RNA Dependent RNA Polymerases of Severe Acute Respiratory Syndrome-Related Coronaviruses- An Insight into their Active Sites and Mechanism of Action

Palanivelu, Peramachi

doi:10.9734/ijbcrr/2020/v29i1030236

Cited by 2 publications

(4 citation statements)

References 32 publications

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“…The N/Q of the triad -YAN/Q-with the dual hydrogen bonding capacity can recognize the 2'-OH group of incoming NTPs and thus, discriminate NTPs and dNTPs during RNA synthesis. It is interesting to note that the YAN/Q type of motif is also found in the RdRps of Dengue, Zika, and Yellow Fever viruses too (data not shown) (11). However, it is intriguing to know that a similar triad is not found in the influenza C virus.…”

Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 91%

“…The -YAQ-triad is found only in influenza A and B viruses which is similar to the invariant -YAN 691 -found in SARS-CoV-1, SARS-CoV-2 and other SARS-related CoVs. It is located in the palm domain and suggested to be involved in the nucleotide selection [11,12]. The N/Q of the triad -YAN/Q-with the dual hydrogen bonding capacity can recognize the 2'-OH group of incoming NTPs and thus, discriminate NTPs and dNTPs during RNA synthesis.…”

Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 99%

“…It is interesting to note that a similar characteristic, highly conserved methioninerich peptide -897 GHMLDMYSVML-or (-X2MX2MX3M-) is also found in the RdRps of SARS-CoV-1, SARS-CoV-2 and other SARS-related CoVs. This methionine-rich motif at the template entry site is suggested to be involved in stabilizing the base pair between the template and the incoming NTP [6,11].…”

Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 99%

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An insight into the active sites of the catalytic basic protein subunit PB1 of the RNA polymerase of human influenza viruses

Palanivelu¹

2023

World J. Adv. Res. Rev.

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RNA polymerase from human influenza viruses is a heterotrimeric enzyme and performs the crucial functions of both transcription and replication for multiplication of the viruses in human cells. The heterotrimeric enzyme is made up of two basic protein subunits (PB1 and PB2) and an acidic protein subunit (PA). All the three subunits perform well-defined function(s) in the transcription and replication processes in the human cells. The basic protein subunit PB1 is shown to possess the polymerization activity, whereas the PB2 and the PA subunits are found to be involved in the cap-snatching and proofreading (PR) activities, respectively. The polymerase activity in the catalytic subunit, PB1, is found to be an RNA-dependent RNA polymerase (RdRp). Multiple sequence alignment (MSA) analysis of the PB1 subunits from all the three human influenza viruses, A, B and C shows large number of highly conserved peptides, amino acid motifs and invariant amino acids. Site-directed mutagenesis (SDM) analysis and X-ray crystallographic data have shown that two completely conserved motifs, viz. –GDN- and –SDD-, are involved in binding to the catalytic Mg2+ ion. These data are in close agreement with the MSA analysis data of the polymerases from all the three human influenza viruses. Furthermore, two highly conserved polymerase catalytic regions are identified in the PB1 subunits by sequence similarity to other DNA/RNA polymerases and hence, are proposed to function in the nucleotidyl transfer activities. Presence of the two catalytic regions suggest that the polymerase may function in a dual mode, i.e., in phase I, in association with the cap-snatching subunit PB2, it could be involved in the synthesis of mRNAs (transcription mode) and once enough proteins are made from the mRNAs, in the second phase, in association with PR exonuclease subunit PA, it could switch to the replication mode to synthesize error-free, exact copies of the viral genome. For both the activities, it could use the same invariant catalytic Mg2+-binding –GDN- and –SDD- motifs.

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Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 91%

Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 99%

Section: Clustal O (124) Msa Of the Pb1 Catalytic Subunits Of The Rdr...mentioning

confidence: 99%

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An insight into the active sites of the catalytic basic protein subunit PB1 of the RNA polymerase of human influenza viruses

Palanivelu¹

2023

World J. Adv. Res. Rev.

