ProteinsSubunitOligonucleotide-bindPhylogenetic TreeTransferaseMitochondrialGenomeSequenceTRNARegulationPolymerase activityEnzymeOrganismBacterialAnnotationReplicationMetabolismDatasetsEukaryoticENSEMBLSuperfamilySequencesPathwayMammalianEnzymesCatalyticNovoEncodesInvolvementRecombinationStrandNucleotideTranscriptionActivityLigaseViralSpecificityStructuralPutativeTaxonomicDamageStrainsLigation
Proteins3
- gag gene codes for structural proteins which forms the 'body' of the viral particle, among other proteins. (proteopedia.org)
- Pol gene on the other hand codes for three essential enzymes which are Reverse Transcriptase (RT), Integrase (IN) and Protease (PR), among other proteins. (proteopedia.org)
- env gene codes for viral envelop proteins. (proteopedia.org)
Subunit4
- Identification and DNA sequence of the large subunit of the capping enzyme from Shope fibroma virus. (ox.ac.uk)
- This protein was found to also interact with DNA polymerase alpha/primase and mediate the phosphorylation of the large p180 subunit, which suggests a regulatory role in DNA replication during the S-phase of the cell cycle. (cancerindex.org)
- Plasmids for generating marked mutants and mutant strains can be searched for by gene Name/Accession (e.g. 'sll1226' or '1513_sll1226-sacB'), gene homology (e.g. 'hydrogenase large subunit'), Gene ID (e.g. hoxH), or by a portion of the gene coding sequence Sequence (CDS). (cyanosource.ac.uk)
- DNA-directed RNA polymerase, subunit 2, hybrid-binding. (ntu.edu.sg)
Oligonucleotide-bind2
- The next coupling of adenylation to DNA ligation is dependent upon downstream DNA-binding domains, such as an oligonucleotide-binding fold (OB fold) and a helix-hairpin-helix (HhH) domain. (conferencedequebec.org)
- NAD + dependent ligases have a central ligase catalytic core which is composed of oligonucleotide binding fold domain and nucleotidyltransferase domain. (microbenotes.com)
Phylogenetic Tree1
- Score represents the degree of relatedness of a KO to the query gene based on the clustering in the phylogenetic tree of protein sequences ( see below for the tree ). (umassmed.edu)
Transferase2
- The DNA-independent adenylyl transfer activity resides inside the amino-terminal adenylation website, which comprises an amino-terminal Ia area that is particular to NAD+-reliant DNA ligases and a nucleotidyl transferase (NTase) area that is common among DNA and RNA ligases. (conferencedequebec.org)
- DNA ligase belongs to the nucleotide transferase superfamily, including RNA ligases and mRNA capping enzymes. (microbenotes.com)
Mitochondrial3
- Predominant cellular mitochondrial dysfunction in the TOP3A gene-caused Bloom syndrome-like disorder. (nih.gov)
- This is the most common of the hereditary sideroblastic anemias, followed by mitochondrial transporter defects such as SLC25A38 gene mutation discussed below. (medscape.com)
- T can be summarized as follows: This mutation firstly loses the appropriate base pair interaction, from Watson-Crick to T-G mismatching, in the anticodon-stem of MT-TW gene and induces defects in mitochondrial tRNATrp-associated translation machinery most likely due to inadequate anticodon recognition of mitochondrial tryptophan by its altered conformation [1]. (rnacentral.org)
Genome4
- Rare mutations in genome sequence that result from failed DNA repair are transmitted across generations through DNA replication during each cell division. (nature.com)
- HIV genome contains three main genes: gag, pol, and env. (proteopedia.org)
- Repetitive content contributes to difficulty in multicellular Eukaryotic genome assembly as well [ 4 ], but the problem becomes more complicated in metagenome assembly [ 5 ] due to the wide range of abundance among bacterial species and strains, and the presence of other environmental DNA (e.g., plants, protists). (biomedcentral.com)
- This database contains entries for 3,572 known and predicted gene coding sequences in Synechocystis sp PCC 6803 based on the Kazusa genome sequence and nomenclature ( http://genome.microbedb.jp/cyanobase/GCA_000009725.1 ). (cyanosource.ac.uk)
Sequence5
- The parts of the gene sequence that carry out the different functions of the GENES. (umassmed.edu)
- The panel covered known genetic causes of channelopathies and cardiomyopathies and included a sequence analysis and copy number variation analysis of various genes [3]. (rnacentral.org)
