A0MD28 (RPOA_PRRSS) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Replicase polyprotein 1ab Alternative name(s): ORF1ab polyprotein Cleaved into the following 12 chains: Nsp1 EC=3.4.22.- Nsp1-alpha papain-like cysteine proteinase EC=3.4.22.- Alternative name(s): PCP1-alpha Nsp1-beta papain-like cysteine proteinase EC=3.4.22.- Alternative name(s): PCP1-beta Nsp2 cysteine proteinase EC=3.4.19.12 EC=3.4.22.- Alternative name(s): CP2 Short name=CP Non-structural protein 3 Short name=Nsp3 3C-like serine proteinase Short name=3CLSP EC=3.4.21.- Alternative name(s): Nsp4 Non-structural protein 5-6-7 Short name=Nsp5-6-7 Non-structural protein 8 Short name=Nsp8 RNA-directed RNA polymerase Short name=Pol Short name=RdRp EC=2.7.7.48 Alternative name(s): Nsp9 Helicase Short name=Hel EC=3.6.4.12 EC=3.6.4.13 Alternative name(s): Nsp10 Non-structural protein 11 Short name=Nsp11 Non-structural protein 12 Short name=Nsp12
Organism	Porcine reproductive and respiratory syndrome virus (isolate Pig/United States/SD 01-08/2001) (PRRSV) [Complete proteome]
Taxonomic identifier	857306 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Nidovirales › Arteriviridae › Arterivirus › Porcine reproductive and respiratory syndrome virus
Virus host	Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	3838 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The replicase polyprotein 1ab is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products By similarity. Ref.3 Nsp1 is essential for viral subgenomic mRNA synthesis By similarity. Ref.3 Nsp1-alpha inhibits IFN-beta production. Counteracts the action of NF-kappaB by decreasing the phosphorylation of IkappaB-alpha, such that the degradation of IkappaB-alpha is suppressed. This leads to the blockage of NF-kappaB nuclear translocation and thus interference of NF-kappaB activation. Also seems to inhibit IRF3-dependent pathways By similarity. Ref.3 Nsp2 cysteine proteinase which cleaves the nsp2/nsp3 site in the polyprotein. Also displays deubiquitinating and deISGylase activities. The deubiquitinating activity cleaves both ubiquitinated and ISGylated products and may therefore regulate ubiquitin and ISG15 dependent host innate immunity By similarity. Deubiquitinates host NFKBIA, thereby interfering with NFKBIA degradation and impairing subsequent NF-kappa-B activation. Ref.3 The 3C-like serine proteinase chain is responsible for the majority of cleavages as it cleaves the C-terminus of the polyprotein By similarity. Ref.3 The helicase chain, which contains a zinc finger structure, displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity By similarity. Ref.3
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). ATP + H2O = ADP + phosphate. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Subcellular location	Nsp1: Host nucleus By similarity. Host cytoplasm By similarity. Nsp1-alpha papain-like cysteine proteinase: Host nucleus By similarity. Host cytoplasm By similarity. Nsp1-beta papain-like cysteine proteinase: Host cytoplasm By similarity. Nsp2 cysteine proteinase: Host membrane; Multi-pass membrane protein Potential. Non-structural protein 3: Host membrane; Multi-pass membrane protein Potential. Non-structural protein 5-6-7: Host membrane; Multi-pass membrane protein Potential. 3C-like serine proteinase: Host cytoplasm Potential. RNA-directed RNA polymerase: Host cytoplasm › host perinuclear region Potential. Helicase: Host cytoplasm › host perinuclear region Potential.
Domain	The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane By similarity. The OTU-like region is responsible for the deubiquitinating and deISGylation activities of Nsp2 Probable.
Post-translational modification	Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. Nsp1 is autocleaved into two subunits, Nsp1-alpha and Nsp1-beta. There are two alternative pathways for processing. Either nsp4-5 is cleaved, which represents the major pathway or the nsp5-6 and nsp6-7 are processed, which represents the minor pathway. The major pathway occurs when nsp2 acts as cofactor for nsp4 By similarity.
Sequence similarities	Belongs to the arteriviridae polyprotein family. Contains 1 (+)RNA virus helicase ATP-binding domain. Contains 1 (+)RNA virus helicase C-terminal domain. Contains 1 AV MBD (arterivirus metal-binding) domain. Contains 1 peptidase C31 domain. Contains 1 peptidase C32 domain. Contains 1 peptidase C33 domain. Contains 1 peptidase S32 domain. Contains 1 RdRp catalytic domain.
