Structural analysis of ribosomal protein L7/L12 by the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate.

Abstract:

:The structure of the dimeric form of the protein L7/L12 from ribosomes from Escherichia coli was studied by using the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate. The imidate group of the cross-linker reacts very specifically with Lys-51 of L7/L12. Subsequent cross-linking of this modified L7/L12 by reductive alkylation of the aldehyde group of the cross-linker results in the formation of a covalent cross-link between both polypeptide chains of the L7/L12 dimer. This covalently cross-linked dimer is fully active in reconstitution of elongation factor G dependent GTP hydrolysis of 50S cores lacking L7/L12, suggesting a conformation of the cross-linked protein similar to the conformation of native L7/L12. Analysis of the tryptic peptides of cross-linked L7/L12 shows the points of attachment of the cross-linker to be Lys-51 in one polypeptide chain and Lys-29 in the other. On the basis of a combination of this result with published data, a structure for the N-terminal region of L7/L12 dimers is proposed. The important feature of this model is a shifted parallel alignment of both polypeptide chains resulting in one free N-terminal stretch for each L7/L12 dimer which attaches the protein to the ribosome via protein L10.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Maassen JA,Schop EN,Möller W

doi

10.1021/bi00507a057

subject

Has Abstract

pub_date

1981-02-17 00:00:00

pages

1020-5

issue

4

eissn

0006-2960

issn

1520-4995

journal_volume

20

pub_type

杂志文章
  • DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein: promoter-dependent differences in the thermodynamics and kinetics of binding.

    abstract::The equilibrium binding and association kinetics of the Saccharomyces cerevisiae TATA Binding Protein (TBP) to the E4 and Major Late promoters of adenovirus (TATATATA and TATAAAAG, respectively), have been directly compared by quantitative DNase I titration and quench-flow "footprinting". The equilibrium binding of TB...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi981072u

    authors: Petri V,Hsieh M,Jamison E,Brenowitz M

    更新日期:1998-11-10 00:00:00

  • Biosynthesis of prolyl hydroxylase: evidence for two separate dolichol-media pathways of glycosylation.

    abstract::Prolyl hydroxylase is a glycoprotein containing two nonidentical subunits, alpha and beta. The alpha subunit of prolyl hydroxylase isolated from 13-day-old chick embryos contains a single high mannose oligosaccharide having seven mannosyl residues. Two forms of alpha subunit have been shown to exist in enzyme purified...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00342a041

    authors: Kedersha NL,Tkacz JS,Berg RA

    更新日期:1985-10-08 00:00:00

  • The structure of a soluble chemoreceptor suggests a mechanism for propagating conformational signals.

    abstract::Transmembrane chemoreceptors, also known as methyl-accepting chemotaxis proteins (MCPs), translate extracellular signals into intracellular responses in the bacterial chemotaxis system. MCP ligand binding domains control the activity of the CheA kinase, situated approximately 200 A away, across the cytoplasmic membran...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801727m

    authors: Pollard AM,Bilwes AM,Crane BR

    更新日期:2009-03-10 00:00:00

  • Fluorescence-detected circular dichroism of ethidium in vivo and bound to deoxyribonucleic acid in vitro.

    abstract::Fluorescence-detected circular dichroism (FDCD) spectra are reported for ethidium in Escherichia coli cells and bound to E. coli DNA in vitro. FDCD bands are observed at 325 and 385 nm. These bands change amplitude as the ethidium to DNA ratio changes. Spectra are similar for in vivo and in vitro measurements. However...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00333a001

    authors: Lamos ML,Turner DH

    更新日期:1985-06-04 00:00:00

  • Downscaling Fourier transform infrared spectroscopy to the micrometer and nanogram scale: secondary structure of serotonin and acetylcholine receptors.

    abstract::High signal-to-noise Fourier transform infrared (FTIR) spectra of the 5-hydroxytryptamine (serotonin) receptor (5-HT(3)R) and the nicotinic acetylcholine receptor (nAChR) were obtained by microscope FTIR spectroscopy using micrometer-sized, fully hydrated protein films. Because this novel procedure requires only nanog...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi035113k

    authors: Rigler P,Ulrich WP,Hovius R,Ilegems E,Pick H,Vogel H

    更新日期:2003-12-02 00:00:00

  • Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.

