthase via rapid-scanning ultraviolet-visible spectroscopy.

    abstract::The pre-steady-state reaction of indole and L-serine with the alpha 2 beta 2 complex of Escherichia coli tryptophan synthase has been investigated under different premixing conditions with rapid-scanning stopped-flow (RSSF) UV-visible spectroscopy for the spectral range 300-550 nm. When alpha 2 beta 2 was mixed with i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00357a032

    authors: Drewe WF Jr,Dunn MF

    更新日期:1986-05-06 00:00:00

  • Solution structure and molecular determinants of hemoglobin binding of the first NEAT domain of IsdB in Staphylococcus aureus.

    abstract::The human pathogen Staphylococcus aureus acquires heme iron from hemoglobin (Hb) via the action of a series of iron-regulated surface determinant (Isd) proteins. The cell wall anchored IsdB protein is recognized as the predominant Hb receptor, and is comprised of two NEAr transporter (NEAT) domains that act in concert...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi5005188

    authors: Fonner BA,Tripet BP,Eilers BJ,Stanisich J,Sullivan-Springhetti RK,Moore R,Liu M,Lei B,Copié V

    更新日期:2014-06-24 00:00:00

  • Mechanism of enolase: the crystal structure of enolase-Mg2(+)-2-phosphoglycerate/phosphoenolpyruvate complex at 2.2-A resolution.

    abstract::Enolase in the presence of Mg2+ catalyzes the elimination of H2O from 2-phosphoglyceric acid (PGA) to form phosphoenolpyruvate (PEP) and the reverse reaction, the hydration of PEP to PGA. The structure of the ternary complex yeast enolase-Mg2(+)-PGA/PEP has been determined by X-ray diffraction and refined by crystallo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00225a012

    authors: Lebioda L,Stec B

    更新日期:1991-03-19 00:00:00

  • Function of the MexB efflux-transporter divided into two halves.

    abstract::The MexA-MexB-OprM efflux pump exports structurally and functionally diverse xenobiotics and confers multi-drug resistance on Pseudomonas aeruginosa cells. The MexB transporter traverses the inner membrane twelve times, bears two large periplasmic domains and has two homologous tandem repeats. To test whether two homo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0300074

    authors: Eda S,Yoneyama H,Nakae T

    更新日期:2003-06-17 00:00:00

  • Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.

    abstract::Previous studies of the low molecular mass family 11 xylanase from Bacillus circulans show that the ionization state of the nucleophile (Glu78, pK(a) 4.6) and the acid/base catalyst (Glu172, pK(a) 6.7) gives rise to its pH-dependent activity profile. Inspection of the crystal structure of BCX reveals that Glu78 and Gl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:

    authors: Joshi MD,Sidhu G,Nielsen JE,Brayer GD,Withers SG,McIntosh LP

    更新日期:2001-08-28 00:00:00

  • Fast cytochrome bo from Escherichia coli binds two molecules of nitric oxide at CuB.

    abstract::The reaction of nitric oxide (NO) with fast cytochrome bo from Escherichia coli has been studied by electronic absorption, MCD, and EPR spectroscopy. Titration of the enzyme with NO showed the formation of two distinct species, consistent with NO binding stoichiometries of 1:1 and 2:1 with observed dissociation consta...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971481a

    authors: Butler CS,Seward HE,Greenwood C,Thomson AJ

    更新日期:1997-12-23 00:00:00

  • Hemes a and a3 environments of plant cytochrome c oxidase.

    abstract::The structures of hemes a and a3 of maize and wheat germ cytochrome c oxidase were investigated by resonance Raman spectroscopy. Comparison between the plant and mammalian cytochrome oxidases revealed that (i) the vinyl groups associated with hemes a and a3 vibrate at higher frequencies in the plant enzyme than in the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00489a028

    authors: de Paula JC,Peiffer WE,Ingle RT,Centeno JA,Ferguson-Miller S,Babcock GT

    更新日期:1990-09-18 00:00:00

  • Mapping of the cleavage-associated bleomycin binding site on DNA with a new method based on site-specific blockage of the minor groove with N2-isobutyrylguanine.