Sequence caution	The sequence AAR37017.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Host-virus interaction Inhibition of host ISG15 by virus Inhibition of host NF-kappa-B by virus Inhibition of host STAT1 by virus Inhibition of host innate immune response by virus Inhibition of host interferon signaling pathway by virus Modulation of host ubiquitin pathway by viral deubiquitinase Modulation of host ubiquitin pathway by virus Viral RNA replication Viral immunoevasion
Cellular component	Host cytoplasm Host membrane Host nucleus Membrane
Coding sequence diversity	Ribosomal frameshifting
Domain	Transmembrane Transmembrane helix Zinc-finger
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Serine protease Thiol protease Transferase
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological_process	modulation by virus of host protein ubiquitination Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host ISG15 activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host NF-kappaB transcription factor activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host STAT1 activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon-mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro viral protein processing Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell host cell perinuclear region of cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro helicase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW serine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Isoform Replicase polyprotein 1ab (identifier: A0MD28-1)

Also known as: pp1ab;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Produced by -1 ribosomal frameshifting at the 1a-1b genes boundary.

Isoform Replicase polyprotein 1a (identifier: A0MD28-2)

Also known as: pp1a; ORF1a polyprotein;

The sequence of this isoform differs from the canonical sequence as follows:
     2380-3838: Missing.

Note: Produced by conventional translation.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 3838	3838	Replicase polyprotein 1ab By similarity		PRO_0000397084
	Chain	1 – 384	384	Nsp1 By similarity		PRO_0000410830
	Chain	1 – 180	180	Nsp1-alpha papain-like cysteine proteinase Potential		PRO_0000397085
	Chain	181 – 385	205	Nsp1-beta papain-like cysteine proteinase Potential		PRO_0000397086
	Chain	386 – 1446	1061	Nsp2 cysteine proteinase By similarity		PRO_0000397087
	Chain	1447 – 1676	230	Non-structural protein 3 By similarity		PRO_0000397088
	Chain	1677 – 1879	203	3C-like serine proteinase By similarity		PRO_0000397089
	Chain	1880 – 2334	455	Non-structural protein 5-6-7 By similarity		PRO_0000397090
	Chain	2335 – 3020	686	RNA-directed RNA polymerase By similarity		PRO_0000397091
