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At least 1,153 records · Page 64Linked to original sources
PubMed2005

Expression and assay of glycoprotein-specific ubiquitin ligases.

N-linked glycosylation of proteins that takes place in the endoplasmic reticulum (ER) plays a key role in protein quality control. Misfolded proteins or unassembled protein complexes that fail to achieve their functional states in the ER are retrotranslocated into the cytosol and degraded by the ubiquitin-proteasome system in a process called ER-associated degradation (ERAD). N-linked glycoprotein-specific ubiquitin ligase complexes, SCF(Fbs1) and SCF(Fbs2), appear to participate in ERAD for selective elimination of aberrant glycoproteins in the cytosol. This chapter describes methods employed for the isolation and oligosaccharide-binding assay of Fbs proteins that are the substrate-recognition components of the SCF(Fbs) complex and the in vitro ubiquitylation assay of the SCF(Fbs) ubiquitin ligase complexes.

Animals↗
PubMed2005

Assays for high-throughput screening of E2 AND E3 ubiquitin ligases.

We developed a series of assays for biochemical activities involving ubiquitin. These assays use electrochemiluminescence detection to measure the ubiquitylation of target proteins. To enable electrochemiluminescence detection, the target proteins were prepared as bacterially expressed fusion proteins and captured on the surface of specially designed microtiter plates having integrated electrodes. Ubiquitylation was quantitated directly, through the use of ubiquitin labeled with an electrochemiluminescent label, or indirectly, through the use of labeled antiubiquitin antibodies. Assays were carried out in both 96-well and 384-well plates. The success of the assay with this variety of formats allowed the selection of optimal work flows for specific applications on the basis of ease of use and overall reagent consumption and availability. We used our ubiquitylation assays to measure the activities of E2 ubiquitin-conjugating enzymes and E3 class ubiquitin ligases. Signal/background ratios for many of our assays were greater than 50, significantly facilitating their conversion to high-throughput practice in a convenient manner. The speed, sensitivity, and convenience of the assay formats makes them well suited for comprehensive interrogations of libraries of compounds or genes in applications like drug and substrate discovery for ubiquitin ligases.

Electrochemistry↗
PubMed1996

Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.

The crystal structure of the ATP-dependent DNA ligase from bacteriophage T7 has been solved at 2.6 A resolution. The protein comprises two domains with a deep cleft running between them. The structure of a complex with ATP reveals that the nucleotide binding pocket is situated on the larger N-terminal domain, at the base of the cleft between the two domains of the enzyme. Comparison of the overall domain structure with that of DNA methyltransferases, coupled with other evidence, suggests that DNA also binds in this cleft. Since this structure is the first of the nucleotidyltransferase superfamily, which includes the eukaryotic mRNA capping enzymes, the relationship between the structure of DNA ligase and that of other nucleotidyltransferases is also discussed.

Adenosine Triphosphate↗
PubMed1996

tRNA ligase is required for regulated mRNA splicing in the unfolded protein response.

The accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers an intracellular signaling pathway, the unfolded protein response (UPR), that leads to increased transcription of genes encoding ER-resident proteins. Transcriptional activation is mediated by a dedicated transcription factor, Hac1p, whose activity is controlled by regulated splicing of its mRNA. We have identified a mutation in tRNA ligase that disrupts the UPR in the yeast Saccharomyces cerevisiae. In this mutant, splicing of HAC1 mRNA, but not tRNA, is blocked. In contrast, HAC1 mRNA splicing is not impaired in cells that are blocked in spliceosome-mediated mRNA splicing. Furthermore, the splice junctions of HAC1 mRNA do not conform to the consensus sequences of other yeast pre-mRNAs. Our results suggest that the regulated splicing of HAC1 mRNA occurs by a novel pathway, involving tRNA ligase and bypassing the spliceosome.

Base Sequence↗
PubMed2003

COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases.

COP9 Signalosome (CSN) is a fascinating protein complex whose biochemical and physiological functions are only beginning to be understood. It is conserved throughout eukaryotes and is critical to the proper development of all multicellular organisms in which its function has been explored. Recent work suggests that CSN plays a key role in sustaining the activity of SCF and other cullin-based ubiquitin ligases, which may account for its essential roles in development. Here, we summarize what is known about CSN, and discuss hypotheses for how CSN promotes the activity of SCF ubiquitin ligases.

