SARS-2-CoV nsp5 (3CL-PRO) proteiini-proteiini interaktioista

* Mitä tietoja Swiss modul antaa nyt nsp5  koronavirusproteiinista, joka on SARS-virusten pääentsyymi.  Nsp5 pystyy pilkkomaan  replikaasi-polyproteiinia 11 eri kohdasta, joten se tuottaa  useimmat   viruksen työkaluproteiineista, kun on päässyt itse  pilkkoutumaan  replikaasista esiin. https://covid-19.uniprot.org/uniprotkb/P0DTD1

 3C-like proteinase (EC:3.4.22.691 Publication)

Short name: 3CL-PRO

Short name: 3CLp

Alternative name(s):

nsp5 ( sequence)

>sp|P0DTD1|3264-3569
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

3C-like proteinase:Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291, PubMed:32272481). Also able to bind an ADP-ribose-1''-phosphate (ADRP).

Inhibited by pyridone-containing alpha-ketoamides compounds 13a and 13b. In turn, alpha-ketoamide 13b (tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate) inhibits SARS-CoV-2 replication in human lung cells (PubMed:32198291). Inhibited ex vivo by michael acceptor inhibitor N3 (PubMed:32272481)"

* https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf 

"The SARS-CoV-2 interactome reveals novel aspects of SARS-CoV-2 biologyOur study highlighted interactions between SARS-CoV-2 proteins and human proteins with a range of functions including DNA replication (Nsp1), epigenetic and gene expression regulators (Nsp5, Nsp8, Nsp13, E), vesicle trafficking (Nsp6, Nsp7, Nsp10, Nsp13, Nsp15, Orf3a, E, Orf8), lipid modification (Spike), RNA processing and regulation (Nsp8, N), ubiquitin ligases (Orf10), signaling (Nsp8, Nsp13, N, Orf9b), nuclear transport machinery (Nsp9, Nsp15, Orf6), cytoskeleton (Nsp1, Nsp13), mitochondria (Nsp4, Nsp8, Orf9c), and extracellular matrix (Nsp9) (Fig.3)"

 SARS-2-CoV  nsp5  proteiiniinteraktio  ihmisen  HDAC2-proteiinien kanssa.
( histonideasetylaasi 2)  
 ja  
SARS-2-CoV nsp5) proteiininteraktio  ihmisen TRMT1-proteiinin kanssa  (tRNA-metyylitransferaasi 1)

"We identified protein-protein interactions with the main protease Nsp5, using both wild-type and catalytic dead(C145A) constructs. 
For wild-type Nsp5, we identified one high-confidence interaction, the epigenetic regulator histone deacetylase 2 (HDAC2), and predicted a cleavage site between the HDAC domain and the nuclear localization sequence, suggesting that Nsp5 may inhibit HDAC2 transport into the nucleus (Extended Data Fig. 7), potentially impacting the published functions of HDAC2 in mediating inflammation and interferon response38,39.
 We also identified an interaction of Nsp5 (C145A) with tRNA methyltransferase 1 (TRMT1), which is responsible for synthesis of the dimethylguanosine (m2,2G) base modification on both nuclear and mitochondrial tRNAs40. We predict TRMT1 is also cleaved by Nsp5, removing its zinc finger and nuclear localization signal and likely resulting in an exclusively mitochondrial localization (Extended Data Fig. 7).

• HDAC2 (6q21)

(Histonideasetylaasi2.

Tämän entsyymin tehtävänä on poistaa  acetyl ryhmiä (Ac)  lysiinitähteistä (de-asetyloida histonien  N-terminaalisia lysiineitä(K).  Lisäksi entsyymissä on nitroso-cysteiinikohtia ( nitrosyloituvia). HDAC2:n    aktiivissa kohdassa on sinkkiä sitovaa kykyä, mikä on olennaista  entsyymiaktiivisuudelle.  Tämä HDAC2 -proteiini muodostaa transkriptiota vaimentavan kompleksin liittyessään  esim.  YY1 -sinkkisormiproteiiniin.  SARS- CoV nsp5  mutiloi näitä  stabiileja sinkkisormimuodostumia, mikä  epästabiloi proteiinin struktuuria ja samalla  hävittää entsyymiaktiivisuuden. Myös  tumaan lokalisoiva  signaali  häviää proteiinista ja se ei pääse DNA:n  histoneille, vaan jäänee mitokondriaan). 