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“…It has been well established that zinc acts as the cofactor for >450 enzymes and proteins, where it plays both structural and catalytic roles. It is interesting to note that zinc is also an integral component of both prokaryotic and eukaryotic DNA and RNA polymerases and is found to be essential for their function [34,35]. As the Znmediated reactions are exceedingly faster and efficient, many enzymes use Zn 2+ as the catalytic metal ion.…”

Section: A Unified Mechanism Of Action For the Pr Exonucleases Of Msu Rnapsmentioning

confidence: 99%

An Insight into the Proofreading Functions of Multisubunit DNA-Dependent RNA Polymerases and Their Catalytic Mechanism

Palanivelu

2021

IJBcRR

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Aim: To analyze the active sites of the proofreading (PR) functions in the multisubunit DNA-dependent RNA polymerases (MSU RNAPs) from prokaryotes, chloroplasts and eukaryotes, and propose a plausible unified catalytic mechanism for these enzymes. Study Design: Data collected on these enzymes from bioinformatics, biochemical, site-directed mutagenesis (SDM), X-ray crystallography and cryo-electron microscopy (cryo-EM) were used for the analyses. Methodology: The protein sequence data of MSU RNAPs from prokaryotes, prokaryotic-types (plant chloroplasts) and eukaryotes were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available from biochemical and SDM experiments, and X-ray crystallographic and cryo-EM data on these enzymes are also used to confirm the possible amino acids involved in the active site of the PR function in these MSU RNAPs Results: All the seven types of MSU RNAPs (I-VII) reported from prokaryotes to eukaryotes were analyzed by the multiple sequence alignment (MSA) software, Clustal Omega, to find out conservations among them. The MSA analysis showed many conserved amino acid motifs including small and large peptide regions from the MSU RNAPs of prokaryotes, eukaryotes and plant chloroplasts. Interestingly, the catalytic amino acid and template-binding pairs are highly conserved in all these polymerases, with a few exceptions. Most of them use a basic amino acid (R/K/H) for initiating catalysis and an -YG/FG- pair for template-binding. Some odd type of catalytic amino acids and template-binding pairs are observed in human pathogens, parasites and organisms which cannot ferment sugars. In all the MSU RNAPs, the proposed polymerase catalytic region also possessed three invariant Cs and an invariant H within it. The invariant Cs is shown to bind a zinc atom and proposed to involve in the PR function by excising any misincorporated nucleotide during the transcription process. In the plant-specific MSU RNAPs IV and V, which involve in transcriptional gene silencing in plants, the catalytic and template-binding pairs do not follow the regular distance conservations as observed with other five of the MSU RNAPs. Their polymerase/PR active site regions are similar to RNAP III rather than to RNAP II, as all three make only low molecular weight RNAs. Conclusions: All the known MSU RNAPs possess three invariant Cs and an invariant H embedded within the polymerase active site itself. The three invariant Cs are shown to bind a zinc atom and the invariant H could act as the proton acceptor from a metal-bound water molecule, for initiating excision of the mismatches by a Zn-mediated hydrolysis. Thus, the PR function in MSU RNAPs is integrated within the polymerase active site itself, which is in sharp contrast to the PR functions reported in DNA-dependent DNA polymerases and RNA-dependent RNA polymerases. Therefore, all the seven MSU RNAPs from prokaryotes and eukaryotes are proposed to follow a unified mechanism to excise the mismatches during transcription. The discovery of intrinsic self-correcting RNA transcription mechanism fulfils the missing link in molecular evolution.

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RNA Dependent RNA Polymerases of Severe Acute Respiratory Syndrome-Related Coronaviruses- An Insight into their Active Sites and Mechanism of Action

Cited by 2 publications

References 32 publications

An insight into the active sites of the catalytic basic protein subunit PB1 of the RNA polymerase of human influenza viruses

An insight into the active sites of the catalytic basic protein subunit PB1 of the RNA polymerase of human influenza viruses

An Insight into the Proofreading Functions of Multisubunit DNA-Dependent RNA Polymerases and Their Catalytic Mechanism

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