# Nsp12

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{{Short description|Protein in the Coronavirus genome}}

'''Nsp12''' is a non-structural protein in the [Coronavirus](/source/Coronavirus) genome. Its gene is part of the [ORF1ab](/source/ORF1ab) [reading frame](/source/reading_frame) and it is part of the pp1ab polyprotein; it is cleaved by [3CL<sup>pro</sup>](/source/3CLpro).<ref name=":0">{{Citation |last1=Snijder |first1=E.J. |chapter=The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing |date=2016 |title=Advances in Virus Research |volume=96 |pages=59–126 |publisher=Elsevier |language=en |doi=10.1016/bs.aivir.2016.08.008 |isbn=978-0-12-804736-1 |pmc=7112286 |pmid=27712628 |last2=Decroly |first2=E. |last3=Ziebuhr |first3=J.}}</ref>

Nsp12 is a multi-domain subunit: it consists of an [N-terminal](/source/N-terminal) [nidovirus](/source/nidovirus)-specific extension (NiRAN) domain, an interface domain, and a [C-terminal](/source/C-terminal) [RNA-dependent RNA-polymerase](/source/RNA-dependent_RNA_polymerase) domain. The N-terminal portion of SARS-CoV-2 nsp12 additionally contains a [β-hairpin](/source/%CE%B2-hairpin) which is sandwiched between the NiRAN and RdRp domain.<ref name=":1">{{Cite journal |last1=Jiang |first1=Yi |last2=Yin |first2=Wanchao |last3=Xu |first3=H. Eric |date=2021-01-29 |title=RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 |journal=Biochemical and Biophysical Research Communications |language=en |volume=538 |pages=47–53 |doi=10.1016/j.bbrc.2020.08.116 |issn=0006-291X |pmc=7473028 |pmid=32943188}}</ref>
thumb|289x289px|A representation of the SARS genome with ORF1A, ORF1AB, and the ribosomal frameshift shown. Coronavirus nsp12 is identified and expanded; RdRp, NiRAN domains as well as the interface domain are identified.
Coronavirus nsp12 also plays a role in host immune evasion; research has demonstrated that nsp12 inhibits the nuclear translocation of [IRF3](/source/IRF3).<ref>{{Cite journal |last1=Wang |first1=Wenjing |last2=Zhou |first2=Zhuo |last3=Xiao |first3=Xia |last4=Tian |first4=Zhongqin |last5=Dong |first5=Xiaojing |last6=Wang |first6=Conghui |last7=Li |first7=Li |last8=Ren |first8=Lili |last9=Lei |first9=Xiaobo |last10=Xiang |first10=Zichun |last11=Wang |first11=Jianwei |date=April 2021 |title=SARS-CoV-2 nsp12 attenuates type I interferon production by inhibiting IRF3 nuclear translocation |journal=Cellular & Molecular Immunology |language=en |volume=18 |issue=4 |pages=945–953 |doi=10.1038/s41423-020-00619-y |issn=1672-7681 |pmc=7907794 |pmid=33637958}}</ref>

== RdRp Domain ==
The RNA-dependent RNA polymerase domain of nsp12 is C-terminal. In [SARS-CoV-2](/source/SARS-CoV-2) the domain spans residues 366 to 920.<ref name=":2">{{Cite journal |last1=Yin |first1=Wanchao |last2=Mao |first2=Chunyou |last3=Luan |first3=Xiaodong |last4=Shen |first4=Dan-Dan |last5=Shen |first5=Qingya |last6=Su |first6=Haixia |last7=Wang |first7=Xiaoxi |last8=Zhou |first8=Fulai |last9=Zhao |first9=Wenfeng |last10=Gao |first10=Minqi |last11=Chang |first11=Shenghai |last12=Xie |first12=Yuan-Chao |last13=Tian |first13=Guanghui |last14=Jiang |first14=He-Wei |last15=Tao |first15=Sheng-Ce |date=2020-06-26 |title=Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir |journal=Science |language=en |volume=368 |issue=6498 |pages=1499–1504 |doi=10.1126/science.abc1560 |issn=0036-8075 |pmc=7199908 |pmid=32358203|bibcode=2020Sci...368.1499Y }}</ref> The structure of the RdRp domain shares common structural features with eukaryotic [RNA polymerases](/source/RNA_polymerase): the structure consists of a cupped right hand with subdomains referred to as fingers, palms, and thumbs.<ref name=":0" /> RdRp activity is dependent on two key zinc ions and conserved metal binding motifs of a [histidine](/source/histidine) and two cysteines each.<ref name=":1" />