Animals↗
PubMed2000

Cloning and characterization of the proximal promoter region of the mouse glutamate-L-cysteine ligase regulatory subunit gene.

We describe upregulation of the mRNA for the mouse glutamate-cysteine ligase regulatory subunit gene (Glcl-r) in Hepa-1 cells treated with beta-napthoflavone (BNF) and tert-butylhydroquinone (tBHQ). A 2-kb fragment of the proximal promoter region of the gene was cloned and sequenced, and sequence analysis reveals a high degree of homology when compared to the human glutamate-cysteine ligase regulatory subunit gene promoter. Primer extension analysis indicates a major transcription start site 218 bp upstream of the translation start codon in a CpG-rich region, suggesting that transcription is Sp1 mediated. Reporter constructs containing nested deletion fragments of the Glcl-r promoter demonstrate that regulatory elements sufficient for basal and tBHQ-inducible expression lie between -273 and -787 bp relative to the translation start codon and that the distal promoter may contain negative regulatory elements.

Animals↗
PubMed2003

Expanded divalent metal-ion tolerance of evolved ligase ribozymes.

Class I ligases are artificial ribozymes that catalyze the joining of two single-stranded RNAs. These ribozymes are between 120 and 160 nucleotides in length, making them intermediate in size for catalytic RNAs. Previous characterization of the b1-207 ribozyme suggests that it behaves similar to larger ribozymes in terms of divalent metal-ion dependence. This molecule displays a strong preference for magnesium for catalysis, and is inactive in any other metal except manganese, which actually inhibits its operation in magnesium. Here, we sought to examine the metal-ion usages of two ligases that were obtained through continuous evolution in vitro from the b1-207 sequence framework. We found an expanded catalytic range for the E(100)(#3) and B(16)(#19) ribozymes, as they are both catalytically active in calcium and strontium, and less inhibited by manganese. Though not selected for activity in these salts, the evolved ribozymes exhibit several adaptations to in vitro catalysis, and their ability to accommodate metals other than magnesium can be viewed as an example of a molecular exaptation.

Base Sequence↗
PubMed2003

Association of polymorphism in glutamate-cysteine ligase catalytic subunit gene with coronary vasomotor dysfunction and myocardial infarction.

OBJECTIVES: The purpose of this study was to test the hypothesis that polymorphisms in the promoter region of the glutamate-cysteine ligase catalytic subunit (GCLC) gene may be associated with coronary endothelial vasomotor dysfunction and myocardial infarction (MI). BACKGROUND: Glutamate-cysteine ligase is a rate-limiting enzyme for synthesis of glutathione (GSH) that plays a crucial role in the intracellular antioxidant defense systems. Oxidants transcriptionally upregulate the GCLC gene for GSH synthesis, providing a protective mechanism against oxidant-induced endothelial dysfunction or activation, which plays a pathogenetic role in cardiovascular diseases. METHODS: The association of the possible polymorphisms with coronary arterial diameter responses to acetylcholine was determined in 62 male subjects. The frequency of polymorphisms was compared between 255 male patients with MI and 179 male control subjects. RESULTS: We found a polymorphism (-129C/T) in which the T allele showed lower promoter activity (50% to 60% of the activity of the C allele) in response to H(2)O(2) in human endothelial cells. Endothelium-dependent dilation of coronary arteries was impaired in subjects with the -129T allele (n = 31), as compared with the age-matched subjects without the -129T allele (n = 31). The T allele was highly frequent in patients with MI as compared with control subjects, and it was a significant risk factor for MI, independent of traditional coronary risk factors (odds ratio [OR] 1.81, 95% confidence interval [CI] 1.08 to 3.03; p = 0.03). CONCLUSIONS: The -129T polymorphism of the GCLC gene may suppress the GCLC gene induction response to an oxidant, and it is implicated in coronary endothelial vasomotor dysfunction and MI.

Adult↗
PubMed2001

Correlation between urine and cervical specimens for the detection of cervical Chlamydia trachomatis and Neisseria gonorrhoeae using ligase chain reaction in a cohort of HIV infected and uninfected adolescents.

