SARS-2 CoV nsp1 (Host translation inhibitor) interaktio ihmisen proteiinien kanssa

https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf
SARS-2 nsp1

 Vahva interaktiokandidaatti:

(5) POLA1 (Xp22.11-p21.3)
https://www.ncbi.nlm.nih.gov/gene/5422
( DNApolymeraasi alfa1  katalyyttinen alayksikkö)
DNA polymerase alpha 1, catalytic subunit
Also known as NSX; POLA; p180; VEODS
Summary. This gene encodes the catalytic subunit of DNA polymerase, which together with a regulatory and two primase subunits, forms the DNA polymerase alpha complex. The catalytic subunit plays an essential role in the initiation of DNA replication. [provided by RefSeq, Mar 2010] Expression Ubiquitous expression in lymph node (RPKM 2.6), bone marrow (RPKM 2.2) and 25 other tissues

(7)  PRIM2 (6p11.2)
(DNA primaasin  alayksikkö 2)
 https://www.ncbi.nlm.nih.gov/gene/5558
DNA primase subunit 2.  Also known as p58; PRIM2A
Summary. This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014 Expression Broad expression in prostate (RPKM 6.3), lymph node (RPKM 1.3) and 21 other tissues.

Interaktio ei ole vahvaa:

(62) PRIM1, (12q13.3)
DNA primase subunit 1, (DNAprimaasin alayksikkkö 1)
 https://www.ncbi.nlm.nih.gov/gene/5557
DNA primase subunit 1. Also known as p49.
Summary. The replication of DNA in eukaryotic cells is carried out by a complex chromosomal replication apparatus, in which DNA polymerase alpha and primase are two key enzymatic components. Primase, which is a heterodimer of a small subunit and a large subunit, synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. The protein encoded by this gene is the small, 49 kDa primase subunit. [provided by RefSeq, Jul 2008]Expression Broad expression in bone marrow (RPKM 10.3), testis (RPKM 9.4) and 25 other tissues.

(105) COLGALT1 (19p13.11)
(kollageeni beta, (1-O) galactosyylitransferaasi 1)
 https://www.ncbi.nlm.nih.gov/gene/79709
 collagen beta(1-O)galactosyltransferase 1.
Also known as BSVD3; GLT25D1; ColGalT 1
Summary. The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015] Expression Ubiquitous expression in placenta (RPKM 27.5), appendix (RPKM 22.9) and 25 other tissues
Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of Neisseria gonorrhoeae and Lic2A of Haemophilus influenzae. M. catarrhalis Lgt2 catalyzes the addition of galactose (Gal) to the growing chain of LOS on the cell surface. N. gonorrhoeae LgtB and LgtE link Gal-beta(1,4) to GlcNAc (N-acetylglucosamine) and Glc (glucose), respectively. The genes encoding LgtB and LgtE are two genes of a five gene locus involved in the synthesis of gonococcal LOS. LgtE is believed to perform the first step in LOS biosynthesis.

(108) POLA2 (11q13.1)
https://www.ncbi.nlm.nih.gov/gene/23649
(DNA polymeraasin alfa2  lisäalayksikkö)
DNA polymerase alpha 2, accessory subunit.

(176) PKP2 (12p11.21)
plakofiliini2 (placophilin 2)
https://www.ncbi.nlm.nih.gov/gene/5318
Plakophilin 2. Also known as ARVD9.
Summary. This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This gene product may regulate the signaling activity of beta-catenin. Two alternately spliced transcripts encoding two protein isoforms have been identified. A processed pseudogene with high similarity to this locus has been mapped to chromosome 12p13. [provided by RefSeq, Jul 2008]Expression Biased expression in heart (RPKM 72.8), colon (RPKM 29.6) and 12 other tissues
 (useita armadillo-toistoja)

armadillo repeat

Armadillo (ARM)/beta-catenin-like repeats are approximately 40 amino acid long, tandemly repeated sequence motif, first identified in the Drosophila segment polarity gene armadillo. These repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified. ARM repeats are related to HEAT repeats.

ORIGIN      
        1 maapgapaey gyirtvlgqq ilgqldsssl alpseaklkl agssgrggqt vkslriqeqv
       61 qqtlarkgrs svgngnlhrt ssvpeyvynl hlvendfvgg rspvpktydm lkagttatye
      121 grwgrgtaqy ssqksveers lrhplrrlei spdssperah ythsdyqysq rsqaghtlhh
      181 qesrraallv ppryarseiv gvsragttsr qrhfdtyhrq yqhgsvsdtv fdsipanpal
      241 ltyprpgtsr smgnlleken yltagltvgq vrplvplqpv tqnrasrssw hqssfhstrt
      301 lreagpsvav dssgrrahlt vgqaaaggsg nllterstft dsqlgnadme mtleravsml
      361 eadhmlpsri saaatfiqhe cfqksearkr vnqlrgilkl lqllkvqned vqravcgalr
      421 nlvfedndnk levaelngvp rllqvlkqtr dletkkqitg llwnlssndk lknlmiteal
      481 ltlteniiip fsgwpegdyp kanglldfdi fynvtgclrn mssagadgrk amrrcdglid
      541 slvhyvrgti adyqpddkat encvcilhnl syqleaelpe kysqniyiqn rniqtdnnks
      601 igcfgsrsrk vkeqyqdvpm peeksnpkgv ewlwhsivir mylsliaksv rnytqeaslg
      661 alqnltagsg pmptsvaqtv vqkesglqht rkmlhvgdps vkktaisllr nlsrnlslqn
      721 eiaketlpdl vsiipdtvps tdlliettas acytlnniiq nsyqnardll ntggiqkima
      781 isagdayasn kaskaasvll yslwahtelh haykkaqfkk tdfvnsrtak ayhslkd
//

SARS-2 tekee interaktioita ainakin yli 300 ihmisen proteiiniin

 
Katson  tänään lukemastani interaktioproteiiniluettelosta muutaman interaktioproteiinin. ensin otsikkona SARS-2 proteiini ja alla  jokunen ihmisen interaktioiproteiini ( ihmisen proteiinin geeni mainittuna) Keskeneräinen ...

