Abstract:
:Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lu CT,Huang KY,Su MG,Lee TY,Bretaña NA,Chang WC,Chen YJ,Chen YJ,Huang HDdoi
10.1093/nar/gks1229subject
Has Abstractpub_date
2013-01-01 00:00:00pages
D295-305issue
Database issueeissn
0305-1048issn
1362-4962pii
gks1229journal_volume
41pub_type
杂志文章abstract::The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure, but may be involved in the initiation of SV40 DNA replication in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1989-11-25 00:00:00
abstract::Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks741
更新日期:2012-10-01 00:00:00
abstract::Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni118
更新日期:2005-07-26 00:00:00
abstract::Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki636
更新日期:2005-06-07 00:00:00
abstract::Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl423
更新日期:2006-07-13 00:00:00
abstract::NF-IL6beta regulates gene expression and plays function roles in many tissues. The EGF-regulated cyclooxygenase-2 (cox-2) expression is mediated through p38(MAPK) signaling pathway and positively correlates with NF-IL6beta expression in A431 cells. NF-IL6beta coordinated with c-Jun on cox-2 transcriptional activation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj422
更新日期:2006-01-05 00:00:00
abstract::Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku580
更新日期:2014-07-01 00:00:00
abstract::Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. Here, we show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx058
更新日期:2017-05-05 00:00:00
abstract::During erythropoiesis in the chick, the nucleosome repeat length increases from 190 base pairs to 212 base pairs. This increase is correlated with a dramatic increase in the concentration of the red cell specific histone H5 (from 0.2 molecules per nucleosome to 1 molecule per nucleosome) and with no change in the conc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.4.1179
更新日期:1978-04-01 00:00:00
abstract::Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2457
更新日期:1998-05-15 00:00:00
abstract::The delivery of site-specific post-translational modifications to histones generates an epigenetic regulatory network that directs fundamental DNA-mediated processes and governs key stages in development. Methylation of histone H4 lysine-20 has been implicated in DNA repair, transcriptional silencing, genomic stabilit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt776
更新日期:2014-01-01 00:00:00
abstract::GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg057
更新日期:2003-01-01 00:00:00
abstract::We have previously described programs for a variety of types of sequence analysis (1-4). These programs have now been integrated into a single package. They are written in the standard C programming language and run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running unde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.443
更新日期:1986-01-10 00:00:00
abstract::Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE-DNA interactions. Here we synthesi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku535
更新日期:2014-08-01 00:00:00
abstract::Saccharomyces cerevisiae chl1 mutants have a significant increase in the rate of chromosome missegregation. CHL1 encodes a 99 kDa predicted protein with an ATP binding site consensus, a putative helix-turn-helix DNA binding motif, and homology to helicases. Using site-directed mutagenesis, I show that mutations that a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.16.3056
更新日期:2000-08-15 00:00:00
abstract::The somatic V(D)J recombination for the assembly of the Ig and TCR genes is mediated by the recombination signal sequences (Rss) and the V(D)J recombinase. A cDNA clone was isolated from a lambda gt11 expression library made from mouse thymocyte poly(A)+ RNA, using the Rss as a ligand. The deduced amino acid sequence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.22.5067
更新日期:1993-11-11 00:00:00
abstract::The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1044
更新日期:2012-01-01 00:00:00
abstract::The bZip proteins GCN4 and C/EBP differ in their DNA binding specificities: GCN4 binds well to the pseudopalindromic AP1 site 5'-A4T3G2A1C0T1C2'A3'T4'-3' and to the palindromic ATF/CREB sequence 5'-A4T3G2A1-C0*G0'T1'C2'A3'T4'-3'; C/EBP preferentially recognizes the palindromic sequence 5'-A4T3T2G1C0*G0'C1'A2'-A3'T4'-3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.20.4162
更新日期:1995-10-25 00:00:00
abstract::The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.10.1758
更新日期:1995-05-25 00:00:00
abstract::With the abundant mammalian lncRNAs identified recently, a comprehensive annotation resource for these novel lncRNAs is an urgent need. Since its first release in November 2016, AnnoLnc has been the only online server for comprehensively annotating novel human lncRNAs on-the-fly. Here, with significant updates to mult...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa368
更新日期:2020-07-02 00:00:00
abstract::Although Dicer is essential for general microRNA (miRNA) biogenesis, vertebrate mir-451 is Dicer independent. Instead, its short pre-miRNA hairpin is 'sliced' by Ago2, then 3'-resected into mature miRNAs. Here, we show that Drosophila cells and animals generate functional small RNAs from mir-451-type precursors. Howev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1038
更新日期:2014-02-01 00:00:00
abstract::A feature of Haemophilus influenzae genomes is the presence of several loci containing tracts of six or more identical tetranucleotide repeat units. These repeat tracts are unstable and mediate high frequency, reversible alterations in the expression of surface antigens. This process, termed phase variation (PV), enab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki180
更新日期:2005-01-14 00:00:00
abstract::The human embryonal carcinoma cell line NEC14 can be induced to differentiate by the addition of 10(-2)M N,N'-hexamethylene-bis-acetamide (HMBA). A subtractive cDNA library specific to undifferentiated NEC14 cells was constructed using oligo(dT)30-Latex and polymerase chain reaction (PCR). The method was designed to i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.25.7097
更新日期:1991-12-01 00:00:00
abstract::Histone H2B O-GlcNAcylation is an important post-translational modification of chromatin during gene transcription. However, how this epigenetic modification is regulated remains unclear. Here we found that the energy-sensing adenosine-monophosphate-activated protein kinase (AMPK) could suppress histone H2B O-GlcNAcyl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku236
更新日期:2014-05-01 00:00:00
abstract::Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.921
更新日期:1987-02-11 00:00:00
abstract::The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx244
更新日期:2017-05-19 00:00:00
abstract::A computer program has been developed which aids in the determination of restriction enzyme recognition sequences. This is achieved by cleaving DNAs of known sequence with a restriction endonuclease and comparing the fragmentation pattern with a computer-generated set of patterns. The feasibility of this approach has ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.11.4105
更新日期:1978-11-01 00:00:00
abstract::DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz653
更新日期:2019-09-19 00:00:00
abstract::Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.21.4969
更新日期:1980-11-11 00:00:00
abstract::Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky098
更新日期:2018-04-20 00:00:00