    abstract::Although the binding of various forms of bleomycin to DNA has been studied extensively, the transient nature of the activated bleomycin species which ultimately attacks DNA has largely precluded direct examination of its physical interactions with DNA. In an attempt to map the minimum binding site required for this sp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962957d

    authors: Suh D,Povirk LF

    更新日期:1997-04-08 00:00:00

  • Structural Insight into the Discrimination between 8-Oxoguanine Glycosidic Conformers by DNA Repair Enzymes: A Molecular Dynamics Study of Human Oxoguanine Glycosylase 1 and Formamidopyrimidine-DNA Glycosylase.

    abstract::hOgg1 and FPG are the primary DNA repair enzymes responsible for removing the major guanine (G) oxidative product, namely, 7,8-dihydro-8-oxoguanine (OG), in humans and bacteria, respectively. While natural G adopts the anti conformation and forms a Watson-Crick pair with cytosine (C), OG can also adopt the syn conform...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b01292

    authors: Sowlati-Hashjin S,Wetmore SD

    更新日期:2018-02-20 00:00:00

  • Biochemical characterization of the L-plastin-actin interaction shows a resemblance with that of alpha-actinin and allows a distinction to be made between the two actin-binding domains of the molecule.

    abstract::Actin interaction with L-plastin, a plastin/fimbrins isoform of the alpha-actinin family of molecules, is poorly characterized, from the biochemical point of view. Besides, molecular modeling of the T-isoform has recently provided a complete model of interaction with filamentous actin [Volkmann, N., DeRosier, D., Mats...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi030151p

    authors: Lebart MC,Hubert F,Boiteau C,Ventéo S,Roustan C,Benyamin Y

    更新日期:2004-03-09 00:00:00

  • Effects of ouabain on the rotational dynamics of renal Na,K-ATPase studied by saturation-transfer EPR.

    abstract::The interaction of a nitroxide spin-labeled derivative of ouabain with sheep kidney Na,K-ATPase and the motional behavior of the ouabain spin label-Na,K-ATPase complex have been studied by means of electron paramagnetic resonance (EPR) and saturation-transfer EPR (ST-EPR). Spin-labeled ouabain binds with high affinity...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00122a019

    authors: Mahaney JE,Grisham CM

    更新日期:1992-02-25 00:00:00

  • Hypertriglyceridemic VLDL decreases plasminogen binding to endothelial cells and surface-localized fibrinolysis.

    abstract::The effect of normo (NTG)- and hypertriglyceridemic (HTG)-VLDL on cultured human umbilical vein endothelial cell (HUVEC) surface-localized fibrinolysis was examined following pre-incubation with NTG-, HTG-VLDL, LDL (1-20 micrograms/mL) or buffer (control). Ligand binding assays, using 125I-labeled tcu-PA, t-PA, or Glu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi952032i

    authors: Li XN,Koons JC,Benza RL,Parks JM,Varma VK,Bradley WA,Gianturco SH,Taylor KB,Grammer JR,Tabengwa EM,Booyse FM

    更新日期:1996-05-14 00:00:00

  • Transmembrane calcium movements mediated by ionomycin and phosphatidate in liposomes with Fura 2 entrapped.

    abstract::A novel liposomal method permits studies of Ca movements across the bilayers of multilamellar vesicles (MLV) which had entrapped the Ca-dependent, fluorescent indicator dye Fura 2. Ionomycin-mediated Ca translocation across MLV of phosphatidylcholine (PC)/dicetyl phosphate (DCP), 9:1, obeyed simple first-order kinetic...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00415a040

    authors: Blau L,Weissmann G

    更新日期:1988-07-26 00:00:00

  • Basic proline-rich proteins from human parotid saliva: complete covalent structures of proteins IB-1 and IB-6.

