The arginine finger loop of yeast and human GAP is a determinant for the specificity toward Ras GTPase.

Abstract:

:In this work, we have studied the role of the arginine finger region in determining the specificity of the GTPase activating proteins (GAPs) Saccharomyces cerevisiae Ira2p and human p120-GAP toward yeast Ras2p and human Ha-Ras p21. It is known that p120-GAP can enhance both Ras2p and Ha-Ras GTPase activities, whereas Ira2p is strictly specific for Ras2p and fails to activate Ha-Ras GTPase. Substitution in Ira2p of the arginine following the arginine finger with alanine, the residue found in the corresponding position of p120-GAP, or by glycine as found in neurofibromin, evokes a low but significant stimulation of Ha-Ras GTPase. The stimulatory activity of Ira2p on Ha-Ras increased by substituting segments of the finger loop region with p120-GAP residues, especially with the six residues forming the tip of the arginine loop. In p120-GAP, substitution of the entire finger loop with the corresponding region of Ira2p led to a construct completely inactive on Ha-Ras GTPase but active on yeast Ras2p GTPase. Analysis of these results and modeling of Ira2p.Ras complexes emphasize the importance of the finger loop region not only for the catalytic activity but also as a structural determinant involved in the specificity of GAPs toward Ras proteins from different organisms.

journal_name

Biochemistry

journal_title

Biochemistry

authors

te Biesebeke R,Krab IM,Parmeggiani A

doi

10.1021/bi010027a

subject

Has Abstract

pub_date

2001-06-26 00:00:00

pages

7474-9

issue

25

eissn

0006-2960

issn

1520-4995

pii

bi010027a

journal_volume

40

pub_type

杂志文章
  • Direct tests of the energetic basis of abortive cycling in transcription.

    abstract::Although the synthesis of RNA from a DNA template is (and must be) a generally very stable process to enable transcription of kilobase transcripts, it has long been known that during initial transcription of the first 8-10 bases of RNA complexes are relatively unstable, leading to the release of short abortive RNA tra...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200620q

    authors: Vahia AV,Martin CT

    更新日期:2011-08-16 00:00:00

  • Preparation and characterization of N-(1-pyrenyl)iodoacetamide-labeled Escherichia coli RNA polymerase.

    abstract::N-(1-Pyrenyl)iodoacetamide has been used to introduce fluorescent probes into Escherichia coli RNA polymerase. After an incubation time of 15 min, approximately 2 pyrene equiv was introduced per enzyme molecule. There was no further increase in modification after more extended periods of incubation. Neither calf thymu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00215a028

    authors: Johnson RS,Bowers M,Eaton Q

    更新日期:1991-01-08 00:00:00

  • Characterizing the response of calcium signal transducers to generated calcium transients.

    abstract::Cellular Ca2+ transients and Ca2+-binding proteins regulate physiological phenomena as diverse as muscle contraction, neurosecretion, and cell division. When Ca2+ is rapidly mixed with slow Ca2+ chelators, EGTA, or Mg2+/EDTA, artificial Ca2+ transients (ACTs) of varying duration (0.1-50 ms half-widths (hws)) and ampli...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982495z

    authors: Davis JP,Tikunova SB,Walsh MP,Johnson JD

    更新日期:1999-03-30 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

  • The amino- and carboxyl-terminal fragments of the Bacillus thuringensis Cyt1Aa toxin have differential roles in toxin oligomerization and pore formation.

    abstract::The Cyt toxins produced by the bacteria Bacillus thuringiensis show insecticidal activity against some insects, mainly dipteran larvae, being able to kill mosquitoes and black flies. However, they also possess a general cytolytic activity in vitro, showing hemolytic activity in red blood cells. These proteins are comp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi101239r

    authors: Rodriguez-Almazan C,Ruiz de Escudero I,Cantón PE,Muñoz-Garay C,Pérez C,Gill SS,Soberón M,Bravo A

    更新日期:2011-01-25 00:00:00

  • Identification of the C=O stretching vibrations of FMN and peptide backbone by 13C-labeling of the LOV2 domain of Adiantum phytochrome3.

    abstract::Phototropin, a blue-light photoreceptor in plants, has two FMN-binding domains named LOV1 and LOV2. We previously observed temperature-dependent FTIR spectral changes in the C=O stretching region (amide-I vibrational region of the peptide backbone) for the LOV2 domain of Adiantum phytochrome3 (phy3-LOV2), suggesting p...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061837v

    authors: Iwata T,Nozaki D,Sato Y,Sato K,Nishina Y,Shiga K,Tokutomi S,Kandori H

    更新日期:2006-12-26 00:00:00

  • Ligand-dependent aggregation and cooperativity: a critique.