PURPOSE: (a) To examine the concordance between ligase chain reaction (LCR) results from urine and cervical samples for Chlamydia trachomatis and Neisseria gonorrhoeae in HIV infected and uninfected adolescent women, and (b) to examine factors that may influence the concordance of LCR results in this population. METHODS: Baseline specimens from 269 of 334 female subjects enrolled in a longitudinal study of HIV infection in adolescents were analyzed for C. trachomatis and N. gonorrhoeae using ligase chain reaction (LCR) assays in a central laboratory. Concordance was measured using kappa coefficient with permutation analyses to calculate the difference between HIV status groups. Discordant LCR results were examined for the co-infection with the other microorganism, bacterial vaginosis, or Trichomonas vaginalis. RESULTS: The prevalence of C. trachomatis detected by LCR in the HIV infected and uninfected groups was 19.3% and 12.2%, respectively (p = .16); the prevalence of N. gonorrhoeae was 7.0% and 2.4%, respectively (p = .16). Urine LCR assay sensitivity to detect cervical C. trachomatis infection was 86% (95% CI: 68%-96%) in the HIV infected group and 100% (95% CI: 69%-100%) in the HIV uninfected group. Urine LCR assay sensitivity to detect cervical N. gonorrhoeae infection was 92% (95% CI: 62%-100%) in the HIV infected group. There were only 2 N. gonorrhoeae infections in the HIV uninfected group, and both were urine LCR positive. Differences in sensitivity between HIV infected and HIV uninfected subjects were not statistically significant. Coinfection with N. gonorrhoeae, bacterial vaginosis or Trichomonas vaginalis was not associated with the concordance of urine and cervical LCR results. CONCLUSION: The relatively high sensitivity of urine LCR testing overall suggests that urine screening may be reasonable for sexually active adolescent females with or without HIV infection in situations in which urine screening may be more acceptable than pelvic examinations.

Adolescent↗
PubMed2002

The SCF ubiquitin ligase: an extended look.

The SCF E3 ubiquitin ligases select specific proteins for ubiquitination (and typically destruction) by coupling variable adaptor (F box) proteins that bind protein substrates to a conserved catalytic engine containing a cullin, Cul1, and the Rbx1/Roc1 RING finger protein. A new crystal structure of the SCF(Skp2) ubiquitin ligase shows the molecular organization of this complex and raises important questions as to how substrate ubiquitination is accomplished.

Cell Cycle Proteins↗
PubMed2004

A putative ariadne-like E3 ubiquitin ligase (PAUL) that interacts with the muscle-specific kinase (MuSK).

Formation of the postsynaptic membrane at the skeletal neuromuscular junction (NMJ) requires activation of the muscle-specific receptor tyrosine kinase (MuSK). Few intracellular mediators or modulators of MuSK actions are known. E3 ubiquitin ligases may serve this role, because activities of several receptor tyrosine kinases, G-protein-coupled receptors and channels are modulated by ubiquitination. Here, we report identification of a putative Ariadne-like ubiquitin ligase (PAUL) that binds to the cytoplasmic domain of MuSK. PAUL is expressed in numerous tissues of developing and adult mice, and is present at NMJs in muscle fibers but is not confined to them.

Amino Acid Sequence↗
PubMed1992

Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases.

We have deduced the nucleotide sequence of the genes encoding the three components of 4-chlorobenzoate (4-CBA) dehalogenase from Pseudomonas sp. CBS-3 and examined the origin of these proteins by homology analysis. Open reading frame 1 (ORF1) encodes a 30-kDa 4-CBA-coenzyme A dehalogenase related to enoyl-coenzyme A hydratases functioning in fatty acid beta-oxidation. ORF2 encodes a 57-kDa protein which activates 4-CBA by acyl adenylation/thioesterification. This 4-CBA:coenzyme A ligase shares significant sequence similarity with a large group of proteins, many of which catalyze similar chemistry in beta-oxidation pathways or in siderophore and antibiotic synthetic pathways. These proteins have in common a short stretch of sequence, (T,S)(S,G)G(T,S)(T,E)G(L,X)PK(G,-), which is particularly highly conserved and which may represent an important new class of "signature" sequence. We were unable to find any proteins homologous in sequence to the 16-kDa 4-hydroxybenzoate-coenzyme A thioesterase encoded by ORF3. Analysis of the chemistry and function of the proteins found to be structurally related to the 4-CBA:coenzyme A ligase and the 4-CBA-coenzyme A dehalogenase supports the proposal that they evolved from a beta-oxidation pathway.