    abstract::In Escherichia coli, the PurT-encoded glycinamide ribonucleotide transformylase, or PurT transformylase, catalyzes an alternative formylation of glycinamide ribonucleotide (GAR) in the de novo pathway for purine biosynthesis. On the basis of amino acid sequence analyses, it is known that the PurT transformylase belong...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000926j

    authors: Thoden JB,Firestine S,Nixon A,Benkovic SJ,Holden HM

    更新日期:2000-08-01 00:00:00

  • How does GAP catalyze the GTPase reaction of Ras? A computer simulation study.

    abstract::The formation of a complex between p21(ras) and GAP accelerates the GTPase reaction of p21(ras) and terminates the signal for cell proliferation. The understanding of this rate acceleration is important for the elucidation of the role of Ras mutants in tumor formation. In principle there are two main options for the o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000640e

    authors: Glennon TM,Villà J,Warshel A

    更新日期:2000-08-15 00:00:00

  • Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.

    abstract::Protocatechuate 3,4-dioxygenase (3,4-PCD) utilizes a ferric ion to catalyze the aromatic ring cleavage of 3,4-dihydroxybenzoate (PCA) by incorporation of both atoms of dioxygen to yield beta-carboxy-cis, cis-muconate. The crystal structures of the anaerobic 3,4-PCD.PCA complex, aerobic complexes with two heterocyclic ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970469f

    authors: Orville AM,Lipscomb JD,Ohlendorf DH

    更新日期:1997-08-19 00:00:00

  • Histone redistribution and conformational effect on chromatin induced by formaldehyde.

    abstract::Histone redistributions between endogenous DNA in calf thymus chromatin and exogenous DNA from Clostridium perfringens (69% A + T) or from Micrococcus luteus (30% A + T) induced by 0.6 M NaCl or by 2% formaldehyde were studied by thermal denaturation. The observed redistribution occurred on histone Hl when the exogeno...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00666a002

    authors: Polacow I,Cabasso L,Li HJ

    更新日期:1976-10-19 00:00:00

  • Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.

    abstract::Nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of H(2)O(2) and nitrite. The flavoenzyme is a new member of the acyl-CoA dehydrogenase (ACAD) family, but it does not react with acyl-CoA substrates. We presen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051966w

    authors: Nagpal A,Valley MP,Fitzpatrick PF,Orville AM

    更新日期:2006-01-31 00:00:00

  • Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family.

    abstract::In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understood. Here, we use evolutionary sequence variation in the α-lytic protease (αLP) p...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.0c00720

    authors: Nixon CF,Lim SA,Sailer ZR,Zheludev IN,Gee CL,Kelch BA,Harms MJ,Marqusee S

    更新日期:2021-01-26 00:00:00

  • Kinetic studies of guinea pig liver transglutaminase reveal a general-base-catalyzed deacylation mechanism.

    abstract::Guinea pig liver transglutaminase (TGase) reacts with 0.1 mM N-Cbz-L-Glu(gamma-p-nitrophenyl ester)Gly (5, prepared herein, K(M) = 0.02 mM) to undergo rapid acylation that can be followed spectrophotometrically at 400 nm (pH 7.0, 25 degrees C). Deacylation of the transiently formed thiolester acyl enzyme intermediate ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0024097

    authors: Leblanc A,Gravel C,Labelle J,Keillor JW

    更新日期:2001-07-27 00:00:00

  • Molecular Basis for Fe(III)-Independent Curcumin Potentiation of Cystic Fibrosis Transmembrane Conductance Regulator Activity.

    abstract::Curcumin potentiates the phosphorylation-dependent activity of human cystic fibrosis transmembrane conductance regulator (CFTR) in Fe(3+)-dependent and Fe(3+)-independent manners. Although the Fe(3+)-dependent curcumin potentiation results from removal of endogenous inhibitory Fe(3+) at the interface of the regulatory...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00219

    authors: Wang G

    更新日期:2015-05-12 00:00:00

  • Mechanistic insight into the photosensory versatility of DXCF cyanobacteriochromes.