 https://www.ncbi.nlm.nih.gov/gene/3066
 Histone deacetylase 2. Also known as HD2; RPD3; YAF1; KDAC2
Summary This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger ( Znf) transcription factor. Thus, it plays an important role in transcriptional regulation, cell cycle progression and developmental events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010] Expression. Ubiquitous expression in testis (RPKM 14.8), endometrium (RPKM 10.6) and 25 other tissues See more
Preferred Names:histone deacetylase 2.
Names: YY1-associated factor 1.
transcriptional regulator homolog RPD3. 
FEATURES:https://www.ncbi.nlm.nih.gov/protein/NP_001518.3
Active site: Comment:Active site consists of a long narrow tunnel (that apparently serves for substrate binding) and a cavity with Zn ion (that is important for catalysis). In this structure, the tunnel is filled by the aliphatic chain of the inhibitor.
  Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC2 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. It forms transcriptional repressor complexes by associating with several proteins, including the mammalian zinc-finger transcription factor YY1, thus playing an important role in transcriptional regulation, cell cycle progression and developmental events. Additionally, a few non-histone HDAC2 substrates have been found. HDAC2 plays a role in embryonic development and cytokine signaling important for immune response, and is over-expressed in several solid tumors including oral, prostate, ovarian, endometrial and gastric cancer. It participates in DNA-damage response, along with HDAC1; together, they can promote DNA non-homologous end-joining. HDAC2 is considered an important cancer prognostic marker. Inhibitors specifically targeting HDAC2 could be a therapeutic drug option.
https://www.ncbi.nlm.nih.gov/pubmed/31545224

Biomed Pharmacother. 2019 Oct;118:109380. doi: 10.1016/j.biopha.2019.109380. Epub 2019 Aug 30. Expression of GR-α and HDAC2 in steroid-Sensitive and steroid-Insensitive interstitial lung disease.Bin YF¹, Wu LJ¹ et al.

(Tämä proteiiniperhe  kiinnostaa muitakin viruksia:Esim: 

HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages).

• TRMT1 (19p13.13)

(tRNA- metyylitransferaasi 1.
 Muita nimiä TRM1 ja MRT68. Tämä geeni koodaa tRNA:ta modifioivaa entsyymiä ja toimii  dimetyylitransferaasina,  joka  modifioi tRNA:n guaniinitähteen 26- asemassa. Entsyymi voi siirtää   yhden  tai  kaksi metyyliryhmää (Me)  ja käyttää  aktivoitua metioniinia(SAM) metyylin (Me) antajana.  Geenimutaatio assosioituu leukomalasiaan ja mikrokefaliaan)


https://www.ncbi.nlm.nih.gov/gene/55621 
 tRNA methyltransferase 1. Also known as TRM1; MRT68.
Summary. This gene encodes a tRNA-modifying enzyme that acts as a dimethyltransferase, modifying a single guanine residue at position 26 of the tRNA. The encoded enzyme has both mono- and dimethylase activity when exogenously expressed, and uses S-adenosyl methionine (SAM) as a methyl donor. The C-terminal region of the encoded protein has both a zinc finger motif (Znf), and an arginine/proline-rich region. Mutations in this gene have been implicated in autosomal recessive intellectual disorder (ARID). Alternative splicing results in multiple transcript variants encoding different isoforms. There is a pseudogene of this gene on the X chromosome. [provided by RefSeq, May 2017] Expression Ubiquitous expression in spleen (RPKM 12.4), lymph node (RPKM 11.5) and 25 other tissues. Preferred Names tRNA (guanine(26)-N(2))-dimethyltransferase
Names:N(2),N(2)-dimethylguanosine tRNA methyltransferase,
TRM1 tRNA methyltransferase 1 homolog,
tRNA 2,2-dimethylguanosine-26 methyltransferase,
tRNA methyltransferase 1 homolog,
tRNA(guanine-26,N(2)-N(2)) methyltransferase,
tRNA(m(2,2)G26)dimethyltransferase.

FEATURES: NP_001129507.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 1.

Conserved Domains (3) summary

smart00356
Location:600 → 626

ZnF_C3H1; zinc finger

pfam02005
Location:45 → 500

TRM; N2,N2-dimethylguanosine tRNA methyltransferase

cl25637
Location:571 → 624

DFRP_C; DRG Family Regulatory Proteins, Tma46.

Ref.   https://www.ncbi.nlm.nih.gov/pubmed/30289604/



 Lähdeartikkelin listasta  löytyy maininta  myös:

SARS-2- CoV nsp5 (C145A) 
 tekee interaktion
ihmisen  GPX1 -proteiinin kanssa ( joka on glutationiperoksidaasi 1) .