	Chain	2335 – 2379	45	Non-structural protein 8 By similarity		PRO_0000397092
	Chain	3021 – 3462	442	Helicase By similarity		PRO_0000397093
	Chain	3463 – 3686	224	Non-structural protein 11 By similarity		PRO_0000397094
	Chain	3687 – 3838	152	Non-structural protein 12 By similarity		PRO_0000397095
Regions
	Transmembrane	1094 – 1114	21	Helical; Potential
	Transmembrane	1117 – 1137	21	Helical; Potential
	Transmembrane	1162 – 1182	21	Helical; Potential
	Transmembrane	1211 – 1231	21	Helical; Potential
	Transmembrane	1235 – 1255	21	Helical; Potential
	Transmembrane	1450 – 1470	21	Helical; Potential
	Transmembrane	1526 – 1546	21	Helical; Potential
	Transmembrane	1556 – 1576	21	Helical; Potential
	Transmembrane	1592 – 1612	21	Helical; Potential
	Transmembrane	1875 – 1895	21	Helical; Potential
	Transmembrane	1916 – 1936	21	Helical; Potential
	Transmembrane	1960 – 1980	21	Helical; Potential
	Transmembrane	2003 – 2023	21	Helical; Potential
	Transmembrane	2029 – 2048	20	Helical; Potential
	Domain	69 – 180	112	Peptidase C31
	Domain	269 – 385	117	Peptidase C32
	Domain	420 – 527	108	Peptidase C33
	Domain	1677 – 1879	203	Peptidase S32
	Domain	2765 – 2899	135	RdRp catalytic
	Domain	3021 – 3084	64	AV MBD
	Domain	3134 – 3293	160	(+)RNA virus helicase ATP-binding
	Domain	3294 – 3423	130	(+)RNA virus helicase C-terminal
	Zinc finger	8 – 28	21	C4-type; atypical
	Nucleotide binding	3168 – 3175	8	ATP By similarity
	Region	69 – 182	114	PCP1-alpha By similarity
	Region	269 – 384	116	PCP1-beta By similarity
	Region	418 – 505	88	OTU-like
	Region	1132 – 1255	124	HD1 By similarity
	Region	1310 – 1334	25	WCCH By similarity
	Region	1451 – 1612	162	HD2 By similarity
	Region	1902 – 2023	122	HD3 By similarity
Sites
	Active site	76	1	For Nsp1-alpha papain-like cysteine proteinase activity By similarity
	Active site	146	1	For Nsp1-alpha papain-like cysteine proteinase activity By similarity
	Active site	276	1	For Nsp1-beta papain-like cysteine proteinase activity By similarity
	Active site	345	1	For Nsp1-beta papain-like cysteine proteinase activity By similarity
	Active site	429	1	For Nsp2 cysteine proteinase activity By similarity
	Active site	498	1	For Nsp2 cysteine proteinase activity By similarity
	Active site	1715	1	Charge relay system; for 3C-like serine proteinase activity By similarity
	Active site	1740	1	Charge relay system; for 3C-like serine proteinase activity By similarity
	Active site	1793	1	Charge relay system; for 3C-like serine proteinase activity By similarity
	Site	180 – 181	2	Cleavage; by autolysis Potential
	Site	385 – 386	2	Cleavage; by autolysis By similarity
	Site	1446 – 1447	2	Cleavage; by CP2 Potential
	Site	1676 – 1677	2	Cleavage; by 3CLSP By similarity
	Site	1879 – 1880	2	Cleavage; by 3CLSP By similarity
