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Entry version 130 (02 Jun 2021)
Sequence version 3 (10 Aug 2010)
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Protein

Replicase polyprotein 1ab

Gene

rep

Organism
Porcine reproductive and respiratory syndrome virus (strain 16244B) (PRRSV)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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.

Nsp1 is essential for viral subgenomic mRNA synthesis.

By similarity

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).

By similarity

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. Deubiquitinates host NFKBIA, thereby interfering with NFKBIA degradation and impairing subsequent NF-kappa-B activation (By similarity).

By similarity

The 3C-like serine proteinase chain is responsible for the majority of cleavages as it cleaves the C-terminus of the polyprotein.

By similarity

The helicase chain, which contains a zinc finger structure, displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity.

By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • 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). EC:3.4.19.12

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei76For Nsp1-alpha papain-like cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei146For Nsp1-alpha papain-like cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei270For Nsp1-beta papain-like cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei339For Nsp1-beta papain-like cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei437For Nsp2 cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei506For Nsp2 cysteine proteinase activityPROSITE-ProRule annotation1
Active sitei1848Charge relay system; for 3C-like serine proteinase activityPROSITE-ProRule annotation1
Active sitei1873Charge relay system; for 3C-like serine proteinase activityPROSITE-ProRule annotation1
Active sitei1927Charge relay system; for 3C-like serine proteinase activityPROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi3151Zinc 1PROSITE-ProRule annotation1
Metal bindingi3154Zinc 1PROSITE-ProRule annotation1
Metal bindingi3164Zinc 2PROSITE-ProRule annotation1
Metal bindingi3169Zinc 1PROSITE-ProRule annotation1
Metal bindingi3172Zinc 1PROSITE-ProRule annotation1
Metal bindingi3174Zinc 2PROSITE-ProRule annotation1
Metal bindingi3176Zinc 2PROSITE-ProRule annotation1
Metal bindingi3178Zinc 2PROSITE-ProRule annotation1
Metal bindingi3185Zinc 3PROSITE-ProRule annotation1
Metal bindingi3187Zinc 3PROSITE-ProRule annotation1
Metal bindingi3194Zinc 3PROSITE-ProRule annotation1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei3195Involved in mRNA transcription processBy similarity1
Metal bindingi3197Zinc 3PROSITE-ProRule annotation1
Active sitei3714PROSITE-ProRule annotation1
Active sitei3729PROSITE-ProRule annotation1
Active sitei3758PROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri8 – 28C4-type; atypicalAdd BLAST21
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi3298 – 3305ATPBy similarity8

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionEndonuclease, Helicase, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Serine protease, Thiol protease, Transferase
Biological processHost-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host interferon signaling pathway by virus, Inhibition of host ISG15 by virus, Inhibition of host NF-kappa-B by virus, Inhibition of host STAT1 by virus, Modulation of host ubiquitin pathway by viral deubiquitinase, Modulation of host ubiquitin pathway by virus, Viral immunoevasion, Viral RNA replication
LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Replicase polyprotein 1ab
Alternative name(s):
ORF1ab polyprotein
Cleaved into the following 16 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 (EC:3.4.21.-)
Short name:
3CLSP
Alternative name(s):
Nsp4
Non-structural protein 5-6-7
Short name:
Nsp5-6-7
Non-structural protein 5
Short name:
Nsp5
Non-structural protein 6
Short name:
Nsp6
Non-structural protein 7-alpha
Short name:
Nsp7-alpha
Non-structural protein 7-beta
Short name:
Nsp7-beta
Non-structural protein 8
Short name:
Nsp8
RNA-directed RNA polymerase (EC:2.7.7.48)
Short name:
Pol
Short name:
RdRp
Alternative name(s):
Nsp9
Helicase (EC:3.6.4.12, EC:3.6.4.13)
Short name:
Hel
Alternative name(s):
Nsp10
Non-structural protein 11
Short name:
Nsp11
Non-structural protein 12
Short name:
Nsp12
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rep
ORF Names:1a-1b
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiPorcine reproductive and respiratory syndrome virus (strain 16244B) (PRRSV)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri300561 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesRiboviriaOrthornaviraePisuviricotaPisoniviricetesNidoviralesArnidovirineaeArteriviridaeunclassified Arteriviridae
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiSus scrofa (Pig) [TaxID: 9823]