    abstract::Cyanobacteriochromes (CBCRs) are photosensory proteins related to the red/far-red phytochromes. Like phytochromes, CBCRs use linear tetrapyrrole (bilin) chromophores covalently attached via a thioether linkage to a conserved Cys residue also found in plant and cyanobacterial phytochromes. Unlike almost all phytochrome...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300171s

    authors: Rockwell NC,Martin SS,Lagarias JC

    更新日期:2012-05-01 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

  • Evidence for partial secondary structure formation in the transition state for arc repressor refolding and dimerization.

    abstract::Structure formation and dimerization are concerted processes in the refolding of Arc repressor. The integrity of secondary structure in the transition state of Arc refolding has been investigated here by determining the changes in equilibrium stability and refolding/unfolding kinetics for a set of Ala --> Gly mutation...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000423d

    authors: Srivastava AK,Sauer RT

    更新日期:2000-07-18 00:00:00

  • A new subfamily of agmatinases present in methanogenic Archaea is Fe(II) dependent.

    abstract::Here we report that the Methanocaldococcus jannaschii enzyme derived from the MJ0309 gene is an Fe(II) dependent agmatinase (SpeB). This is the first report of an iron-dependent agmatinase. We demonstrate that aerobically isolated recombinant enzyme contains two disulfide bonds and only a trace amount of any metal and...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300039f

    authors: Miller D,Xu H,White RH

    更新日期:2012-04-10 00:00:00

  • Zn(2+)-dependent misfolding of the p53 DNA binding domain.

    abstract::The DNA binding domain (DBD) of p53 folds by a complex mechanism that involves parallel pathways and multiple intermediates, both on- and off-pathway. This heterogeneity renders DBD particularly susceptible to misfolding and aggregation. The origins of parallel folding mechanisms are not well understood. DBD folding h...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi062106y

    authors: Butler JS,Loh SN

    更新日期:2007-03-13 00:00:00

  • The thermodynamic and structural differences among the catalytically active complexes of phosphoglucomutase: metal ion effects.

    abstract::When the identity of the metal ion activator, M, is changed within the series, Zn2+, Co2+, Mg2+, Ni2+, Mn2+, and Cd2+, the equilibrium distribution among the central complexes in the phosphoglucomutase system is markedly altered. (The central complexes are Ep-M-Glc-6-P, ED-M-Glc-1,6-P2, and Ep-M-Glc-1-P, where Ep and ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00663a016

    authors: Ray WJ Jr,Long JW

    更新日期:1976-09-07 00:00:00

  • Purification and characterization of the human erythrocyte band 3 protein C-terminal domain.

    abstract::To clarify the function of the hydrophilic carboxyl-terminal tail of human erythrocyte membrane band 3 protein (HEM-B3), we purified two peptides, C1 (Ala893-Val911) and KS4 (Gly647-Arg656), from human erythrocyte band 3 protein preparations. Purified C1 peptides at concentrations from 5 to 80 microM were incubated wi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi035281c

    authors: Fu G,Wang T,Yang B,Lv F,Shi C,Jiang X,Tian L,Yu W,Hamasaki N

    更新日期:2004-02-17 00:00:00

  • Conformational changes in human hepatitis C virus NS3 protease upon binding of product-based inhibitors.

    abstract::One of the most promising approaches to anti-hepatitis C virus drug discovery is the development of inhibitors of the virally encoded protease NS3. This chymotrypsin-like serine protease is essential for the maturation of the viral polyprotein, and processing requires complex formation between NS3 and its cofactor NS4...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi991220w

    authors: Bianchi E,Orrù S,Dal Piaz F,Ingenito R,Casbarra A,Biasiol G,Koch U,Pucci P,Pessi A

    更新日期:1999-10-19 00:00:00

  • Effects of a surfactant-associated protein and calcium ions on the structure and surface activity of lung surfactant lipids.

    abstract::Previous studies have demonstrated that lung-specific proteins are associated with surfactant lipids, particularly the highly surface active subfraction known as tubular myelin. We have isolated a surfactant-associated protein complex with molecular weight components of 36 000, 32 000, and 28 000 and reassembled it wi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00322a026

    authors: Hawgood S,Benson BJ,Hamilton RL Jr

    更新日期:1985-01-01 00:00:00

  • Correlation of beta-amyloid aggregate size and hydrophobicity with decreased bilayer fluidity of model membranes.