    abstract::Ligand-dependent site-site (or subunit-subunit) interactions provide the basis for explaining cooperativity in chemical reactions. Even in the simplest possible nonaggregating system, interpretation of the interactions in terms of structural details requires an explicit assumption (or model) for the binding of the lig...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi00106a004

    authors: Saroff HA

    更新日期:1991-10-22 00:00:00

  • Time-resolved fluorescence investigations of the interaction of the voltage-sensitive probe RH421 with lipid membranes and proteins.

    abstract::Fluorescence lifetimes and fluorescence anisotropy decays of the voltage-sensitive styryl-pyridinium dye RH421 have been measured in the presence of dimyristoylphosphatidylcholine vesicles, the water soluble enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco), and Na+,K(+)-ATPase-containing membrane fragm...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00037a015

    authors: Visser NV,van Hoek A,Visser AJ,Frank J,Apell HJ,Clarke RJ

    更新日期:1995-09-19 00:00:00

  • Conformational states of the bacteriophage P22 capsid subunit in relation to self-assembly.

    abstract::The formation of closed icosahedral capsids from a single species of coat protein subunit requires that the subunits assume different conformations at different lattice positions. In the double-stranded DNA bacteriophage P22, formation of correctly dimensioned capsids is mediated by interaction between coat protein su...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00475a030

    authors: Prevelige PE Jr,Thomas D,King J,Towse SA,Thomas GJ Jr

    更新日期:1990-06-12 00:00:00

  • Soluble phosphatidylserine binds to a single identified site in the C2 domain of human factor Va.

    abstract::Factor V(a) (FV(a)) is a cofactor for the serine protease factor X(a) that activates prothrombin to thrombin in the presence of Ca(2+) and a membrane surface. FV(a) is a heterodimer composed of one heavy chain (A1 and A2 domains) and one light chain (A3, C1, and C2 domains). We use fluorescence, circular dichroism, an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010449k

    authors: Srivastava A,Quinn-Allen MA,Kim SW,Kane WH,Lentz BR

    更新日期:2001-07-27 00:00:00

  • pH dependence and structural interpretation of the reactions of Coprinus cinereus peroxidase with hydrogen peroxide, ferulic acid, and 2,2'-azinobis.

    abstract::Steady-state and transient-state analysis of Coprinus cinereus peroxidase, CIP (identical to Arthromyces ramosus peroxidase), was used to characterize the kinetics of the three fundamental steps in heme peroxidase catalysis: compound I (cpd I) formation, cpd I reduction, and compound II (cpd II) reduction. The rate co...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970387r

    authors: Abelskov AK,Smith AT,Rasmussen CB,Dunford HB,Welinder KG

    更新日期:1997-08-05 00:00:00

  • Replication, repair, and translesion polymerase bypass of N⁶-oxopropenyl-2'-deoxyadenosine.

    abstract::The oxidative stress products malondialdehyde and base propenal react with DNA bases forming the adduction products 3-(2'-deoxy-β-D-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one (M1dG) and N(6)-(oxypropenyl)-2'-deoxyadenosine (OPdA). M1dG is mutagenic in vivo and miscodes in vitro, but little work has been do...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi401103k

    authors: Maddukuri L,Shuck SC,Eoff RL,Zhao L,Rizzo CJ,Guengerich FP,Marnett LJ

    更新日期:2013-12-03 00:00:00

  • Probing structural factors stabilizing antisense oligonucleotide duplexes: NMR studies of a DNA.DNA duplex containing a formacetal linkage.

    abstract::The duplex formed by annealing the formacetal backbone modified dodecamer d-(CGCGTTOCH2OTTGCGC) to its complementary strand, d(GCGCAAAACGCG) (duplex I), has been studied by NMR techniques and analyzed with reference to its unmodified counterpart (duplex II). Comparison of parameters such as 2D cross-peak intensities, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00142a009

    authors: Gao X,Brown FK,Jeffs P,Bischofberger N,Lin KY,Pipe AJ,Noble SA

    更新日期:1992-07-14 00:00:00

  • 2-Hydroxy-2'-deoxyadenosine 5'-triphosphate enhances A.T --> C.G mutations caused by 8-hydroxy-2'-deoxyguanosine 5'-triphosphate by suppressing its degradation upon replication in a HeLa extract.

