Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “LIGASES”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources
PubMed2000

The F-box protein Skp2 is a ubiquitylation target of a Cul1-based core ubiquitin ligase complex: evidence for a role of Cul1 in the suppression of Skp2 expression in quiescent fibroblasts.

The ubiquitin protein ligase SCF(Skp2) is composed of Skp1, Cul1, Roc1/Rbx1 and the F-box protein Skp2, the substrate-recognition subunit. Levels of Skp2 decrease as cells exit the cell cycle and increase as cells re-enter the cycle. Ectopic expression of Skp2 in quiescent fibroblasts causes mitogen-independent S-phase entry. Hence, mechanisms must exist for limiting Skp2 protein expression during the G(0)/G(1) phases. Here we show that Skp2 is degraded by the proteasome in G(0)/G(1) and is stabilized when cells re-enter the cell cycle. Rapid degradation of Skp2 in quiescent cells depends on Skp2 sequences that contribute to Cul1 binding and interference with endogenous Cul1 function in serum-deprived cells induces Skp2 expression. Furthermore, recombinant Cul1-Roc1/Rbx1-Skp1 complexes can catalyse Skp2 ubiquitylation in vitro. These results suggest that degradation of Skp2 in G(0)/G(1) is mediated, at least in part, by an autocatalytic mechanism involving a Skp2-bound Cul1-based core ubiquitin ligase and imply a role for this mechanism in the suppression of SCF(Skp2) ubiquitin protein ligase function during the G(0)/G(1) phases of the cell cycle.

Amino Acid Motifs↗
PubMed1995

NPl1, an essential yeast gene involved in induced degradation of Gap1 and Fur4 permeases, encodes the Rsp5 ubiquitin-protein ligase.

When yeast cells growing on a poor nitrogen source are supplied with NH4+ ions, several nitrogen permeases including the general amino acid permease (Gap1p) are rapidly and completely inactivated. This report shows that inactivation by NH4+ of the Gap1 permease is accompanied by its degradation. A functional NPl1 gene product is required for both inactivation and degradation of Gap1p. Molecular analysis of the NPl1 gene showed that it is identical to RSP5. The RSP5 product is a ubiquitin-protein ligase (E3 enzyme) whose physiological function was, however, unknown. Its C-terminal region is very similar to that of other members of the E6-AP-like family of ubiquitin-protein ligases. Its N-terminal region contains a single C2 domain that may be a Ca(2+)-dependent phospholipid interaction motif, followed by several copies of a recently identified domain called WW(P). The Npi1/Rsp5 protein has a homologue both in humans and in mice, the latter being involved in brain development. Stress-induced degradation of the uracil permease (Fur4p), a process in which ubiquitin is probably involved, was also found to require a functional NPl1/RSP5 product. Chromosomal deletion of NPl1/RSP5 showed that this gene is essential for cell viability. In the viable npi1/rsp5 strain, expression of NPl1/RSP5 is reduced as a result of insertion of a Ty1 element in its 5' region. Our results show that the Npi1/Rsp5 ubiquitin-protein ligase participates in induced degradation of at least two permeases, Gap1p and Fur4p, and probably also other proteins.

Amino Acid Sequence↗
PubMed2003

Overproduction of polypeptides corresponding to the amino terminus of the F-box proteins Cdc4p and Met30p inhibits ubiquitin ligase activities of their SCF complexes.

Ubiquitin ligases direct the transfer of ubiquitin onto substrate proteins and thus target the substrate for proteasome-dependent degradation. SCF complexes are a family of ubiquitin ligases composed of a common core of components and a variable component called an F-box protein that defines substrate specificity. Distinct SCF complexes, defined by a particular F-box protein, target different substrate proteins for degradation. Although a few have been identified to be involved in important biological pathways, such as the cell division cycle and coordinating cellular responses to changes in environmental conditions, the role of the overwhelming majority of F-box proteins is not clear. Creating inhibitors that will block the in vivo activities of specific SCF ubiquitin ligases may provide identification of substrates of these uncharacterized F-box proteins. Using Saccharomyces cerevisiae as a model system, we demonstrate that overproduction of polypeptides corresponding to the amino terminus of the F-box proteins Cdc4p and Met30p results in specific inhibition of their SCF complexes. Analyses of mutant amino-terminal alleles demonstrate that the interaction of these polypeptides with their full-length counterparts is an important step in the inhibitory process. These results suggest a common means to inhibit specific SCF complexes in vivo.