	Site	2049 – 2050	2	Cleavage; by 3CLSP By similarity
	Site	2065 – 2066	2	Cleavage; by 3CLSP By similarity
	Site	2334 – 2335	2	Cleavage; by 3CLSP By similarity
	Site	3020 – 3021	2	Cleavage; by 3CLSP By similarity
	Site	3071	1	Involved in mRNA transcription process By similarity
	Site	3462 – 3463	2	Cleavage; by 3CLSP By similarity
	Site	3686 – 3687	2	Cleavage; by 3CLSP By similarity
Natural variations
	Alternative sequence	2380 – 3838	1459	Missing in isoform Replicase polyprotein 1a.		VSP_039634
	Natural variant	666	1	R → Q in strain: Infectious clone SD 01-08.
	Natural variant	1005	1	R → K in strain: Infectious clone SD 01-08.
	Natural variant	1012	1	N → S in strain: Infectious clone SD 01-08.
	Natural variant	3092	1	P → L in strain: Infectious clone SD 01-08.
	Natural variant	3682	1	Y → H in strain: Infectious clone SD 01-08.
Experimental info
	Mutagenesis	429	1	C → A: Lethal. Ref.3
	Mutagenesis	458	1	D → A: Slight reduction in the ability of Nsp2 to impair NF-kappaB activation. Ref.3
	Mutagenesis	462	1	S → A: Reduction in the ability of Nsp2 to impair NF-kappaB activation. Ref.3
	Mutagenesis	463	1	D → A: Lethal. Ref.3
	Mutagenesis	465	1	D → A: Reduction in the ability of Nsp2 to impair NF-kappaB activation. Ref.3
	Mutagenesis	498	1	H → A: Lethal. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Replicase polyprotein 1ab (pp1ab) [UniParc]. Last modified August 10, 2010. Version 2. Checksum: 07ADB34E6578FFC9	FASTA	3,838	418,948
	10 20 30 40 50 60 MSGTFSRCMC TPAARVFWNA GQVFCTRCLS ARPLLSPELQ DTDLGVVGLF YKPKDKIHWK 70 80 90 100 110 120 VPIGIPQVEC TPSGCCWLSA VFPLARMTSG NHNFLQRLVK VADVLYRDGC LAPRHLRELQ 130 140 150 160 170 180 VYERGCSWYP ITGPVPGMGL FANSMHVSDQ PFPGATHVLT NSPLPQRACR QPFCPFEEAH 190 200 210 220 230 240 SDVYRWKKFV IFTDSSPNGR FRMMWTPESD DSAALEVLPP ELERQVEILT RSFPAHHPIN 250 260 270 280 290 300 LADWELTESP ENGFSFGTSH SCGHIVQNPN VFDGKCWLTC FLGQSAEVCY HEEHLANALG 310 320 330 340 350 360 YQTKWGVHGK YLQRRLQVRG MRAVVDPDGP IHVEALSCSQ SWVRHLTLNN DVTPGFVRLT 370 380 390 400 410 420 SIRIVSNTEP TAFRIFRFGA HKWYGAAGKR ARAKRATKSG KDSALAPKIA PPVPTCGITT 430 440 450 460 470 480 YSPPTDGSCG WHVLAAIVNR MINGDFTSPL PQYNRPEDDW ASDYDLAQAI QCLQLPATVV 490 500 510 520 530 540 RNRACPNAKY LIKLNGVHWE VEVRSGMAPR SLSRECVVGV CSEGCVAPPY PADGLPKRAL 550 560 570 580 590 600 EALASAYRLP SDCVSSGIAD FLADPPPQEF WTLDKMLTSP SPERSGFSSL YKLLLEVVPQ 610 620 630 640 650 660 KCGATEGAFV YAVERMLKDC PSPEQAMALL AKIKVPSSKA PSVSLDECFP AGVPADFEPA 670 680 690 700 710 720 FQERPRSPGA AVALCSPDAK GFEGTASEEA QESGHKAVHA VPLAEGPNNE QVQVVAGEQL 730 740 750 760 770 780 ELGGCGLAIG SAQSSSDSKR ENMHNSREDE PLDLSHPAPA ATTTLVGEQT PDNPGSDASA 790 800 810 820 830 840 LPIAVRGFVP TGPILRHVEH CGTESGDSSS PLDLSFAQTL DQPLDLSLAA WPVKATASDP 850 860 870 880 890 900 GWVRGRCEPV