    abstract::The coexistence effects of multiple kinds of oxidized deoxyribonucleotides were examined using an SV40 origin-dependent in vitro replication system with a HeLa extract. Oxidized dGTP and dATP, 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (8-OH-dGTP) and 2-hydroxy-2'-deoxyadenosine 5'-triphosphate (2-OH-dATP), were used...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi062117r

    authors: Satou K,Kasai H,Masutani C,Hanaoka F,Harashima H,Kamiya H

    更新日期:2007-06-05 00:00:00

  • Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors.

    abstract::Eukaryotic initiation factor 5 (eIF5) plays multiple roles in translation initiation. Its N-terminal domain functions as a GTPase-activator protein (GAP) for GTP bound to eIF2, while its C-terminal region nucleates the interactions between multiple translation factors, including eIF1, which acts to inhibit GTP hydroly...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi052387u

    authors: Conte MR,Kelly G,Babon J,Sanfelice D,Youell J,Smerdon SJ,Proud CG

    更新日期:2006-04-11 00:00:00

  • Energy dependent hydrogen ion accumulation in submitochondrial particles.

    abstract::The fluorescence quenching of 9-aminoacridine (9AA) in suspension of beef heart EDTA submitochondrial particles was studied and was used to calculate the pH gradient between these particles and the medium. This pH gradient, which is energy dependent, is also dependent strongly on the presence of anion species in the m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00683a017

    authors: Rottenberg H,Lee CP

    更新日期:1975-06-17 00:00:00

  • Solution structure and folding characteristics of the C-terminal SH3 domain of c-Crk-II.

    abstract::Crk-II is a signaling adaptor protein that is involved in many cellular processes including apoptosis, proliferation, and differentiation. It has a modular domain architecture consisting of an Src homology 2 domain (SH2) followed by two Src homology 3 (SH3) domains. The structures and ligand-binding properties of the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi060590z

    authors: Muralidharan V,Dutta K,Cho J,Vila-Perello M,Raleigh DP,Cowburn D,Muir TW

    更新日期:2006-07-25 00:00:00

  • Significance of hydrophobic S4-P4 interactions in subtilisin 309 from Bacillus lentus.

    abstract::The subtilisins have an extended substrate binding cleft comprising at least 8 subsites. Two pockets at the S1 and S4 sites are particularly conspicuous, and the interactions between substrate and these two pockets are very important for the substrate specificity. Phe residues have mutationally been introduced at one ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00062a016

    authors: Bech LM,Sørensen SB,Breddam K

    更新日期:1993-03-23 00:00:00

  • Electrostatic control of the rate-determining step of the copper, zinc superoxide dismutase catalytic reaction.

    abstract::The dependence of the activity of bovine Cu,Zn superoxide dismutase on pH and ionic strength was extensively investigated in the ranges of pH 7.4-pH 12.3 and of ionic strength of 0.02-0.25 M. The results obtained indicate that two positively charged groups having pK values of approximately 10.1 and 10.8 are involved i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00385a043

    authors: Argese E,Viglino P,Rotilio G,Scarpa M,Rigo A

    更新日期:1987-06-02 00:00:00

  • Extreme Dynamics in the BamA β-Barrel Seam.

    abstract::BamA is an essential component of the β-barrel assembly machine (BAM) that is responsible for insertion and folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. BamA is an OMP itself, and its β-barrel transmembrane domain is thought to catalyze OMP insertion and folding, although the molecular...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00281

    authors: Doerner PA,Sousa MC

    更新日期:2017-06-20 00:00:00

  • Mutational analysis of the roles in catalysis and substrate recognition of arginines 54 and 305, aspartic acid 309, and tryptophan 317 located at subsites 1 and 2 in glucoamylase from Aspergillus niger.

    abstract::The mutants Arg54-->Leu, Arg54-->Lys, Arg305-->Lys, Asp309-->Glu, and Trp317-->Phe, located at subsites 1 and 2 in glucoamylase from Aspergillus niger, provide insight into the importance of specific hydrogen bonds and hydrophobic interactions in substrate recognition, catalytic mechanism, and stability. As suggested ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00032a009

    authors: Frandsen TP,Christensen T,Stoffer B,Lehmbeck J,Dupont C,Honzatko RB,Svensson B

    更新日期:1995-08-15 00:00:00

  • In the sense of transcription regulation by G-quadruplexes: asymmetric effects in sense and antisense strands.

    abstract::G-Quadruplexes occupy important regulatory regions in the genome. DNA G-quadruplexes in the promoter regions and RNA quadruplexes in the UTRs (untranslated regions) have been individually studied and variously implicated at different regulatory levels of gene expression. However, the formation of G-quadruplexes in the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi401451q

    authors: Agarwal T,Roy S,Kumar S,Chakraborty TK,Maiti S

    更新日期:2014-06-17 00:00:00

  • The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic acid dehalogenase: a kinetic, NMR, and mutational analysis.