Amino Acid Sequence↗
PubMed1989

Subcloning, expression, and purification of the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase: demonstration of enzyme-bound (2,3-dihydroxybenzoyl)adenylate product.

The gene coding for the enzyme 2,3-dihydroxybenzoate-AMP ligase (2,3DHB-AMP ligase), responsible for activating 2,3-dihydroxybenzoic acid in the biosynthesis of the siderophore enterobactin, has been subcloned into the multicopy plasmid pKK223-3 and overproduced in a strain of Escherichia coli. The protein is an alpha 2 dimer with subunit molecular mass of 59 kDa. The enzyme catalyzes the exchange of [32P]pyrophosphate with ATP, dependent upon aromatic substrate with a turnover number of 340 min-1. The enzyme also releases pyrophosphate upon incubation with 2,3-dihydroxybenzoic acid and ATP; an initial burst corresponding to 0.7 nmol of pyrophosphate released per nanomole of enzyme is followed by a slower, continuous release with a turnover number of 0.41 min-1. The 1000-fold difference in rates observed between ATP-pyrophosphate exchange and continuous pyrophosphate release, as well as the close to stoichiometric amount of pyrophosphate released, suggests that intermediates are accumulating on the enzyme surface. Such intermediates have been observed and correspond to enzyme-bond (2,3-dihydroxybenzoyl)adenylate product.

Base Sequence↗
PubMed1978

T4 polynucleotide ligase catalyzed joining of short synthetic DNA duplexes at base-paired ends.

The self-complementary octanucleotide dT-A-G-T-A-C-T-A has been synthesized and its sequence confirmed by two-dimensional fingerprinting. Under conditions used for the T4 polynucleotide ligase reaction, this oligonucleotide forms a dimeric duplex which shows a Tm of 18 degrees C. The optimal rate of joining of the 32P-labeled duplex occurs between 12 and 15 degrees C. The rate is highly concentration dependent, as expected for a bimolecular process. Polyacrylamide gel electrophoretic analysis of this reaction shows the presence of products up to 120 nucleotides in length. In a denaturing gel, each product appears as a double band due to the presence of its 5'-adenylylated activated intermediate. Substrates larger than eight base pairs are utilized more rapidly than the eight base pair duplex, indicating that the T4 ligase has a higher affinity for longer substrates. The low level of nicked intermediates suggests that the joining of both strands requires two steps, the rates of which must be similar.

Base Sequence↗
PubMed1978

T4 polynucleotide ligase catalyzed joining on triple-stranded nucleic acids.

dT1O will form triple-stranded complexes with dAn and these complexes can serve as substrate for T4 polynucleotide ligase (EC 6.5.1.1). The rate of phosphodiester formation was found to be approximately the same as for the double-stranded complex and, furthermore, the rate appears to be similar on the two strands in the complex. Joining of dT1O also took place in the presence of the double-stranded complexes dAn.dTn and dAn.rUn. Polyamines increase the rate of joining catalyzed by T4 polynucleotide ligase under certain conditions.

Coliphages↗
PubMed2001

Solution structure and backbone dynamics of the human DNA ligase IIIalpha BRCT domain.

BRCT (BRCA1 carboxyl terminus) domains are found in a number of DNA repair enzymes and cell cycle regulators and are believed to mediate important protein-protein interactions. The DNA ligase IIIalpha BRCT domain partners with the distal BRCT domain of the DNA repair protein XRCC1 (X1BRCTb) in the DNA base excision repair (BER) pathway. To elucidate the mechanisms by which these two domains can interact, we have determined the solution structure of human ligase IIIalpha BRCT (L3[86], residues 837-922). The structure of L3[86] consists of a beta2beta1beta3beta4 parallel sheet with a two-alpha-helix bundle packed against one face of the sheet. This fold is conserved in several proteins having a wide range of activities, including X1BRCTb [Zhang, X. D., et al. (1998) EMBO J. 17, 6404-6411]. L3[86] exists as a dimer in solution, but an insufficient number of NOE restraints precluded the determination of the homodimer structure. However, 13C isotope-filtered and hydrogen-deuterium exchange experiments indicate that the N-terminus, alpha1, the alpha1-beta2 loop, and the three residues following alpha2 are involved in forming the dimer interface, as similarly observed in the structure of X1BRCTb. NOE and dynamic data indicate that several residues (837-844) in the N-terminal region appear to interconvert between helix and random coil conformations. Further studies of other BRCT domains and of their complexes are needed to address how these proteins interact with one another, and to shed light on how mutations can lead to disruption of function and ultimately disease.

