Abstract:
:The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end guanosine of the downstream RNA template interacts with a fingers domain pocket, with the base sandwiched by H44 and R277 side chains through hydrophobic stacking interactions, and these interactions are still maintained after one in-crystal translocation event induced by nucleotide incorporation, implying that the pocket could regulate the functional properties of the polymerase by interacting with RNA. When mutated, residue R277 showed an impact on virus proliferation in virological studies with residue H44 having a synergistic effect. In vitro biochemical data further suggest that mutations at these two sites affect RNA binding, EC stability, but not polymerase catalytic rate (kcat) and apparent NTP affinity (KM,NTP). We propose that, although rarely captured by crystallography, similar surface pocket interaction with nucleobase may commonly exist in nucleic acid motor enzymes to facilitate their processivity. Potential applications in antiviral drug and vaccine development are also discussed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shi W,Ye HQ,Deng CL,Li R,Zhang B,Gong Pdoi
10.1093/nar/gkz1170subject
Has Abstractpub_date
2020-02-20 00:00:00pages
1392-1405issue
3eissn
0305-1048issn
1362-4962pii
5682902journal_volume
48pub_type
杂志文章abstract::Non-coding RNAs (ncRNAs) have diverse essential biological functions in all organisms, and in eukaryotes, two such classes of ncRNAs are the small nucleolar (sno) and small nuclear (sn) RNAs. In this study, we have identified and characterized a collection of sno and snRNAs in Giardia lamblia, by exploiting our discov...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks887
更新日期:2012-11-01 00:00:00
abstract::Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the alpha-subunit. The epsilon-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to alpha via a segment of 57 addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn489
更新日期:2008-09-01 00:00:00
abstract::A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq750
更新日期:2011-01-01 00:00:00
abstract::The proposition that the 2-amino group of guanine plays a critical role in determining how antibiotics recognise their binding sites in DNA has been tested by relocating it, using tyrT DNA derivative molecules substituted with inosine plus 2,6-diaminopurine (DAP). Irrespective of their mode of interaction with DNA, su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.6.885
更新日期:1995-03-25 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::LRPPRC is a protein that has attracted interest both for its role in post-transcriptional regulation of mitochondrial gene expression and more recently because numerous mutated variants have been characterized as causing severe infantile mitochondrial neurodegeneration. LRPPRC belongs to the pentatricopeptide repeat (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw575
更新日期:2016-08-19 00:00:00
abstract::Denaturing gradient gel electrophoresis (DGGE) is based upon the different melting behaviors of DNA molecules in a chemical denaturant gradient according to their sequences. This technique has recently become a widespread tool to detect mutations. The introduction of a GC-clamp enables the detection of most single bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.12.3331
更新日期:1991-06-25 00:00:00
abstract::TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1043
更新日期:2007-01-01 00:00:00
abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.245
更新日期:1974-02-01 00:00:00
abstract::Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.1943
更新日期:1986-03-11 00:00:00
abstract::High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku370
更新日期:2014-07-01 00:00:00
abstract::The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.17.4239
更新日期:1981-09-11 00:00:00
abstract::Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr697
更新日期:2012-01-01 00:00:00
abstract::In Saccharomyces cerevisiae, the DNA damage response (DDR) is activated by the spatio-temporal colocalization of Mec1-Ddc2 kinase and the 9-1-1 clamp. In the absence of direct means to monitor Mec1 kinase activation in vivo, activation of the checkpoint kinase Rad53 has been taken as a proxy for DDR activation. Here, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1222
更新日期:2010-04-01 00:00:00
abstract::A hybrid plasmid was constructed containing beta-lactamase gene of plasmid pBR322 and cloned coding sequences of bovine growth hormone (BGH). The constructed plasmid contains all DNA sequences required to encode BGH, and when used as a hybridization probe it detects one growth hormone gene in the bovine genome. The cl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.1.19
更新日期:1981-01-10 00:00:00
abstract::A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.13.3136
更新日期:1998-07-01 00:00:00
abstract::Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky264
更新日期:2018-05-18 00:00:00
abstract::Human cytomegalovirus (HCMV) terminase is composed of subunits pUL56 (130 kDa) and pUL89 ( approximately 75 kDa), encoded by the UL56 and UL89 genes. In a recent investigation, we demonstrated that the main ATPase activity is associated with the large terminase subunit pUL56. The protein has two putative ATP-binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg229
更新日期:2003-03-01 00:00:00
abstract::A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.19.7327
更新日期:1984-10-11 00:00:00
abstract::Three new proteins which selectively bind to UV-damaged DNA were identified and purified to near homogeneity from UV-irradiated Drosophila melanogaster embryos through several column chromatographies. These proteins, tentatively designated as D-DDB P1, P2 and P3, can be identified as different complex bands in a gel s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2600
更新日期:1995-07-25 00:00:00
abstract::MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks460
更新日期:2012-07-01 00:00:00
abstract::Most small nucleolar RNAs (snoRNAs) guide rRNA nucleotide modifications, some participate in pre-rRNA cleavages, and a few have both functions. These activities involve direct base-pairing of the snoRNA with pre-rRNA using different domains. It is not known if the modification and processing functions occur independen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq043
更新日期:2010-06-01 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by forming a covalent bond with the 6-position...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.10.2459
更新日期:1993-05-25 00:00:00
abstract::Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural orga...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8427
更新日期:1986-11-11 00:00:00
abstract::MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky306
更新日期:2018-06-20 00:00:00
abstract::VL30 genetic elements constitute a murine multicopy gene family that is retrovirus-like, despite the lack of sequence homology with any known retrovirus. Over one hundred copies of VL30 units are dispersed throughout the mouse genome. We report here that the mouse genome also contains 'solo' VL30 long terminal repeats...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.5.2273
更新日期:1984-03-12 00:00:00
abstract::Previous studies have shown that the yeast Candida albicans encodes a unique seryl-tRNA(CAG) that should decode the leucine codon CUG as serine. However, in vitro translation of several different CUG-containing mRNAs in the presence of this unusual seryl-tRNA(CAG) result in an apparent increase in the molecular weight...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1481
更新日期:1995-05-11 00:00:00
abstract::The eukaryotic mismatch repair protein Msh6 shares five domains in common with other MutS members. However, it also contains several hundred additional residues at its N-terminus. A few of these residues bind to PCNA, but the functions of the other amino acids in the N-terminal region (NTR) are unknown. Here we demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm409
更新日期:2007-01-01 00:00:00
abstract::Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1003
更新日期:2018-01-04 00:00:00