    abstract::trans-3-Chloroacrylic acid dehalogenase (CaaD) converts trans-3-chloroacrylic acid to malonate semialdehyde by the addition of H(2)O to the C-2, C-3 double bond, followed by the loss of HCl from the C-3 position. Sequence similarity between CaaD, an (alphabeta)(3) heterohexamer (molecular weight 47,547), and 4-oxalocr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi030241u

    authors: Azurmendi HF,Wang SC,Massiah MA,Poelarends GJ,Whitman CP,Mildvan AS

    更新日期:2004-04-13 00:00:00

  • Structural determinants of HscA peptide-binding specificity.

    abstract::The Hsp70-class molecular chaperone HscA interacts specifically with a conserved (99)LPPVK(103) motif of the iron-sulfur cluster scaffold protein IscU. We used a cellulose-bound peptide array to perform single-site saturation substitution of peptide residues corresponding to Glu(98)-Ile(104) of IscU to determine posit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0606187

    authors: Tapley TL,Cupp-Vickery JR,Vickery LE

    更新日期:2006-07-04 00:00:00

  • Substrate recognition determinants for rhodopsin kinase: studies with synthetic peptides, polyanions, and polycations.

    abstract::Rhodopsin kinase phosphorylates serine- and threonine-containing peptides from bovine rhodopsin's carboxyl-terminal sequence. Km's for the peptides decrease as the length of the peptide is increased over the range 12-31 amino acids, reaching 1.7 mM for peptide 318-348 from the rhodopsin sequence. The Km for phosphoryl...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00448a013

    authors: Palczewski K,Arendt A,McDowell JH,Hargrave PA

    更新日期:1989-10-31 00:00:00

  • Analysis of the ternary interaction of the red cell membrane skeletal proteins spectrin, actin, and 4.1.

    abstract::Spectrin dimers interact weakly with F-actin under physiological solvent conditions (with an association constant of about 5 X 10(3) M-1 at 20 degrees C). In the presence of the membrane skeletal constituent, protein 4.1, strong binding is observed; an analysis of the profiles for formation of a ternary complex leads ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00314a027

    authors: Ohanian V,Wolfe LC,John KM,Pinder JC,Lux SE,Gratzer WB

    更新日期:1984-09-11 00:00:00

  • Conformational Dynamics and Protein-Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations.

    abstract::ATP-binding cassette (ABC) transporters are ubiquitous in all three kingdoms of life and are implicated in many clinically relevant physiological processes. They couple the energy released by ATP hydrolysis to facilitate substrate translocation across cell membranes. The crystal structures of type II ABC importers hav...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00386

    authors: Pan C,Weng J,Wang W

    更新日期:2016-12-13 00:00:00

  • Human class I alcohol dehydrogenases catalyze the interconversion of alcohols and aldehydes in the metabolism of dopamine.

    abstract::The class I human liver alcohol dehydrogenases (ADHs) catalyze the interconversion of the intermediary alcohols and aldehydes of dopamine metabolism in vitro, whereas those of the class II and class III do not. The individual, homogeneous class I isozymes oxidize (3,4-dihydroxyphenyl)ethanol and (4-hydroxy-3-methoxyph...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00371a005

    authors: Mårdh G,Vallee BL

    更新日期:1986-11-18 00:00:00

  • Phospholipids chiral at phosphorus. Dramatic effects of phosphorus chirality on the deuterium NMR properties of the choline head group of phospholipids in the liquid crystalline phase.

    abstract::To probe the motional and conformational properties of the choline head group of 1,2-dipalmitoyl-sn-glycero-3-thiophosphocholine (DPPsC), the Rp, Sp, and Rp + Sp isomers of [alpha-D2]DPPsC, [beta-D2]DPPsC, and [delta-D9]DPPsC in the subgel, gel, and liquid crystalline phases were investigated with deuterium NMR, and t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00501a008

    authors: Loffredo WM,Jiang RT,Tsai MD

    更新日期:1990-12-11 00:00:00

  • The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR.

    abstract::We have studied the competition between Na+ and K+ for coordination by G quartets using the oligonucleotide d(G3T4G3) as a model system. d(G3T4G3) forms a dimeric foldback structure containing three G quartets in the presence of either NaCl or KCl. Proton chemical shifts, which are particular to the species of coordin...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9620565

    authors: Hud NV,Smith FW,Anet FA,Feigon J

    更新日期:1996-12-03 00:00:00