    abstract::beta-amyloid peptide (Abeta) is the primary constituent of senile plaques, a defining feature of Alzheimer's disease. Aggregated Abeta is toxic to neurons, but the mechanism of toxicity remains unproven. One proposal is that Abeta toxicity results from relatively nonspecific Abeta-membrane interactions. We hypothesize...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0001980

    authors: Kremer JJ,Pallitto MM,Sklansky DJ,Murphy RM

    更新日期:2000-08-22 00:00:00

  • Structural details on the binding of antihypertensive drugs captopril and enalaprilat to human testicular angiotensin I-converting enzyme.

    abstract::Angiotensin converting enzyme (ACE) plays a critical role in the circulating or endocrine renin-angiotensin system (RAS) as well as the local regulation that exists in tissues such as the myocardium and skeletal muscle. Here we report the high-resolution crystal structures of testis ACE (tACE) in complex with the firs...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049480n

    authors: Natesh R,Schwager SL,Evans HR,Sturrock ED,Acharya KR

    更新日期:2004-07-13 00:00:00

  • Identification of a region of the ileal-type sodium/bile acid cotransporter interacting with a competitive bile acid transport inhibitor.

    abstract::Drug intervention that prevents reabsorption of circulating bile acids by the apical (ileal) sodium/bile acid cotransporter (ASBT) may be a promising new therapy for lowering of plasma cholesterol. 2164U90 is a benzothiazepine-based competitive inhibitor of bile acid transport with K(i) values of approximately 10 and ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0205404

    authors: Hallén S,Björquist A,Ostlund-Lindqvist AM,Sachs G

    更新日期:2002-12-17 00:00:00

  • Organellar Na+/H+ exchangers: novel players in organelle pH regulation and their emerging functions.

    abstract::Mammalian Na+/H+ exchangers (NHEs) play a fundamental role in cellular ion homeostasis. NHEs exhibit an appreciable variation in expression, regulation, and physiological function, dictated by their dynamics in subcellular localization and/or interaction with regulatory proteins. In recent years, a subgroup of NHEs co...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi101082e

    authors: Ohgaki R,van IJzendoorn SC,Matsushita M,Hoekstra D,Kanazawa H

    更新日期:2011-02-01 00:00:00

  • Phosphoryl transfer between phosphorylated histidine-containing protein and histidine-containing protein is not autocatalytic.

    abstract::Histidine-containing protein, HPr, is a phosphocarrier protein that is part of the bacterial phosphoenolpyruvate:sugar phosphotransferase system. HPr is phosphorylated by enzyme I, and P-HPr transfers the phosphoryl group to the IIA domain of a number of sugar-specific enzyme II complexes. Autocatalytic phosphoryl tra...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00073a025

    authors: Anderson JW,Waygood EB

    更新日期:1993-06-08 00:00:00

  • DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils.

    abstract::Human uracil DNA glycosylase (hUNG) plays a central role in DNA repair and programmed mutagenesis of Ig genes, requiring it to act on sparsely or densely spaced uracil bases located in a variety of contexts, including U/A and U/G base pairs, and potentially uracils within single-stranded DNA (ssDNA). An interesting qu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi301562n

    authors: Schonhoft JD,Stivers JT

    更新日期:2013-04-16 00:00:00

  • Structural studies of acetylated and control inner core histones.

    abstract::The role of acetylation on the conformation and association state of the inner core histone octamer isolated from HeLa cells was examined. Preparation of suitable quantities of pure acetylated and control inner core histones from HeLa cells required the development of a new preparative procedure. The results from size...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00384a041

    authors: Prevelige PE Jr,Fasman GD

    更新日期:1987-05-19 00:00:00

  • Steady-state and transient kinetic analyses of taurine/alpha-ketoglutarate dioxygenase: effects of oxygen concentration, alternative sulfonates, and active-site variants on the FeIV-oxo intermediate.

    abstract::Taurine/alpha-ketoglutarate (alphaKG) dioxygenase (TauD), an archetype alphaKG-dependent hydroxylase, is a non-heme mononuclear Fe(II) enzyme that couples the oxidative decarboxylation of alphaKG with the conversion of taurine to aminoacetaldehyde and sulfite. The crystal structure of taurine-alphaKG-Fe(II)TauD is kno...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi048746n

    authors: Grzyska PK,Ryle MJ,Monterosso GR,Liu J,Ballou DP,Hausinger RP

    更新日期:2005-03-15 00:00:00