• SARS-2 nsp8: 

MRPS5 (2q11.1)
https://www.ncbi.nlm.nih.gov/gene/6496
Also known as S5mt; MRP-S5.Summary Mammalian mitochondrial ribosomal proteins(MRP-S)  are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S5P family. Pseudogenes corresponding to this gene are found on chromosomes 4q, 5q, and 18q. [provided by RefSeq, Jul 2008] Expression Ubiquitous expression in kidney (RPKM 9.5), duodenum (RPKM 9.0) and 25 other tissues.
https://string-db.org/network/9606.ENSP00000272418

MRSP27
MRSP2
MRSP25 

•  SARS-2 nsp12:

USP54  (10q32.2)   deubikitinaasi USP ryhmätsä, ubikitiinispesifinen peptidaasi  54

(Näissä  Deubikitinaaseissa DUB, ainakin joissain niistä,   tapaa olla entsyymifunktiolle tärkeä  ZnF- rakenne, vaikka se ei ole proteiinin struktuurissa erityisesti  mainittu) .
https://www.ncbi.nlm.nih.gov/gene/159195
 https://doi.org/10.1002/pro.2415

PRRC2B (9q34.13),  isohko peptidi, jossa on runsaasti  proliineja ja fosforylaatiokohtia. Tämän proteiinin  kliinisestä  merkityksestä on muutama maininta.

 Proline Rich Coiled-Coil 2B ^{2 3 5}

KIAA0515 ^{2 3 4}  , HLA-B-Associated Transcript 2-Like 1 ^{3 4}
Proline-Rich Coiled-Coil Protein 2B ^{3 4}
HLA-B Associated Transcript 2-Like ^{2 3}
Protein PRRC2B ^{3 4}
BAT2L1 ^{3 4}
BAT2L ^{3 4}
HLA-B Associated Transcript 2-Like 1 ²
Proline-Rich Coiled-Coil 2B ²
Protein BAT2-Like 1 ³
LQFBS-1 ³

GeneCards Summary for PRRC2B Gene

PRRC2B (Proline Rich Coiled-Coil 2B) is a Protein Coding gene. Diseases associated with PRRC2B include Spinocerebellar Ataxia, Autosomal Recessive, With Axonal Neuropathy 2 and Spinocerebellar Ataxia 36. An important paralog of this gene is PRRC2C.

•  SARS-2 nsp13

FYCO1,  ZFYVE7 (3p21.31)  FYVE-tyyppinen sinkkisormiproteiini.
https://www.ncbi.nlm.nih.gov/gene/79443
(ZFYVE ryhmän Zn finger rakenne  on C-x-C-x-C-x-C-xxx-C-x-C-H-x-C)
FYCO1, Also known as  CATC2; RUFY3; ZFYVE7; CTRCT18 Summary: This gene encodes a protein that contains a RUN domain, FYVE-type zinc finger domain and Golgi dynamics (GOLD) domain. The encoded protein plays a role in microtubule plus end-directed transport of autophagic vesicles through interactions with the small GTPase Rab7, phosphatidylinositol-3-phosphate (PI3P) and the autophagosome marker LC3. Mutations in this gene are a cause of autosomal recessive congenital cataract-2 (CATC2). [provided by RefSeq, Dec 2011]Expression  Ubiquitous expression in heart (RPKM 22.7), endometrium (RPKM 12.6) and 25 other tissues.


CEP350 (1q25.2)  ( 350 kDa) Sentrosomaalinen proteiini350.

Also known as

GM133; CAP350

Summary  The product of this gene is a large protein with a CAP-Gly domain typically found in cytoskeleton-associated proteins. The encoded protein primarily localizes to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. The encoded protein directly interacts with another large centrosomal protein and is required to anchor microtubules at the centrosome. It is also implicated in the regulation of a class of nuclear hormone receptors in the nucleus. Several alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]  https://www.ncbi.nlm.nih.gov/pubmed/17878239/ 

• SARS-2 nsp14:

Sirtuiini SIRT5 (6p23) https://www.ncbi.nlm.nih.gov/gene/23408 This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity. The protein encoded by this gene is included in class III of the sirtuin family. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2010] Expression Ubiquitous expression in heart (RPKM 3.7), liver (RPKM 2.6) and 25 other tissues

 Sinkkiä sitova motiivi: C-xx-C-x(11) -C -x(12)C

  Site            order(166,169,181,194)
                     /site_type="other"
                     /note="Zn binding site [ion binding]"
                     /db_xref="CDD:238703"

• SARS-2 M:

SLC25A21, MTDPS18, ODC, ODC1    https://www.ncbi.nlm.nih.gov/gene/89874

Preferred Names  mitochondrial 2-oxodicarboxylate carrier. Names  oxodicarboxylate carrier solute carrier family 25 (mitochondrial oxoadipate carrier);  member 21; solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21.

HIV-1 Vif downregulates the expression of solute carrier family 25, member 21 (SLC25A21) in Vif-expression T cells