- Score represents the degree of relatedness of a KO to the query gene based on the Smith-Waterman alignment of protein sequence with most similar sequences from all organisms in the KEGG database. (umassmed.edu)
- However, longer repetitive regions are only capable of being completely resolved by long reads of equal or greater size to the repeat, which makes input DNA quality a priority in sequence library construction. (biomedcentral.com)
- Energy is required for the joining of nicks (nicks lack the phosphodiester linkage between the nucleotide sequence) of DNA. (microbenotes.com)
TRNA4
- tRNA-nucleotidyltransferase 1, is an enzyme that in humans is encoded by the TRNT1 gene. (wikipedia.org)
- A eubacterial origin for the human tRNA nucleotidyltransferase? (wikipedia.org)
- This CCA deactivation is reversible and quickly repairable by the CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase]. (prolekarniky.cz)
- Some bacteria carry tRNA genes encoding CCA termini, thus the CCA-adding enzyme is primarily involved in repairing damaged CCA ends in these organisms [9] . (prolekarniky.cz)
Regulation3
- This gene thus plays a role in both cell-cycle and epigenetic regulation. (cancerindex.org)
- Lu D , Zhai J # , Xi M # (2022) Regulation of DNA Methylation During Plant Endosperm Development. (jixianzhai.org)
- Protein citrullination is associated with several physiological processes, including the epigenetic regulation of gene expression, neutrophil extracellular trap formation and DNA damage-induced apoptosis. (bvsalud.org)
Polymerase activity2
- Molecular function: DNA-directed 5'-3' RNA polymerase activity. (expasy.org)
- Any process that activates or increases the frequency, rate or extent of DNA-directed DNA polymerase activity. (mcw.edu)
Enzyme9
- The enzyme consists of a protein component with reverse transcriptase activity, encoded by this gene, and an RNA component which serves as a template for the telomere repeat. (nih.gov)
- This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. (nih.gov)
- This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one another, thus reducing the number of supercoils and altering the topology of DNA. (nih.gov)
- Structural research from the adenylation website have exposed conformational transitions that accompany the adenylation routine (8), and structural research from the full-length enzyme destined to DNA-adenylate offers identified specific connections between your DNA-binding domains as well as the DNA duplex substrate close to the nicked ligation site (20). (conferencedequebec.org)
- Thg1 is the only enzyme known to catalyze nucleotide addition to a polynucleotide chain in the 3'-5' direction, opposite to the direction of nucleotide addition in all known DNA or RNA polymerases, and the mechanism by which Thg1 catalyzes this reaction is unknown. (osu.edu)
- DNA ligase is an enzyme that catalyzes the ligation reaction, ligation is the process of joining various types of DNA fragments. (microbenotes.com)
- The enzyme DNA ligases were firstly isolated from E. coli in 1967, and several DNA ligases were discovered in 1967and 1968. (microbenotes.com)
- DNA ligases are classified into two categories based on source, the enzyme requires either ATP or NAD + as a cofactor. (microbenotes.com)
- The enzyme found in Haemophilus influenza consists of 268 amino acids, and larger cellular ligases such as human DNA ligase I consist of 912 amino acids, and IV consist of 844 amino acids. (microbenotes.com)
Organism1
- The size of DNA ligases is different from organism to organism. (microbenotes.com)
Bacterial4
- LigA is certainly 113359-04-9 supplier well conserved among eubacterial types, is certainly architecturally and biochemically distinctive in the ATP-dependent DNA ligases of eukaryotic cells, and continues to 113359-04-9 supplier be found to become needed for bacterial viability wherever analyzed (13, 14, 15, 17, 31). (conferencedequebec.org)
- Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. (frontiersin.org)
- This can present a problem in metagenomic samples as material-adherent bacterial populations produce tough extracellular capsules that require vigorous mechanical stress for lysis, resulting in substantial DNA fragmentation and single-strand nicks [ 8 ]. (biomedcentral.com)
- Bacterial DNA ligases are NAD + dependent ligases. (microbenotes.com)