Base Sequence↗
PubMed1979

The phylogenetic distribution of tubulin:tyrosine ligase.

The post-translational addition of tyrosine to alpha-tubulin, catalyzed by tubulin:tyrosine ligase, has been previously reported in mammals and birds. The present study demonstrated that significant ligase activity was present in representative organisms from several other major vertebrate classes (chondrichthyes through reptiles) and that both substrate and enzyme from all vertebrates investigated were compatible with mammalian ligase and tubulin in the tyrosination reaction. None of the invertebrate tissues examined showed incorporation of tyrosine, phenylalanine or dihydroxyphenylalanine into alpha tubulin under conditions allowing significant incorporation of these compounds in vertebrate supernatant samples. The failure of invertebrate tubulin to incorporate tyrosine in vitro did not appear to be due to saturation of the carboxyl terminal position with tyrosine or the presence of a soluble inhibitor of ligase activity. Although tubulin amino acid composition has been highly conserved throughout evolution, a major evolutionary divergence is described based upon biochemical differences whereby invertebrate tubulin cannot be tyrosinated or post-translationally modified with phenylalanine or dihydroxyphenylalanine under conditions suitable for the incorporation of these compounds by vertebrate alpha tubulin.

Animals↗
PubMed1996

Evolution of structure and substrate specificity in D-alanine:D-alanine ligases and related enzymes.

The D-alanine:D-alanine-ligase-related enzymes can have three preferential substrate specificities. Usually, these enzymes synthesize D-alanyl-D-alanine. In vancomycin-resistant Gram-positive bacteria, structurally related enzymes synthesize D-alanyl-D-lactate or d-alanyl-d-serine. The sequence of internal fragments of eight structural d-alanine:d-alanine ligase genes from enterococci has been determined. Alignment of the deduced amino acid sequences with those of other related enzymes from Gram-negative and Gram-positive bacteria revealed the presence of four distinct sequence patterns in the putative substrate-binding sites, each correlating with specificity to a particular substrate (D-alanine:D-lactate ligases exhibited two patterns). Phylogenetic analysis showed different clusters. The enterococcal subtree was largely superimposable on that derived from 16S rRNA sequences. In lactic acid bacteria, structural divergence due to differences in substrate specificity was observed. Glycopeptide resistance proteins VanA and VanB, the VanC-type ligases, and DdlA and DdlB from enteric bacteria and Haemophilus influenzae constituted separate clusters.

Amino Acid Sequence↗
PubMed2006

Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp.

Genomic analysis of a hyperthermophilic archaeon, Thermococcus sp. NA1, revealed an ORF of 1689 bases encoding 562 amino acids that showed a high similarity to DNA ligases from other hyperthermophilic archaea. The ligase, which was designated TNA1_lig (Thermococcus sp. NA1 ligase), was cloned and expressed in Escherichia coli. The recombinant TNA1_lig was purified by metal affinity chromatography. The optimum ligase activity of the recombinant TNA1_lig occurred at 80 degrees C and pH 7.5. The enzyme was activated by MgCl2 and ZnCl2 but was inhibited by MnCl2 and NiCl2. Additionally, the enzyme was activated by either ATP or NAD+.

Adenosine Triphosphate↗
PubMed1997

D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.

The crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.

Binding Sites↗
PubMed1989

(3-Amino-2-oxoalkyl)phosphonic acids and their analogues as novel inhibitors of D-alanine:D-alanine ligase.

The dipeptide D-alanyl-D-alanine is an essential precursor of bacterial peptidoglycan; thus, blocking its formation is a possible target for the design of novel antibacterial agents. The synthesis of this dipeptide by bacterial D-alanine:D-alanine ligase requires ATP. In analogy with glutamine synthetase, we hypothesized a mechanism for this enzyme involving the intermediacy of D-alanyl phosphate. Several (3-amino-2-oxoalkyl)phosphonic acids and their analogues have been synthesized as possible inhibitory mimics of this proposed intermediate. The most active of them, (3(R)-amino-2-oxobutyl)phosphonic acid (8a) and the corresponding aza analogue (22), were effective ligase inhibitors although they had no significant antibacterial activity. The ligase inhibition of these compounds is consistent with an acyl phosphate displacement step in the mechanism of DAla-DAla ligase.

