دانلود رایگان مقاله لاتین پردازش فرم ssdnaاز سایت الزویر
عنوان فارسی مقاله:
پردازش فرم ssDNA توسط گروه مرموز RNase H اگزونوکلئاز PF 2046
عنوان انگلیسی مقاله:
Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046
سال انتشار : 2016
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مقدمه انگلیسی مقاله:
1. Introduction
Pyrococcus furiosus is a hyperthermophilic archaeon and can grow optimally at 98 C and tolerate temperature of 103 C [1]. Owing to resistance to heat and radiation, P. furiosus is an attractive experimental model for DNA repair research. One study showed that P. furiosus can tolerate ionizing radiation because of an unknown DNA repair system [2]. In an effort to elucidate the mechanism of this robust DNA repair system, ssDNA-specific nucleases have been screened for these unusual properties, and thus PF2046 was identified as an ssDNA-specific exonuclease [3]. The structure of PF2046 has been determined previously and found to contain an RNase H fold [4], which was not inferred from its amino acid sequence. Because of this homology to the RNase H family of proteins, PF2046 was predicted to function as a ribonuclease. Structural analysis, however, did not lead to functional annotation and the function of PF2046 was identified later in the aforementioned study involving the search for DNA repair enzymes in P. furiosus [3]. In that study, the authors were looking for ssDNA-specific nucleases in a P. furiosus genomic library expressed in Escherichia coli and found PF2046 to have a 30 -50 ssDNA-specific exonuclease activity. PF2046 has unique substrate specificity: it prefers a series of dT over a series of dC or dA. Furthermore, PF2046 shows an unusual catalytic mechanism, namely, it removes dinucleotide units from the 30 end. Recently, structures of PhoExo I (PDB ID: 4YOX), a PF2046 homolog from Pyrococcus abyssi have been reported to explain the structural basis of two-nucleotide removal [5]. The RNase H fold is defined as three layersda/b/a structure with a five-strand b-sheetdthe second strand being antiparallel to the rest, according to the SCOP database [6]. RNase H is classified into three classes depending on the amino acid sequence homology [7]. RNases HI and HIII are Mg2þ dependent and cleave only the RNA strand of a RNA/DNA hybrid duplex. RNase HII is catalytically less efficient and nicks the 50 side of a ribonucleotide present in DNA. Compared to RNase HI, RNase HII contains additional helices at the C terminus, which is involved in binding to a substrate [8]. RNase H containing proteins have other domains relevant for functions [9] and reaction mechanism follows two-metal ion catalysis [10]. In addition to simple ribonucleases, an RNase H fold is also found in the functional domain of larger proteins driving various cellular processes such as DNA replication, DNA repair, and posttranscriptional modifications involved in RNA interference [RNAi] [11]. Phylogenetic analyses suggest that during evolution, RNase H proteins diverged to be readily detected by amino acid sequence homology; unexpected proteins with an RNase H fold are still being reported to take part in novel cellular processes. The best example is the RNase H fold proteins participating in RNAi, such as the argonaute protein of P. furiosus [12]. Its cryptic RNase H fold, also known as the Piwi domain, can bind double-stranded RNA and cleave complementary viral mRNA, thus implementing RNAi. To understand the structural basis for the preference of PF2046 of a stretche of dTs over dAs, our aim was to determine the crystal structure of PF2046 complexed with poly-dT. The structure revealed that all three protomers of PF2046 bind ssDNA dT4. Oligos bind mainly via interaction with sugar backbone atoms, and the N3 atom is hydrogen-bonded to the main-chain carbonyl group of Thr53, thus explaining the preference for thymidines over cytosine residues. The binding pocket for the 30 nucleotide is flanked by Pro19 and Phe220, which are applying van der Waals strain to bases and give rise to the A-form DNA, which may pose further restriction on substrate binding.
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کلمات کلیدی:
Processing of A-form ssDNA by cryptic RNase H fold exonuclease ... iranarze.ir/wp-content/uploads/2016/10/E351.pdf Aug 3, 2016 - second nucleotide from the 30 end of ssDNA and prefers poly-dT over ... A-form ssDNA binding by PF2046 should disfavor the processing of ... Publication: Processing of A-form ssDNA by cryptic RNase H fold ... https://www.researchgate.net/.../305823973_Processing_of_A-form_ssDNA_by_cryptic... RNase H fold protein PF2046 of Pyrococcus furiosus is a 3′-5′ ssDNA exonuclease that cleaves after the second nucleotide from the 3′ end of ssDNA and ... Processing of A-form ssDNA by cryptic RNase H fold ... - DeepDyve https://www.deepdyve.com/.../processing-of-a-form-ssdna-by-cryptic-rnase-h-fold-ex... Read "Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046, World Development" on DeepDyve, the largest online rental service for ... SciLit | Article - Processing of A-form ssDNA by cryptic RNase H fold ... www.scilit.net/article/10.1016/j.abb.2016.08.001 Aug 1, 2016 - Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. Junsoo Kim, Gerelt-Od Sambalkhundev, Jonghyeon Son, Ah-reum ... An overview of the transformation process. : Bacterial transformation ... www.nature.com/nrmicro/journal/v12/n3/fig_tab/nrmicro3199_F2.html Feb 10, 2014 - Internalized ssDNA is presumably bound by DprA (DNA processing protein A), ... The transformation heteroduplex that forms can be a fully ... Dynamics of Histone H2AX Phosphorylation in Response to a Defined ... https://books.google.com/books?isbn=0549351493 Jung-Ae Kim - 2007 Ligation can occur without processing DNA ends at all. ... the exonuclease activity executes at DSBs to form ssDNA and HR is chosen to repair DSBs (Ira et al., ... Medical Microbiology - Page 22 - Google Books Result https://books.google.com/books?isbn=1859962548 William L. Irving, Dlawer A. A. Ala'Aldeen, Tim Boswell - 2005 - Medical Viral entry into the host cell is a separate and distinct process which follows ... to generate positive ssRNA (i.e. mRNA), which can be appropriately processed by the ... no further processing, as it is already in a form recognizable by ribosomes.