Amino Acid Sequence↗
PubMed2002

Metal ion requirements for structure and catalysis of an RNA ligase ribozyme.

The class I ligase, a ribozyme previously isolated from random sequence, catalyzes a reaction similar to RNA polymerization, positioning its 5'-nucleotide via a Watson-Crick base pair, forming a 3',5'-phosphodiester bond between its 5'-nucleotide and the substrate, and releasing pyrophosphate. Like most ribozymes, it requires metal ions for structure and catalysis. Here, we report the ionic requirements of this self-ligating ribozyme. The ligase requires at least five Mg(2+) for activity and has a [Mg(2+)](1/2) of 70-100 mM. It has an unusual specificity for Mg(2+); there is only marginal activity in Mn(2+) and no detectable activity in Ca(2+), Sr(2+), Ba(2+), Zn(2+), Co(2+), Cd(2+), Pb(2+), Co(NH(3))(6)(3+), or spermine. All tested cations other than Mg(2+), including Mn(2+), inhibit the ribozyme. Hill analysis in the presence of inhibitory cations suggested that Ca(2+) and Co(NH(3))(6)(3+) inhibit by binding at least two sites, but they appear to productively fill a subset of the required sites. Inhibition is not the result of a significant structural change, since the ribozyme assumes a nativelike structure when folded in the presence of Ca(2+) or Co(NH(3))(6)(3+), as observed by hydroxyl-radical mapping. As further support for a nativelike fold in Ca(2+), ribozyme that has been prefolded in Ca(2+) can carry out the self-ligation very quickly upon the addition of Mg(2+). Ligation rates of the prefolded ribozyme were directly measured and proceed at 800 min(-1) at pH 9.0.

Base Sequence↗
PubMed2004

Generation of a thermostable and denaturant-resistant peptide ligase.

The construction and characterization of a novel, thermostable, peptide ligase are described. Three amino acid substitutions were introduced into the secreted bacterial protease Streptomyces griseus protease B (SGPB). Mutations were chosen on the basis of two separate observations: (i) that a single substitution of the nucleophilic serine (S195A) created an enzyme with significant peptide-ligation activity, albeit greatly reduced stability [(2000) Chem. Biol. 7, 163], and (ii) that a pair of substitutions in the substrate-binding pocket (T213L and F228H) greatly increased the thermostability of the wild-type enzyme [(1996) J. Mol. Biol. 257, 233]. The triple mutant, named streptoligase, was found to catalyze peptide ligation (aminolysis of both a thiobenzyl ester and a p-nitroanilide-activated peptide) efficiently in nondenaturing and denaturing conditions including SDS (0.5% w/v) and guanidine hydrochloride (4.0 M). Moreover, streptoligase exhibited a half-live for unfolding of 16.3 min at 55 degrees C in the absence of stabilizing substrates. The fraction of the streptoligase-catalyzed reaction that gave coupled product with the acceptor peptide FAASR-NH(2) was greater for the p-nitroanilide donor (Sc-AAPF-pNA) than for the benzyl thioester substrate (Sc-AAPF-SBn). These observations are consistent with ligation proceeding through an acyl-enzyme intermediate involving histidine-57. In the case of the thioester donor the triple mutant promotes the direct attack of water on the thioester carbonyl carbon, in addition to hydrolysis occurring at the stage of the acyl-enzyme intermediate. The strategy of multiple point mutations outlined in this study may provide a general means of converting enzymes with chymotrypsin-like protein folds into peptide ligases.

Enzyme Stability↗