Anti-Bacterial Agents↗
PubMed1997

Bacterial resistance to vancomycin: overproduction, purification, and characterization of VanC2 from Enterococcus casseliflavus as a D-Ala-D-Ser ligase.

The VanC phenotype for clinical resistance of enterococci to vancomycin is exhibited by Enterococcus gallinarum and Enterococcus casseliflavus. Based on the detection of the cell precursor UDP-N-acetylmuramic acid pentapeptide intermediate terminating in D-Ala-D-Ser instead of D-Ala-D-Ala, it has been predicted that the VanC ligase would be a D-Ala-D-Ser rather than a D-Ala-D-Ala ligase. Overproduction of the E. casseliflavus ATCC 25788 vanC2 gene in Escherichia coli and its purification to homogeneity allowed demonstration of ATP-dependent D-Ala-D-Ser ligase activity. The kcat/Km2 (Km2 = Km for D-Ser or C-terminal D-Ala) ratio for D-Ala-D-Ser/D-Ala-D-Ala dipeptide formation is 270/0.69 for a 400-fold selection against D-Ala in the C-terminal position. VanC2 also has substantial D-Ala-D-Asn ligase activity (kcat/Km2 = 74 mM-1min-1).

Bacterial Proteins↗
PubMed1973

Effect of alanine, leucine and fructose on lysyl-transfer ribonucleic acid ligase activity in a mutant of Escherichia coli K-12.

A mutant of Escherichia coli K-12 was examined which has growth medium-dependent lysyl-transfer ribonucleic acid (tRNA) ligase activity. In minimal medium or 0.5% yeast extract, the activity of the enzyme in the mutant strain was 5 to 10% of wild type. However, when the mutant was grown in a highly enriched medium, such as AC broth (Difco), the activity of the mutant ligase increased 10- to 20-fold. We found that the supplementation of 0.5% yeast extract by l-alanine plus d-fructose replaces the need for the highly enriched medium. Fructose plus l-leucine and fructose plus l-alpha-amino-n-butyric acid were also stimulatory, but not as effective as fructose and alanine. With minimal medium, a combination of carbohydrate (fructose or glucose) plus alanine and leucine was required to replace the enriched medium. The most effective combination was fructose, glucose, alanine, and leucine. Lysyl-tRNA ligase was stimulated 1.5 to 2-fold in the wild-type strain or Hfr H (Hayes) by fructose plus alanine when these strains were cultured in 0.5% yeast extract. Experiments employing the combined technique of density labeling with D(2)O and isopycnic centrifugation in cesium chloride indicated that the increased activity of lysyl-tRNA ligase observed in AC broth or in the presence of fructose, glucose, alanine, and leucine is due to the synthesis of new enzyme.

Alanine↗
PubMed1973

Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase.

The temperature-sensitive Escherichia coli mutant strain ST-640 lyses at the restrictive temperature except when an osmotic stabilizer or a high concentration of d-alanine is present. The presence of dl-alanyl-dl-alanine does not prevent lysis. The rate of murein synthesis, followed in a wall medium, is decreased at both 30 and 42 C. d-Alanyl-d-alanine and uridine diphosphate-N-acetyl-muramyl (UDP-MurNAc)-pentapeptide are synthesized in decreased amounts, accompanied by accumulation of UDP-MurNAc-tripeptide at 42 C but not at 30 C. Uridine nucleotide precursors leak into the medium, especially out of the mutant cells. This leakage is prevented when NaCl is present. The d-alanine: d-alanine ligase (ADP) (EC 6.3.2.4) of the mutant strain, assayed in crude extracts, is temperature sensitive. The impaired ligase is relatively resistant to d-cycloserine and other inhibitors of the enzyme. Combined genetic and enzymatic results show that the low ligase activity is due to a mutation in the ddl gene, the structural gene for d-alanine: d-alanine ligase.

Alanine↗
PubMed2002

Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair.