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei1266 – 1286HelicalSequence analysisAdd BLAST21
Transmembranei1296 – 1316HelicalSequence analysisAdd BLAST21
Transmembranei1345 – 1365HelicalSequence analysisAdd BLAST21
Transmembranei1368 – 1388HelicalSequence analysisAdd BLAST21
Transmembranei1583 – 1603HelicalSequence analysisAdd BLAST21
Transmembranei1650 – 1670HelicalSequence analysisAdd BLAST21
Transmembranei1685 – 1705HelicalSequence analysisAdd BLAST21
Transmembranei1719 – 1739HelicalSequence analysisAdd BLAST21
Transmembranei2012 – 2032HelicalSequence analysisAdd BLAST21
Transmembranei2060 – 2080HelicalSequence analysisAdd BLAST21
Transmembranei2092 – 2112HelicalSequence analysisAdd BLAST21
Transmembranei2137 – 2157HelicalSequence analysisAdd BLAST21
Transmembranei2164 – 2184HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Host cytoplasm, Host membrane, Host nucleus, Membrane

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000366571 – 3961Replicase polyprotein 1abAdd BLAST3961
ChainiPRO_00004108261 – 382Nsp1By similarityAdd BLAST382
ChainiPRO_00000366591 – 180Nsp1-alpha papain-like cysteine proteinaseBy similarityAdd BLAST180
ChainiPRO_0000036660181 – 383Nsp1-beta papain-like cysteine proteinaseBy similarityAdd BLAST203
ChainiPRO_0000036661384 – 1579Nsp2 cysteine proteinaseSequence analysisAdd BLAST1196
ChainiPRO_00000366621580 – 1809Non-structural protein 3By similarityAdd BLAST230
ChainiPRO_00000366631810 – 20133C-like serine proteinaseBy similarityAdd BLAST204
ChainiPRO_00000366642014 – 2458Non-structural protein 5-6-7By similarityAdd BLAST445
ChainiPRO_00004231182014 – 2183Non-structural protein 5By similarityAdd BLAST170
ChainiPRO_00004231192184 – 2199Non-structural protein 6By similarityAdd BLAST16
ChainiPRO_00004231202200 – 2348Non-structural protein 7-alphaBy similarityAdd BLAST149
ChainiPRO_00004231212349 – 2458Non-structural protein 7-betaBy similarityAdd BLAST110
ChainiPRO_00000366652459 – 3144RNA-directed RNA polymeraseBy similarityAdd BLAST686
ChainiPRO_00000366662459 – 2503Non-structural protein 8By similarityAdd BLAST45
ChainiPRO_00000366673145 – 3585HelicaseBy similarityAdd BLAST441
ChainiPRO_00000366683586 – 3808Non-structural protein 11By similarityAdd BLAST223
ChainiPRO_00000366693809 – 3961Non-structural protein 12By similarityAdd BLAST153

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei180 – 181Cleavage; by autolysisBy similarity2
Sitei383 – 384Cleavage; by autolysisBy similarity2
Sitei1579 – 1580Cleavage; by CP2Sequence analysis2
Sitei1809 – 1810Cleavage; by 3CLSPBy similarity2
Sitei2013 – 2014Cleavage; by 3CLSPBy similarity2
Sitei2183 – 2184Cleavage; by 3CLSPBy similarity2
Sitei2199 – 2200Cleavage; by 3CLSPBy similarity2
Sitei2348 – 2349Cleavage; by 3CLSPBy similarity2
Sitei2458 – 2459Cleavage; by 3CLSPBy similarity2
Sitei3144 – 3145Cleavage; by 3CLSPBy similarity2
Sitei3585 – 3586Cleavage; by 3CLSPBy similarity2
Sitei3808 – 3809Cleavage; by 3CLSPBy similarity2

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q9YN02

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

13961
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q9YN02

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini69 – 180Peptidase C31PROSITE-ProRule annotationAdd BLAST112
Domaini263 – 383Peptidase C32PROSITE-ProRule annotationAdd BLAST121
Domaini428 – 535Peptidase C33PROSITE-ProRule annotationAdd BLAST108
Domaini1810 – 2013Peptidase S32PROSITE-ProRule annotationAdd BLAST204
Domaini2488 – 2651NiRANPROSITE-ProRule annotationAdd BLAST164
Domaini2890 – 3024RdRp catalyticPROSITE-ProRule annotationAdd BLAST135
Domaini3145 – 3208AV ZBDPROSITE-ProRule annotationAdd BLAST64
Domaini3265 – 3417(+)RNA virus helicase ATP-bindingAdd BLAST153
Domaini3418 – 3546(+)RNA virus helicase C-terminalAdd BLAST129
Domaini3585 – 3681AV-Nsp11N/CoV-Nsp15MPROSITE-ProRule annotationAdd BLAST97
Domaini3683 – 3805NendoUPROSITE-ProRule annotationAdd BLAST123