Annotation2
- Association scores for KOs best matching to the query gene according to each annotation predictor, and for the accepted KO if there is any (rightmost columns). (umassmed.edu)
- See above for the final decision on the annotation of this gene. (umassmed.edu)
Replication3
- In Cryptococcus neoformans , where changes in ancestral DNA methylation can potentially persist for millions of years, methyltransferases copy methylation patterns upon DNA replication 6 . (nature.com)
- DNA ligation actions are crucial for multiple DNA procedures in replication and PDK1 fix, including the signing up for of Okazaki fragments right into a constant strand during chromosomal DNA replication. (conferencedequebec.org)
- DNA ligase plays a vital role in DNA replication , DNA repair, and DNA recombination. (microbenotes.com)
Metabolism1
- Using 16S ribosomal RNA gene amplicon sequencing and metagenomics, we resolved the microbial community composition on the North and South Shelves of Iceland, analyzed its evolution from 2011 to 2018, identified frequently occurring taxa, and predicted their potential metabolism. (matis.is)
Datasets3
- Moreover, the expression of STING and antigen-presenting machinery genes is generally downregulated in patient tumours of human lung cancer datasets. (figshare.com)
- Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
- Using single-cell RNA sequencing datasets, we identified a specific enrichment of imprinted gene expression in a recognised "parenting hub", the galanin-expressing neurons of the preoptic area. (bvsalud.org)
Eukaryotic3
- Stress-induced changes of gene expression are crucial for survival of eukaryotic cells. (prolekarniky.cz)
- Whereas eukaryotic DNA ligases are ATP-dependent bacteria, archaea and virus DNA ligases are both NAD+ and ATP dependent. (microbenotes.com)
- Most eukaryotic DNA ligases use ATP as a cofactor, including bacteriophage, archaeal, and eubacteria DNA ligases. (microbenotes.com)
ENSEMBL1
- hydrogen peroxide-inducible genes activator [Ensembl]. (ntu.edu.sg)
Superfamily1
- Chen CC, Simard MJ, Tabara H, Brownell DR, McCollough JA, Mello CC. A member of the polymerase beta nucleotidyltransferase superfamily is required for RNA interference in C. elegans. (umassmed.edu)
Sequences2
- The main module page also shows the location of these motifs within the upstream sequences of the module member genes. (systemsbiology.net)
- cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. (systemsbiology.net)
Pathway4
- Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. (ox.ac.uk)
- Topoisomerase I poison-triggered immune gene activation is markedly reduced in human small-cell lung cancers by impairment of the cGAS/STING pathway. (figshare.com)
- TOP1 poison-induced micronuclei activate the cGAS/STING pathway leading to increased expression of immune genes in HeLa cells, but not in human SCLC cell lines, mainly due to lack of STING and/or cGAS expression. (figshare.com)
- Pathway maps where this gene is represented are listed here. (umassmed.edu)
Mammalian1
- DNA ligase III: It is the only mammalian ligase that is found in mitochondria. (microbenotes.com)
Enzymes2
- Enzymes that are associated with this gene in the WormFlux database, but not included in the current network model . (umassmed.edu)
- SACURE pipeline annotates genes based on a logistic function that converts evidence from multiple resources into a KEGG orthology decision, which is then associated with enzymes and reactions . (umassmed.edu)
Catalytic4
- A) Step one 1, DNA-independent adenylation from the catalytic lysine of LigA (depicted as transfer of pA), using NAD+ (NppA) as the substrate and releasing NMN (pN) item. (conferencedequebec.org)
- Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. (rcsb.org)
- Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. (rcsb.org)
- Many DNA ligases also contain a non-catalytic domain that is conserved, but the function of this domain is unknown. (microbenotes.com)
Novo3
- TOP3A, a new partner gene fused to MLL in an adult patient with de novo acute myeloid leukaemia. (nih.gov)
- Given the considerable time needed to activate new genes and/or de novo synthesize mRNA, the translation of existing mRNAs provides the necessary plasticity for the cell to selectively and rapidly respond to stress [1] , [2] . (prolekarniky.cz)
- cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. (systemsbiology.net)
Encodes1
- This gene encodes an arginine-specific ADP-ribosyltransferase. (nih.gov)
Involvement2
- Abnormalities precipitated by a targeted truncation in the murine gene Brca2 define its involvement in DNA repair. (nih.gov)
- T heteroplasmy in MT-TW gene, was found in a patient exhibiting MELAS with multiple organ involvement [1]. (rnacentral.org)
Recombination2
- 59:4024-4030, 1993) indicates the presence of hybrid transposons and provides evidence for extensive recombination, both between transposon genes and between transposon and mer genes, within these natural populations of bacteria. (lincoln.ac.uk)
- DNA ligase IV: homologous recombination repair and important in immune cell development and other activities critical to a normal cell. (microbenotes.com)
Strand2
- B) Step two 2, covalent transfer of AMP (pA) from LigA towards the 5 phosphate of focus on DNA strand b. (conferencedequebec.org)
- C) Step three 3, ligation of DNA strands a and b with launch of AMP from DNA strand b. (conferencedequebec.org)
Nucleotide1
- It ligates DNA during the process of nucleotide excision repair and recombinant fragment. (microbenotes.com)
Transcription2
- DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (expasy.org)
- Biological process: DNA-templated transcription. (expasy.org)
Activity2
- We report the usage of a known pyridochromanone inhibitor with antibacterial activity to measure the validity of NAD+-reliant DNA ligase (LigA) as an antibacterial focus on in (MSSA and MRSA) strains (MIC = 1. (conferencedequebec.org)
- The protein encoded by this gene is a cyclin-dependent kinase 2 (CDK2) -associated protein which is thought to negatively regulate CDK2 activity by sequestering monomeric CDK2, and targeting CDK2 for proteolysis. (cancerindex.org)
Ligase9
- Launch NAD+-reliant DNA ligase (LigA) continues to be identified by many authors as a stunning potential focus on for broad-spectrum antibacterial chemotherapy (7, 23). (conferencedequebec.org)
- Open up in another windowpane Fig 1 Response plan depicting the three successive adenylyl transfer methods that underlie the DNA ligation response catalyzed by eubacterial NAD+-reliant DNA ligase (LigA). (conferencedequebec.org)
- They inhibit LigA from different bacterias but are inactive against the ATP-dependent individual DNA ligase I (1, 9). (conferencedequebec.org)
- DNA ligase joins the DNA molecule covalently by catalyzing the formation of phosphodiester bonds between adjacent nucleotides. (microbenotes.com)
- The final phosphodiester linkage between the 5'-phosphate group on the DNA chain synthesized by DNA polymerase III and the 3'-hydroxyl group on the chain made by DNA polymerase I is catalyzed by DNA ligase. (microbenotes.com)
- DNA ligase forms a bond between the sugar-phosphate backbone to fully repair the DNA. (microbenotes.com)
- Now day purified DNA ligase is isolated in the laboratory, which is used in gene cloning to join DNA molecules together to form recombinant DNA. (microbenotes.com)
- It is the most widely used DNA ligase derived from the T7 bacteriophage. (microbenotes.com)
- DNA ligase II: purification or excision repair of alternatively spliced form of DNA ligase III found in non-dividing cells. (microbenotes.com)
Viral1
- Viral ATP-dependent DNA ligases are generally small in size. (microbenotes.com)
Specificity1
- Model reactions that follow from the KEGG reactions associated with this gene, but that exclude this gene due to differences in reaction specificity or localization compared to the predictions for this gene. (umassmed.edu)
Structural1
- Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. (biomedcentral.com)
Putative1
- A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. (biomedcentral.com)
Taxonomic1
- A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. (biomedcentral.com)
Damage1
- Increased sensitivity to genotoxic agents, particularly ultraviolet light and methylmethanesulfonate, shows that Brca2 function is essential for the ability to survive DNA damage. (nih.gov)
Strains1
- Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. (frontiersin.org)
Ligation1
- Pyridochromanones had been discovered by high-throughput verification as powerful competitive inhibitors of DNA ligation by LigA from (50% inhibitory focus [IC50] 0.9 M) (1). (conferencedequebec.org)