• GPX1 (3p21.31) 

(Glutationiperoksidaasi 1 on   selenoproteiini  solun redoxsysteemissä.  Sen rakenteessa on harvinainen aminohappo selenocysteiini (Sec) entsyymin atiivissa kohdassa . Se koodautuu UGA-koodilla, joka tavallisesti merkitsee translaation lopetusta. Tällä entsyymin  hienosääteisellä yksityiskohdalla  on kliinistä merkitystä.  

Seleeni on maaperästä  ravintoon tuleva aine ja esim aiemmin  Suomessa oli vajetta seleenistä maaperän seleeniköyhyyden takia.  Joissain paikoissa maailmassa on  taas hyvin  runsaasti seleeniä sisältävää maaperää, mikä ei sekään ole hyvä asia. Seleeni kuuluu ravintosuosituksissa mainittuihin hivenaineisiin. Tässä yhteydessä  ei selviä, miten  SARS-2- CoV nsp5 (C145A) . Selitys lienee lähdeartikkelin tekstissä. Kiinan Anhui provinssissa on korkea seleenipitoisuus. Se on tutkittu Dashan kylästä.  Anhuiprovinssista tuli ensimmäiset COVID-19 potilaat, ja he saivat antiviraalin hoidon eikä kukaan heistä kuollut. https://www.sciencedirect.com/science/article/pii/S1201971220302034. 

Dashan kylän  seleenipitoisuus maaperässä:  https://www.sciencedirect.com/science/article/pii/S1201971220302034

Rakenteellinen aminohappo selenocysteiini (asemassa 49) näyttää merkatun  U kirjaimella. Ensimmistä kertaa huomaan tällaisen merkinnän peptidisekvenssissä).    https://www.ncbi.nlm.nih.gov/pubmed/32179940The dietary Se intake of local residents was estimated to be 261.2 µg day^- 1 and hair Se content varied from 0.34 to 1.35 mg kg^- 1, suggesting that the potential health risk should be concerned. Weathering of carbonaceous rock was speculated to be the primary source of soil Se according to the contents of Se in rocks, the distribution of Se in soil profiles and the relationships between Se and other elements in soils and parent rocks.  
 (Ps. Kun seleeni-innostus tuli Suomeen, oli tarjolla 300 ug tableteita immunoseleenia. Sain jopa ilmaiseksi  apteekista tällaisia! Olin aloitamassa keliakidieettiä siihen aikaan).
Brasilian  selenium tilanteesta. https://www.ncbi.nlm.nih.gov/pubmed/20646739
 https://edition.cnn.com/2020/05/07/americas/amazon-manaus-coronavirus-intl/index.html
COVID 19 on aivan  akuutin katastrofin astetta Brasiliassa vielä päivästä päivään.  Manaus- nimisessä kaupungissa lienee epicentrum.   Tästä seleeniasiasta  johduin   nihin maaperäseikkoihin.

glutathione peroxidase 1

Also known as GPXD; GSHPX1

Summary: The protein encoded by this gene belongs to the glutathione peroxidase family, members of which catalyze the reduction of organic hydroperoxides  and hydrogen peroxide (H2O2) by glutathione, and thereby protect cells against oxidative damage. Other studies indicate that H2O2 is also essential for growth-factor mediated signal transduction, mitochondrial function, and maintenance of thiol redox-balance; therefore, by limiting H2O2 accumulation, glutathione peroxidases are also involved in modulating these processes. Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. This isozyme is the most abundant, is ubiquitously expressed and localized in the cytoplasm, and whose preferred substrate is hydrogen peroxide. It is also a selenoprotein, containing the rare amino acid selenocysteine (Sec) at its active site. Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. This gene contains an in-frame GCG trinucleotide repeat in the coding region, and three alleles with 4, 5 or 6 repeats have been found in the human population. The allele with 4 GCG repeats has been significantly associated with breast cancer risk in premenopausal women. Alternatively spliced transcript variants have been found for this gene. Pseudogenes of this locus have been identified on chromosomes X and 21. [provided by RefSeq, Aug 2017] Expression Ubiquitous expression in fat (RPKM 212.4), spleen (RPKM 100.0) and 24 other tissues See more Orthologs.

FEATURES:https://www.ncbi.nlm.nih.gov/protein/NP_000572.2

ORIGIN      
        1 mcaarlaaaa aaaqsvyafs arplaggepv slgslrgkvl lienvaslug ttvrdytqmn
       61 elqrrlgprg lvvlgfpcnq fghqenakne eilnslkyvr pgggfepnfm lfekcevnga
      121 gahplfaflr ealpapsdda talmtdpkli twspvcrndv awnfekflvg pdgvplrrys
      181 rrfqtidiep dieallsqgp sca
//