Mammalian DNA polymerase mu (pol mu) is related to terminal deoxynucleotidyl transferase, but its biological role is not yet clear. We show here that after exposure of cells to ionizing radiation (IR), levels of pol mu protein increase. pol mu also forms discrete nuclear foci after IR, and these foci are largely coincident with IR-induced foci of gammaH2AX, a previously characterized marker of sites of DNA double-strand breaks. pol mu is thus part of the cellular response to DNA double-strand breaks. pol mu also associates in cell extracts with the nonhomologous end-joining repair factor Ku and requires both Ku and another end-joining factor, XRCC4-ligase IV, to form a stable complex on DNA in vitro. pol mu in turn facilitates both stable recruitment of XRCC4-ligase IV to Ku-bound DNA and ligase IV-dependent end joining. In contrast, the related mammalian DNA polymerase beta does not form a complex with Ku and XRCC4-ligase IV and is less effective than pol mu in facilitating joining mediated by these factors. Our data thus support an important role for pol mu in the end-joining pathway for repair of double-strand breaks.

Antigens, Nuclear↗
PubMed1994

2-Amino-3-ketobutyrate-CoA ligase from beef liver mitochondria. Purification and partial sequence.

2-Amino-3-ketobutyrate-CoA ligase (EC 2.3.1.29), or aminoacetone synthetase, has been purified by a nine-step procedure from 1.0 kg of beef liver to yield 8.8 mg of homogeneous enzyme. The homogeneous form of the enzyme, a monomer of M(r) = 44,000, shows unusually high absorption at 430 nm, with a ratio of absorbance at 280 and 430 nm of 2.6. On storage a species with an additional absorption peak at 332 is formed. Neither the 430-nm peak nor the 332-430 ratio is affected by pH or substrates. The peak at 430 nm and enzyme activity are both reduced by borohydride reduction and treatment with cysteine. The first 21 amino acids at the NH2-terminal of the ligase occur in the sequence Ser-Ala-Leu-Ala-Gln-Leu-Arg-Gly-Ile-Leu-Glu-Glu-Glu-Leu-Glu-Ser-Ile-Arg- Gly-Ala - Gly. No homology is detectable in the first 20 amino acids of the Escherichia coli and beef liver mitochondria enzymes. However, homology is found around the lysine residue to which the pyridoxal 5'-phosphate is attached in the two enzymes. A very hydrophobic peptide containing pyridoxal phosphate having the following sequence Leu-Leu-Gly-Val-Met-Asp-Gln-Val-Thr-Ile-Ile-Asn-Ser-Thr-Leu-Gly-Lys(P xy)-Ala- Leu-Gly-Gly-Ala-Ser-Gly-Gly-Tyr-Thr-Thr-Gly-Pro-Gly-Ala-Leu-Val has been isolated from the ligase. Fourteen residues around the lysine to which the pyridoxal 5'-phosphate is bound are completely identical with the pyridoxal 5'-phosphate containing peptide isolated from the E. coli 2-amino-3-ketobutyrate-CoA ligase.

Acetyltransferases↗
PubMed1981

Differentiation of thymocytes during chicken ontogeny: occurrence of a specific DNA ligase in relationship to cell size and surface antigens.

The activities of two forms (8.2 and 6.2 S) of DNA ligase have been studied in chicken thymocytes at different stages of development (16 and 18 days of incubation, hatching and one month after birth). Thymocytes have been sorted out on the basis of size and T antigenicity (immunofluorescence) with the activated cell sorter. Three kinds of cells can be distinguished: (a) large, antigenically negative cells of 16 days of incubation, expressing only the "heavy" (8.2 S) form of enzyme. The activity of this form decreases during development and is very low after birth; (b) large, antigenically positive cells without DNA ligase activity and (c) small, antigenically positive cells, expressing the "light" (6.2 S) enzyme. This form of enzyme appears only from 18 days of incubation onwards. These results allow us to consider the 6.2 S DNA ligase activity as an additional marker (with cell reduction and T antigenicity) for thymocyte maturation.

Aging↗
PubMed1987

Relationship between thymus ontogeny and DNA ligase expression in the chicken.

DNA ligase expression was studied in the embryonic chicken thymus. As previously reported, during thymus ontogeny two separate and successive (8S and 6S) forms of enzyme are found. The switch from the heavy to the light form takes place at around 18 days of incubation in situ. The demonstration that two successive generations of thymic lymphoid precursor cells develop in the embryonic bird thymus and that the replacement of the first by the second thymocyte generation takes place at around 18 days suggested the possibility that each form of enzyme could be restricted to a given thymocyte generation. By either culturing or transplanting embryonic thymuses of different ages it appears that the switch from the heavy to the light form of DNA ligase is not related to a change over of the first by the second generation of embryonic thymocytes but rather to some maturation process of the thymic lymphocytes starting from 17 days of embryonic life. The influence of extrathymic factors on the turning on of the expression of the 6 S DNA ligase in the post-natal environment is also suggested.