FLKPRKAFSD GDSALQFGEL SESSSVIEFD QTKDTLVADA PVDLTTSNEA 910 920 930 940 950 960 LSAVDPSEFV ELRRPRHSAQ ALIDRGGPLA DVHAKIKNRV YEQCLQACEP GSRATPATRE 970 980 990 1000 1010 1020 WLDKMWDRVD MKTWRCTSQF QAGRILASLK FLPDMIQDTP PPVPRKNRAS DNAGLKQLVA 1030 1040 1050 1060 1070 1080 RWDKKLSVTP PPKSAGLVLD QTVPPPTDIQ QEDATPSDGL SHASDFSSRV STSWSWKGLM 1090 1100 1110 1120 1130 1140 LSGTRLAGSA GQRLMTWVFE VYSHLPAFIL TLFSPRGSMA PGDWLFAGVV LLALLLCRSY 1150 1160 1170 1180 1190 1200 PILGCLPLLG VFSGSLRRVR LGVFGSWMAF AVFLFSTPSN PVGSSCDHDS PECHAELLAL 1210 1220 1230 1240 1250 1260 EQRQLWEPVR GLVVGPSGLL CVILGKLLGG SRHLWHVILR LCMLTDLALS LVYVVSQGRC 1270 1280 1290 1300 1310 1320 HKCWGKCIRT APAEVALNVF PFSRATRNSL TSLCDRFQTP KGVDPVHLAT GWRGCWRGES 1330 1340 1350 1360 1370 1380 PIHQPHQKPI AYANLDEKKI SAQTVVAVPY DPSQAIKCLK VLQAGGAIVD QPTPEVVRVS 1390 1400 1410 1420 1430 1440 EIPFSAPFFP KVPVNPDCRI VVDSDTFVAA VRCGYSTAQL VLGRGNFAKL NQTPLRDSAS 1450 1460 1470 1480 1490 1500 TKTTGGASYT LAVAQVSVWT LVHFILGLWF TSPQVCGRGT ADPWCSNPFS YPAYGPGVVC 1510 1520 1530 1540 1550 1560 SSRLCVSADG VTLPLFSAVA QLSGREVGIF ILVLVSLTAL AHRLALKADM LVVFSAFCAY 1570 1580 1590 1600 1610 1620 AWPMSSWLIC FFPILLKWVT LHPLTMLWVH SFLVFCMPAA GILSLGITGL LWAVGRFTQV 1630 1640 1650 1660 1670 1680 AGIITPYDIH QYTSGPRGAA AVATAPEGTY MAAVRRAALT GRTLIFTPSA VGSLLEGAFR 1690 1700 1710 1720 1730 1740 THKPCLNTVN VVGSSLGSGG VFTIDGRKTV VTAAHVLNGD TARVTGDSYN RMHTFKTSGD 1750 1760 1770 1780 1790 1800 YAWSHADDWQ GVAPVVKVAK GYRGRAYWQT STGVEPGVIG EGFAFCFTNC GDSGSPVISE 1810 1820 1830 1840 1850 1860 SGDLIGIHTG SNKLGSGLVT TPEGETCAIK ETKLSDLSRH FAGPSVPLGD IKLSPAIVPD 1870 1880 1890 1900 1910 1920 VTSIPSDLAS LLASVPVMEG GLSTVQLLCV FFLLWRMMGH AWTPIVAVGF FLLNEILPAV 1930 1940 1950 1960 1970 1980 LVRAVFSFAL FILAWATPWS AQVLMIRLLT ASLNRNKLSL AFYALGGVVG LAAEIGAFAG 1990 2000 2010 2020 2030 2040 RLPELSQALS TYCFLPRVLA MASYVPIIII GGLHALGVIL WLFKYRCLHN MLVGDGSFSS 2050 2060 2070 2080 2090 2100 AFFLRYFAEG NLRKGVSQSC GMSNESLTAA LACKLSQADL DFLSSLTNFK CFVSASNMKN 2110 2120 2130 2140 2150 2160 AAGQYIEAAY AKALRQELAS LVQVDKMKGI LSKLEAFAET ATPSLDAGDV VVLLGQHPHG 2170 2180 2190 2200 2210 2220 SILDINVGTE RKTVSVQETR SLGGSKFSVC TVVSNTPVDA LTGIPLQTPT PLFENGPRHR 2230 2240 2250 2260 2270 2280 GEEDDLRVER MKKHCVSLGF HNINGKVYCK IWDKSTGDTF YTDDSRYTQD LAFQDRSADY 2290 2300 2310 2320 2330 2340 RDRDYEGVQT APQQGFDPKS ETPIGTVVIG GITYNRYLIK GKEVLVPKPD NCLEAAKLSL 2350 2360 2370 2380 2390 2400 EQALAGMGQT CDLTAAEVEK LRRIISQLQG LTTEQALNCL LAASGLTRCG RGGLVVTETA 2410 2420 2430 2440 2450 2460 VKIVKYHSRT FTLGPLDLKV TSEAEVKKST EQGHAVVANL CSGVILMRPH PPSLVDVLLK 2470 2480 2490 2500 2510 2520 PGLDTKPGIQ PGHGAGNMGV DGSTWDFETA PTKAELELSK QIIQACEVRR GDAPNLQLPY 2530 2540 2550 2560 2570 2580 KLYPVRGDPE RHGGRLINTR FGDLSYKTPQ DTKSAIHAAC CLHPNGAPVS DGKSTLGTTL 