    abstract::The complete amino acid sequences of two basic proline-rich proteins, IB-1 and IB-6, from human parotid saliva have been determined. Fragments for sequence analysis were obtained by enzymatic digestions. The proteins have molecular weights of 9571 (IB-1) and 11,530 (IB-6) and contain 34 and 39 mol % proline, respectiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00357a013

    authors: Kauffman D,Hofmann T,Bennick A,Keller P

    更新日期:1986-05-06 00:00:00

  • Copurification of the FpvA ferric pyoverdin receptor of Pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport.

    abstract::The Pseudomonas aeruginosa FpvA receptor is a TonB-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. Surprisingly, FpvA expressed in P. aeruginosa grown in an iron-deficient medium copurifies with a ligand X that we have characterized by UV, fluorescence, a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990421x

    authors: Schalk IJ,Kyslik P,Prome D,van Dorsselaer A,Poole K,Abdallah MA,Pattus F

    更新日期:1999-07-20 00:00:00

  • Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants.

    abstract::Urease from Klebsiella aerogenes [Jabri et al. (1995) Science 268, 998-1004] is an (alpha beta gamma)3 trimer with each alpha-subunit having an (alpha beta)8-barrel domain containing a binickel active center. Here we examine structure-function relations for urease in more detail through structural analysis of the urea...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi960424z

    authors: Jabri E,Karplus PA

    更新日期:1996-08-20 00:00:00

  • Ionic-strength-dependent effects in protein folding: analysis of rate equilibrium free-energy relationships and their interpretation.

    abstract::The traditional approach to studying protein folding involves applying a perturbation, usually denaturant or mutation, and determining the effect upon the free energy of folding, DeltaG0, and the activation free energy, DeltaG(not equal). Data collected as a function of the perturbation can be used to construct rate e...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi701645g

    authors: Song B,Cho JH,Raleigh DP

    更新日期:2007-12-11 00:00:00

  • Interaction of assembly protein AP-2 and its isolated subunits with clathrin.

    abstract::The clathrin assembly protein complex AP-2 is a multimeric subunit complex consisting of two 100-115-kDa subunits known as alpha and beta and 50- and 16-kDa subunits. The subunits have been dissociated and separated by ion-exchange chromatography in 7.5 M urea. Fractions highly enriched in either the alpha or beta sub...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00236a036

    authors: Prasad K,Keen JH

    更新日期:1991-06-04 00:00:00

  • Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.

    abstract::Oligonucleotides labeled with hexachlorofluorescein (hex) have enabled the interaction of the restriction endonuclease EcoRV with DNA to be evaluated using fluorescence anisotropy. The sensitivity of hex allowed measurements at oligonucleotide concentrations as low as 1 nM, enabling K(D) values in the low nanomolar ra...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi001956p

    authors: Reid SL,Parry D,Liu HH,Connolly BA

    更新日期:2001-02-27 00:00:00

  • A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase.

    abstract::The gene product 61 primase protein from bacteriophage T4 was expressed as an intein fusion and purified to homogeneity. The primase binds one zinc ion, which is coordinated by four cysteine residues to form a zinc ribbon motif. Factors that influence the rate of priming were investigated, and a physiologically releva...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0108554

    authors: Valentine AM,Ishmael FT,Shier VK,Benkovic SJ

    更新日期:2001-12-18 00:00:00

  • Insulin allosteric behavior: detection, identification, and quantification of allosteric states via 19F NMR.

    abstract::The insulin hexamer is an allosteric protein widely used in formulations for the treatment of diabetes. The hexamer exhibits positive and negative cooperativity and apparent half-site binding activity, reflecting the interconversion of three allosteric states, designated as T6, T3R3, and R6. The hexamer contains two s...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi050392s

    authors: Bonaccio M,Ghaderi N,Borchardt D,Dunn MF

    更新日期:2005-05-31 00:00:00

  • Substrate-dependent unfolding of the energy coupling motif of a membrane transport protein determined by double electron-electron resonance.