The active site has seven catalytic motifs that are labeled A through G. Motif B serves as a hinge which allows the active site to associate with template RNA and Motif F directly interacts with the phosphate group of incoming free nucleotides.<ref name=":1" />

RdRp has to interact with [RNA](/source/RNA), which is negatively charged, so multiple subdomains including the primer-template entry site, NTP entry site, and the RNA strand exit routes contain positively charged residues.<ref name=":1" /> RdRp is unique from host RNA polymerases in that it has to associate with RNA instead of DNA, many RdRp residues interact with RNA bases via 2’-OH groups on the ribose ring which provides a possibly structural explanation for its specificity for RNA.<ref name=":2" />

Coronavirus nsp12 cannot function independently; it has two essential cofactor proteins, nsp7 and nsp8, that form a Replication and Transcription Complex (RTC).<ref name=":3">{{Cite journal |last=Ionescu |first=Mihaela Ileana |date=2020-12-01 |title=An Overview of the Crystallized Structures of the SARS-CoV-2 |url=https://doi.org/10.1007/s10930-020-09933-w |journal=The Protein Journal |language=en |volume=39 |issue=6 |pages=600–618 |doi=10.1007/s10930-020-09933-w |issn=1875-8355 |pmc=7584483 |pmid=33098476}}</ref> Structural studies of the RTC indicate that nsp7 and nsp8 form an 8:8 hexadecamer which acts as a [primase](/source/primase) to initiate viral replication.<ref>{{Cite journal |last1=Zhai |first1=Yujia |last2=Sun |first2=Fei |last3=Li |first3=Xuemei |last4=Pang |first4=Hai |last5=Xu |first5=Xiaoling |last6=Bartlam |first6=Mark |last7=Rao |first7=Zihe |date=November 2005 |title=Insights into SARS-CoV transcription and replication from the structure of the nsp7–nsp8 hexadecamer |journal=Nature Structural & Molecular Biology |language=en |volume=12 |issue=11 |pages=980–986 |doi=10.1038/nsmb999 |issn=1545-9993 |pmc=7096913 |pmid=16228002}}</ref>

While nsp12 is relatively well conserved across the ''Coronavirus'' viral species, there are biochemical and structural differences between the RdRp domain of SARS-CoV and SARS-CoV-2. SARS-CoV-2 RdRp has lower enzymatic activity and lower thermal stability compared to the RdRp domain in [SARS-CoV](/source/SARS-CoV-1).<ref>{{Cite journal |last1=Peng |first1=Qi |last2=Peng |first2=Ruchao |last3=Yuan |first3=Bin |last4=Zhao |first4=Jingru |last5=Wang |first5=Min |last6=Wang |first6=Xixi |last7=Wang |first7=Qian |last8=Sun |first8=Yan |last9=Fan |first9=Zheng |last10=Qi |first10=Jianxun |last11=Gao |first11=George F. |last12=Shi |first12=Yi |date=2020-06-16 |title=Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2 |journal=Cell Reports |language=English |volume=31 |issue=11 |article-number=107774 |doi=10.1016/j.celrep.2020.107774 |issn=2211-1247 |pmc=7260489 |pmid=32531208}}</ref>

=== Targeting by Remdesivir ===
Nsp12 is researched as a target for antiviral drugs as it is highly structurally conserved across related viruses and strains, and there are no human proteins with close structural homology.<ref name=":1" /> The emergence of SARS-CoV-2 and associated COVID19 disease led to the investigation of [Remdesivir](/source/Remdesivir) as an [antiviral drug](/source/antiviral_drug) for SARS-CoV-2. Remdesivir is a nucleoside analog which can compete with [ATP](/source/Adenosine_triphosphate) for incorporation into the RNA strand and prematurely terminate RNA synthesis.<ref name=":3" />