2590 2600 2610 2620 2630 2640 QHGFELYVPT VPYSVMEYLD SRPDTPFMCT KHGTSKAAAE DLQKYDLSTQ GFVLPGVLRL 2650 2660 2670 2680 2690 2700 VRRFIFGHIG KAPPLFLPST YPAKNSMAGI NGQRFPTKDV QSIPEIDEMC ARAVKENWQT 2710 2720 2730 2740 2750 2760 VTPCTLKKQY CSKPKTRTIL GTNNFIALAH RSALSGVTQA FMKKAWKSPI ALGKNKFKEL 2770 2780 2790 2800 2810 2820 HCTVAGRCLE ADLASCDRST PAIVRWFVAN LLYELAGCEE YLPSYVLNCC HDLVATQDGA 2830 2840 2850 2860 2870 2880 FTKRGGLSSG DPVTSVSNTV YSLIIYAQHM VLSALKMGHE IGLKFLEEQL KFEDLLEIQP 2890 2900 2910 2920 2930 2940 MLVYSDDLVL YAERPTFPNY HWWVEHLDLM LGFRTDPKKT VITDKPSFLG CRIEAGRQLV 2950 2960 2970 2980 2990 3000 PNRDRILAAL AYHMKAQNAS EYYASAAAIL MDSCACIDHD PEWYEDLICG IARCARQDGY 3010 3020 3030 3040 3050 3060 SFPGPAFFMS MWEKLRSHNE GKKFRHCGIC DAKADHASAC GLDLCLFHSH FHQHCPVTLS 3070 3080 3090 3100 3110 3120 CGHHAGSREC SQCQSPVGAG RSPLDAVLKQ IPYKPPRTVI MKVGNKTTAL DPGRYQSRRG 3130 3140 3150 3160 3170 3180 LVAVKRGIAG NEVDLPDGDY QVVPLLPTCK DINMVKVACN VLLSKFIVGP PGSGKTTWLL 3190 3200 3210 3220 3230 3240 SQVQDDDVIY TPTHQTMFDI VSALKVCRYS IPGASGLPFP PPARSGPWVR LVASGHVPGR 3250 3260 3270 3280 3290 3300 TSYLDEAGYC NHLDILRLLS KTPLVCLGDL QQLHPVGFDS YCYVFDQMPQ KQLTTIYRFG 3310 3320 3330 3340 3350 3360 PNICAAIQPC YREKLESKAR NTRVVFTTWP VAFGQVLTPY HKDRIGSAIT IDSSQGATFD 3370 3380 3390 3400 3410 3420 IVTLHLPSPK SLNKSRALVA ITRARHGLFI YDPHNQLQEF FNLIPERTDC NLVFSRGDDL 3430 3440 3450 3460 3470 3480 VVLSADNAVT TVAKALGTGP SRFRVSDPRC KSLLAACSAS LEGSCMPLPQ VAHNLGFYFS 3490 3500 3510 3520 3530 3540 PDSPAFAPLP KELAPHWPVV THQNNRAWPD RLVASMRPID ARYSKPMVGA GYVVGPSTFL 3550 3560 3570 3580 3590 3600 GTPGVVSYYL TLYIRGEPQA LPETLVSTGR IATDCREYLD AAEEEAAKEL PHAFIGDVKG 3610 3620 3630 3640 3650 3660 TTVGGCHHIT SKYLPRTLPK DSVAVVGVSS PGRAAKAMCT LTDVYLPELR PYLQPETASK 3670 3680 3690 3700 3710 3720 CWKLKLDFRD VRLMVWKGAT AYFQLEGLTW SALPDYARFI QLPKDAVVYI DPCIGPATAN 3730 3740 3750 3760 3770 3780 RKVVRTTDWR ADLAVTPYDY GAQNILTTAW FEDLGPQWKI LGLQPFRRAF GFENTEDWAI 3790 3800 3810 3820 3830 LARRMSDGKD YTDYNWDCVR ERPHAIYGRA RDHTYHFAPG TELQVELGKP RLPPGREP
	Isoform Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [UniParc]. Checksum: 6CAC6C94BDABDF8D	FASTA	2,379	257,784
	10 20 30 40 50 60 MSGTFSRCMC TPAARVFWNA GQVFCTRCLS ARPLLSPELQ DTDLGVVGLF YKPKDKIHWK 70 80 90 100 110 120 VPIGIPQVEC TPSGCCWLSA VFPLARMTSG NHNFLQRLVK VADVLYRDGC LAPRHLRELQ 130 140 150 160 170 180 VYERGCSWYP ITGPVPGMGL FANSMHVSDQ PFPGATHVLT NSPLPQRACR QPFCPFEEAH 190 200 210 220 230 240 SDVYRWKKFV IFTDSSPNGR FRMMWTPESD DSAALEVLPP ELERQVEILT RSFPAHHPIN 250 260 270 280 290 300 LADWELTESP ENGFSFGTSH SCGHIVQNPN VFDGKCWLTC FLGQSAEVCY HEEHLANALG 310 320 330 340 350 360 YQTKWGVHGK YLQRRLQVRG MRAVVDPDGP IHVEALSCSQ SWVRHLTLNN DVTPGFVRLT 370 380 390 400 410 420 SIRIVSNTEP TAFRIFRFGA HKWYGAAGKR ARAKRATKSG