Animals↗
PubMed2006

Ubiquitin ligase gene expression in healthy volunteers with 20-day bedrest.

In animal models, several ubiquitin ligases play an important role in skeletal muscle atrophy caused by unloading. In this study we examined protein ubiquitination and ubiquitin ligase gene expression in quadriceps femoris muscle from healthy volunteers after 20-day bedrest to clarify ubiquitin-dependent proteolysis in human muscles after unloading. During bedrest, thickness and cross-sectional area of the quadriceps femoris muscle decreased significantly by 4.6% and 3.7%, respectively. Ubiquitinated proteins accumulated in these atrophied human muscles. A real-time reverse transcription-polymerase chain reaction system showed that bedrest significantly upregulated expression of two ubiquitin ligase genes, Cbl-b and atrogin-1. We also performed DNA microarray analysis to examine comprehensive gene expression in the atrophied muscle. Bedrest mainly suppressed the expression of muscle genes associated with control of gene expression in skeletal muscle. Our results suggest that, in humans, Cbl-b- or atrogin-1-mediated ubiquitination plays an important role in unloading-induced muscle atrophy, and that unloading stress may preferentially inhibit transcriptional responses in skeletal muscle.

Adaptor Proteins, Signal Transducing↗
PubMed2002

The E3 ubiquitin ligase GREUL1 anteriorizes ectoderm during Xenopus development.

We have identified a family of RING finger proteins that are orthologous to Drosophila Goliath (G1, Gol). One of the members, GREUL1 (Goliath Related E3 Ubiquitin Ligase 1), can convert Xenopus ectoderm into XAG-1- and Otx2-expressing cells in the absence of both neural tissue and muscle. This activity, combined with the finding that XGREUL1 is expressed within the cement gland, suggests a role for GREUL1 in the generation of anterior ectoderm. Although GREUL1 is not a direct inducer of neural tissue, it can activate the formation of ectopic neural cells within the epidermis of intact embryos. This suggests that GREUL1 can sensitize ectoderm to neuralizing signals. In this paper, we provide evidence that GREUL1 is an E3 ubiquitin ligase. Using a biochemical assay, we show that GREUL1 catalyzes the addition of polyubiquitin chains. These events are mediated by the RING domain since a mutation in two of the cysteines abolishes ligase activity. Mutation of these cysteines also compromises GREUL1's ability to induce cement gland. Thus, GREUL1's RING domain is necessary for both the ubiquitination of substrates and for the conversion of ectoderm to an anterior fate.

Amino Acid Sequence↗
PubMed2001

Expression, purification, and biophysical characterization of the BRCT domain of human DNA ligase IIIalpha.

The C-terminal regions of several DNA repair and cell cycle checkpoint proteins are homologous to the breast-cancer-associated BRCA-1 protein C-terminal region. These regions, known as BRCT domains, have been found to mediate important protein-protein interactions. We produced the BRCT domain of DNA ligase IIIalpha (L3[86]) for biophysical and structural characterization. A glutathione S-transferase (GST) fusion with the L3[86] domain (residues 837-922 of ligase IIIalpha) was expressed in Escherichia coli and purified by glutathione affinity chromatography. The GST fusion protein was removed by thrombin digestion and further purification steps. Using this method, (15)N-labeled and (13)C/(15)N-double-labeled L3[86] proteins were prepared to enable a full determination of structure and dynamics using heteronuclear NMR spectroscopy. To obtain evidence of binding activity to the distal BRCT of the repair protein XRCC1 (X1BRCTb), as well as to provide insight into the interaction between these two BRCT binding partners, the corresponding BRCT heterocomplexes were also prepared and studied. Changes in the secondary structures (amount of helix and sheet components) of the two constituents were not observed upon complex formation. However, the melting temperature of the complex was significantly higher relative to the values obtained for the L3[86] or X1BRCTb proteins alone. This increased thermostability imparted by the interaction between the two BRCT domains may explain why cells require XRCC1 to maintain ligase IIIalpha activity.

Amino Acid Sequence↗