== NiRAN Domain ==
Coronavirus nsp12 has an N-terminal nidovirus RdRp-associated [nucleotidyltransferase](/source/nucleotidyltransferase) (NiRAN) domain which is essential for viral replication. The NiRAN domain is capable of transferring nucleotides as functional groups and it contains three key motifs called A, B, and C with seven invariant residues.<ref>{{Cite journal |last1=Gorbalenya |first1=Alexander E. |last2=Enjuanes |first2=Luis |last3=Ziebuhr |first3=John |last4=Snijder |first4=Eric J. |date=April 2006 |title=Nidovirales: Evolving the largest RNA virus genome |journal=Virus Research |language=en |volume=117 |issue=1 |pages=17–37 |doi=10.1016/j.virusres.2006.01.017 |pmc=7114179 |pmid=16503362}}</ref>

The biological function of the nsp12 NiRAN domain is not as well characterized as RdRp, but recent research has elucidated a possible role for the NiRAN domain in viral RNA capping. An additional non-structural protein, nsp9, was shown to associate with nsp12.<ref name=":4">{{Cite journal |last1=Slanina |first1=Heiko |last2=Madhugiri |first2=Ramakanth |last3=Bylapudi |first3=Ganesh |last4=Schultheiß |first4=Karin |last5=Karl |first5=Nadja |last6=Gulyaeva |first6=Anastasia |last7=Gorbalenya |first7=Alexander E. |last8=Linne |first8=Uwe |last9=Ziebuhr |first9=John |date=2021-02-09 |title=Coronavirus replication–transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit |journal=Proceedings of the National Academy of Sciences |language=en |volume=118 |issue=6 |article-number=e2022310118 |doi=10.1073/pnas.2022310118 |issn=0027-8424 |pmc=8017715 |pmid=33472860|bibcode=2021PNAS..11822310S |doi-access=free }}</ref> The biologically active form of nsp9 was additionally shown to be capable of binding nucleic acids with a preference for single-stranded RNA<ref>{{Cite journal |last1=Ponnusamy |first1=Rajesh |last2=Moll |first2=Ralf |last3=Weimar |first3=Thomas |last4=Mesters |first4=Jeroen R. |last5=Hilgenfeld |first5=Rolf |date=2008-11-28 |title=Variable Oligomerization Modes in Coronavirus Non-structural Protein 9 |journal=Journal of Molecular Biology |language=en |volume=383 |issue=5 |pages=1081–1096 |doi=10.1016/j.jmb.2008.07.071 |issn=0022-2836 |pmc=7094590 |pmid=18694760}}</ref> and could cleave nucleotide triphosphates and transfer the resulting nucleotide monophosphates to protein substrates in a process called NMPylation.<ref name=":4" /> Park and colleagues demonstrated that the SARS-CoV-2 NiRAN domain could cleave a [pyrophosphate](/source/pyrophosphate) from the end of an uncapped RNA genome and transfer the monophosphorylated RNA to nsp9 to RNAylate it.<ref name=":5">{{Cite journal |last1=Park |first1=Gina J. |last2=Osinski |first2=Adam |last3=Hernandez |first3=Genaro |last4=Eitson |first4=Jennifer L. |last5=Majumdar |first5=Abir |last6=Tonelli |first6=Marco |last7=Henzler-Wildman |first7=Katie |last8=Pawłowski |first8=Krzysztof |last9=Chen |first9=Zhe |last10=Li |first10=Yang |last11=Schoggins |first11=John W. |last12=Tagliabracci |first12=Vincent S. |date=2022-08-09 |title=The mechanism of RNA capping by SARS-CoV-2 |journal=Nature |volume=609 |issue=7928 |pages=793–800 |language=en |doi=10.1038/s41586-022-05185-z |issn=0028-0836 |pmc=9492545 |pmid=35944563|bibcode=2022Natur.609..793P }}</ref> The domain can then transfer the monophosphorylated RNA from nsp9 to a Guanidine Diphosphate (GDP) to form the initial cap structure for SARS-CoV-2.<ref name=":5" />

== References ==
{{reflist}}

Category:Coronavirus proteins
Category:Viral nonstructural proteins

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Adapted from the Wikipedia article [Nsp12](https://en.wikipedia.org/wiki/Nsp12) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Nsp12?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.