KDSALAPKIA PPVPTCGITT 430 440 450 460 470 480 YSPPTDGSCG WHVLAAIVNR MINGDFTSPL PQYNRPEDDW ASDYDLAQAI QCLQLPATVV 490 500 510 520 530 540 RNRACPNAKY LIKLNGVHWE VEVRSGMAPR SLSRECVVGV CSEGCVAPPY PADGLPKRAL 550 560 570 580 590 600 EALASAYRLP SDCVSSGIAD FLADPPPQEF WTLDKMLTSP SPERSGFSSL YKLLLEVVPQ 610 620 630 640 650 660 KCGATEGAFV YAVERMLKDC PSPEQAMALL AKIKVPSSKA PSVSLDECFP AGVPADFEPA 670 680 690 700 710 720 FQERPRSPGA AVALCSPDAK GFEGTASEEA QESGHKAVHA VPLAEGPNNE QVQVVAGEQL 730 740 750 760 770 780 ELGGCGLAIG SAQSSSDSKR ENMHNSREDE PLDLSHPAPA ATTTLVGEQT PDNPGSDASA 790 800 810 820 830 840 LPIAVRGFVP TGPILRHVEH CGTESGDSSS PLDLSFAQTL DQPLDLSLAA WPVKATASDP 850 860 870 880 890 900 GWVRGRCEPV FLKPRKAFSD GDSALQFGEL SESSSVIEFD QTKDTLVADA PVDLTTSNEA 910 920 930 940 950 960 LSAVDPSEFV ELRRPRHSAQ ALIDRGGPLA DVHAKIKNRV YEQCLQACEP GSRATPATRE 970 980 990 1000 1010 1020 WLDKMWDRVD MKTWRCTSQF QAGRILASLK FLPDMIQDTP PPVPRKNRAS DNAGLKQLVA 1030 1040 1050 1060 1070 1080 RWDKKLSVTP PPKSAGLVLD QTVPPPTDIQ QEDATPSDGL SHASDFSSRV STSWSWKGLM 1090 1100 1110 1120 1130 1140 LSGTRLAGSA GQRLMTWVFE VYSHLPAFIL TLFSPRGSMA PGDWLFAGVV LLALLLCRSY 1150 1160 1170 1180 1190 1200 PILGCLPLLG VFSGSLRRVR LGVFGSWMAF AVFLFSTPSN PVGSSCDHDS PECHAELLAL 1210 1220 1230 1240 1250 1260 EQRQLWEPVR GLVVGPSGLL CVILGKLLGG SRHLWHVILR LCMLTDLALS LVYVVSQGRC 1270 1280 1290 1300 1310 1320 HKCWGKCIRT APAEVALNVF PFSRATRNSL TSLCDRFQTP KGVDPVHLAT GWRGCWRGES 1330 1340 1350 1360 1370 1380 PIHQPHQKPI AYANLDEKKI SAQTVVAVPY DPSQAIKCLK VLQAGGAIVD QPTPEVVRVS 1390 1400 1410 1420 1430 1440 EIPFSAPFFP KVPVNPDCRI VVDSDTFVAA VRCGYSTAQL VLGRGNFAKL NQTPLRDSAS 1450 1460 1470 1480 1490 1500 TKTTGGASYT LAVAQVSVWT LVHFILGLWF TSPQVCGRGT ADPWCSNPFS YPAYGPGVVC 1510 1520 1530 1540 1550 1560 SSRLCVSADG VTLPLFSAVA QLSGREVGIF ILVLVSLTAL AHRLALKADM LVVFSAFCAY 1570 1580 1590 1600 1610 1620 AWPMSSWLIC FFPILLKWVT LHPLTMLWVH SFLVFCMPAA GILSLGITGL LWAVGRFTQV 1630 1640 1650 1660 1670 1680 AGIITPYDIH QYTSGPRGAA AVATAPEGTY MAAVRRAALT GRTLIFTPSA VGSLLEGAFR 1690 1700 1710 1720 1730 1740 THKPCLNTVN VVGSSLGSGG VFTIDGRKTV VTAAHVLNGD TARVTGDSYN RMHTFKTSGD 1750 1760 1770 1780 1790 1800 YAWSHADDWQ GVAPVVKVAK GYRGRAYWQT STGVEPGVIG EGFAFCFTNC GDSGSPVISE 1810 1820 1830 1840 1850 1860 SGDLIGIHTG SNKLGSGLVT TPEGETCAIK ETKLSDLSRH FAGPSVPLGD IKLSPAIVPD 1870 1880 1890 1900 1910 1920 VTSIPSDLAS LLASVPVMEG GLSTVQLLCV FFLLWRMMGH AWTPIVAVGF FLLNEILPAV 1930 1940 1950 1960 1970 1980 LVRAVFSFAL FILAWATPWS AQVLMIRLLT ASLNRNKLSL AFYALGGVVG LAAEIGAFAG 1990 2000 2010 2020 2030 2040 RLPELSQALS TYCFLPRVLA MASYVPIIII GGLHALGVIL WLFKYRCLHN MLVGDGSFSS 2050 2060 2070 2080 2090 2100 AFFLRYFAEG NLRKGVSQSC GMSNESLTAA LACKLSQADL DFLSSLTNFK CFVSASNMKN 2110 2120 2130 2140 2150 2160 AAGQYIEAAY AKALRQELAS LVQVDKMKGI LSKLEAFAET ATPSLDAGDV VVLLGQHPHG 2170 2180 2190 2200 2210 2220 SILDINVGTE RKTVSVQETR SLGGSKFSVC TVVSNTPVDA LTGIPLQTPT PLFENGPRHR 2230 2240 2250 2260 2270 2280 GEEDDLRVER MKKHCVSLGF HNINGKVYCK IWDKSTGDTF YTDDSRYTQD LAFQDRSADY 2290 2300 2310 2320 2330 2340 RDRDYEGVQT APQQGFDPKS ETPIGTVVIG GITYNRYLIK GKEVLVPKPD NCLEAAKLSL 2350 2360 2370 EQALAGMGQT CDLTAAEVEK LRRIISQLQG LTTEQALNC