    abstract::BtuB is a TonB-dependent transport protein that binds and carries vitamin B(12) across the outer membrane of Gram negative bacteria such as Escherichia coli. Previous work has demonstrated that the Ton box, a highly conserved segment near the N-terminus of the protein, undergoes an order-to-disorder transition upon th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061051x

    authors: Xu Q,Ellena JF,Kim M,Cafiso DS

    更新日期:2006-09-12 00:00:00

  • Calmodulin-dependent autophosphorylation of smooth muscle myosin light chain kinase: intermolecular reaction mechanism via dimerization of the kinase and potentiation of the catalytic activity following activation.

    abstract::In the presence of Ca2+ and calmodulin (CM), purified smooth muscle myosin light chain kinase (MLCKase) was found to undergo autophosphorylation at a rate that was about 200-fold slower than its catalytic activity. Up to 1.7 mol of phosphate were incorporated per mole of kinase. Lower levels of incorporation could be ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00037a025

    authors: Sobieszek A

    更新日期:1995-09-19 00:00:00

  • Decrease in ADP-ribosylation of HeLa non-histone proteins from interphase to metaphase.

    abstract::Variations for non-histones in the ADP-ribosylating activities of interphase and metaphase cells were investigated. 32P-Labeled nicotinamide adenine dinucleotide ([32P]NAD), the specific precursor for the modification, was used to radioactively label proteins. Permeabilized interphase and mitotic cells, as well as iso...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00323a017

    authors: Adolph KW,Song MK

    更新日期:1985-01-15 00:00:00

  • Purification and characterization of the chaperonin 10 and chaperonin 60 proteins from Rhodobacter sphaeroides.

    abstract::Two heat-shock proteins that show high identity with the Escherichia coli chaperonin 60 (groEL) and chaperonin 10 (groES) chaperonin proteins were purified and characterized from photolithoautotrophically grown Rhodobacter sphaeroides. The proteins were purified by using sucrose density gradient centrifugation and Mon...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00247a013

    authors: Terlesky KC,Tabita FR

    更新日期:1991-08-20 00:00:00

  • Identification of the GPR55 agonist binding site using a novel set of high-potency GPR55 selective ligands.

    abstract::Marijuana is the most widely abused illegal drug, and its spectrum of effects suggests that several receptors are responsible for the activity. Two cannabinoid receptor subtypes, CB1 and CB2, have been identified, but the complex pharmacological properties of exogenous cannabinoids and endocannabinoids are not fully e...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200010k

    authors: Kotsikorou E,Madrigal KE,Hurst DP,Sharir H,Lynch DL,Heynen-Genel S,Milan LB,Chung TD,Seltzman HH,Bai Y,Caron MG,Barak L,Abood ME,Reggio PH

    更新日期:2011-06-28 00:00:00

  • Recombinant DHX33 Protein Possesses Dual DNA/RNA Helicase Activity.

    abstract::RNA helicase DHX33 has been shown to participate in a variety of cellular activities, including ribosome biogenesis, protein translation, and gene transcription. We and others further discovered that DHX33 is strongly expressed in several types of human cancers and plays important roles in promoting cancer cell prolif...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00166

    authors: Wang X,Ge W,Zhang Y

    更新日期:2019-01-29 00:00:00

  • CO-induced structural rearrangement of the C cluster in Carboxydothermus hydrogenoformans CO dehydrogenase-evidence from Ni K-edge X-ray absorption spectroscopy.

    abstract::We have examined the C cluster in type II CO dehydrogenase (CODH) from Carboxydothermus hydrogenformans using Ni K-edge X-ray absorption near edge spectroscopy and extended X-ray absorption fine structure (EXAFS) spectroscopy. The enzyme was studied under three conditions: "as-isolated" and after treatment with CO or ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi036104e

    authors: Gu W,Seravalli J,Ragsdale SW,Cramer SP

    更新日期:2004-07-20 00:00:00