References

[1]	"Heterogeneity in Nsp2 of European-like porcine reproductive and respiratory syndrome viruses isolated in the United States." Fang Y., Kim D.Y., Ropp S., Steen P., Christopher-Hennings J., Nelson E.A., Rowland R.R. Virus Res. 100:229-235(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region." Fang Y., Rowland R.R., Roof M., Lunney J.K., Christopher-Hennings J., Nelson E.A. J. Virol. 80:11447-11455(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Infectious clone SD 01-08.
[3]	"The cysteine protease domain of porcine reproductive and respiratory syndrome virus nonstructural protein 2 possesses deubiquitinating and interferon antagonism functions." Sun Z., Chen Z., Lawson S.R., Fang Y. J. Virol. 84:7832-7846(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF NSP2 IN DEUBIQUITINATION, MUTAGENESIS OF CYS-429; ASP-458; SER-462; ASP-463; ASP-465 AND HIS-498.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY375474 Genomic RNA. Translation: AAR37016.1. AY375474 Genomic RNA. Translation: AAR37017.1. Different initiation. DQ489311 Genomic RNA. Translation: ABF66340.1. DQ489311 Genomic RNA. Translation: ABF66341.1.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR027351. (+)RNA_virus_helicase_core_dom. IPR008743. Arterivirus_Nsp2_C33. IPR023338. Arterivirus_NSP4_peptidase. IPR027355. AV_MBD_dom. IPR008741. AV_PCPalpha. IPR025773. AV_PCPbeta. IPR008760. EAV_peptidase_S32. IPR027417. P-loop_NTPase. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009003. Trypsin-like_Pept_dom. [Graphical view]
Pfam	PF05410. Peptidase_C31. 1 hit. PF05411. Peptidase_C32. 1 hit. PF05412. Peptidase_C33. 1 hit. PF05579. Peptidase_S32. 1 hit. PF00680. RdRP_1. 1 hit. PF01443. Viral_helicase1. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit. SSF52540. SSF52540. 1 hit.
PROSITE	PS51538. AV_CP. 1 hit. PS51652. AV_MBD. 1 hit. PS51493. AV_NSP4_PRO. 1 hit. PS51539. AV_PCP_ALPHA. 1 hit. PS51540. AV_PCP_BETA. 1 hit. PS51657. PSRV_HELICASE. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPOA_PRRSS

Accession

Primary (citable) accession number: A0MD28
Secondary accession number(s): A0MD29, Q6U9W7, Q6U9W8

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 10, 2010
Last sequence update:	August 10, 2010
Last modified:	May 29, 2013
This is version 31 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program