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni69 – 182PCP1-alphaAdd BLAST114
Regioni263 – 382PCP1-betaAdd BLAST120
Regioni426 – 513OTU-likeAdd BLAST88
Regioni809 – 862DisorderedSequence analysisAdd BLAST54
Regioni898 – 979DisorderedSequence analysisAdd BLAST82
Regioni1153 – 1213DisorderedSequence analysisAdd BLAST61
Regioni1266 – 1388HD1Add BLAST123
Regioni1583 – 1745HD2Add BLAST163
Regioni2036 – 2157HD3Add BLAST122
Regioni2329 – 2358DisorderedSequence analysisAdd BLAST30

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi825 – 840Basic and acidic residuesSequence analysisAdd BLAST16
Compositional biasi953 – 969Polar residuesSequence analysisAdd BLAST17
Compositional biasi1160 – 1179Basic and acidic residuesSequence analysisAdd BLAST20
Compositional biasi1181 – 1198Polar residuesSequence analysisAdd BLAST18
Compositional biasi2329 – 2346Pro residuesSequence analysisAdd BLAST18

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

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.By similarity

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the arteriviridae polyprotein family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri8 – 28C4-type; atypicalAdd BLAST21

Keywords - Domaini

Transmembrane, Transmembrane helix, Zinc-finger

Family and domain databases

Conserved Domains Database

More...
CDDi
cd21410, 1B_av_Nsp10-like, 1 hit
cd21160, NendoU_av_Nsp11-like, 1 hit
cd21166, NTD_av_Nsp11-like, 1 hit
cd21405, ZBD_av_Nsp10-like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.20.58.950, 1 hit
2.40.10.10, 2 hits
3.30.40.20, 1 hit
3.90.70.60, 1 hit
3.90.70.70, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR027351, (+)RNA_virus_helicase_core_dom
IPR031932, Arteri_nsp7a
IPR038451, Arteri_nsp7a_sf
IPR008743, Arterivirus_Nsp2_C33
IPR023338, Arterivirus_NSP4_peptidase
IPR008741, AV_PCPalpha
IPR038155, AV_PCPalpha_sf
IPR025773, AV_PCPbeta
IPR038154, AV_PCPbeta_sf
IPR023183, Chymotrypsin-like_C
IPR043502, DNA/RNA_pol_sf
IPR008760, EAV_peptidase_S32
IPR037227, EndoU-like
IPR043609, NendoU_nidovirus
IPR044348, NSP10_1B_Av
IPR027355, NSP10_Av_ZBD
IPR044320, NSP11_Av_N
IPR044314, NSP11_NendoU_Av
IPR032855, NSP2-B_epitope
IPR027417, P-loop_NTPase
IPR032785, Pdase_C33_assoc
IPR009003, Peptidase_S1_PA
IPR043504, Peptidase_S1_PA_chymotrypsin
IPR001205, RNA-dir_pol_C
IPR007094, RNA-dir_pol_PSvirus

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF16749, Arteri_nsp7a, 1 hit
PF19215, CoV_NSP15_C, 1 hit
PF14757, NSP2-B_epitope, 1 hit
PF14756, Pdase_C33_assoc, 1 hit
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

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF142877, SSF142877, 1 hit
SSF50494, SSF50494, 1 hit
SSF52540, SSF52540, 2 hits
SSF56672, SSF56672, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51538, AV_CP, 1 hit
PS51961, AV_NSP11N_COV_NSP15M, 1 hit
PS51493, AV_NSP4_PRO, 1 hit
PS51539, AV_PCP_ALPHA, 1 hit
PS51540, AV_PCP_BETA, 1 hit
PS51652, AV_ZBD, 1 hit
PS51958, NENDOU, 1 hit
PS51947, NIRAN, 1 hit
PS51657, PSRV_HELICASE, 1 hit
PS50507, RDRP_SSRNA_POS, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (2)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Isoform Replicase polyprotein 1ab (identifier: Q9YN02-1) [UniParc]FASTAAdd to basket
Also known as: pp1ab

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MSGILDRCTC TPNARVFVAE GQVYCTRCLS ARSLLPLNLQ VSELGVLGLF
60 70 80 90 100
YRPEEPLRWT LPRAFPTVEC SPAGACWLSA IFPIARMTSG NLNFQQRMVR
110 120 130 140 150
VAAEIYRAGQ LTPAVLKALQ VYERGCRWYP IVGPVPGVAV FANSLHVSDK
160 170 180 190 200
PFPGATHVLT NLPLPQRPKP EDFCPFECAM ATVYDIGHDA VMYVAEGKIS
210 220 230 240 250
WAPRGGDEVK FEAVPGELKL IANRLRTSFP PHHAVDMSKF AFTAPGCGVS
260 270 280 290 300
MRVERQHGCL PADTVPEGNC WWSLFDLLPL EVQDKEIRHA NQFGYQTKHG
310 320 330 340 350
VSGKYLQRRL QVNGLRAVTD SNGPIVVQYF SVKESWIRHL KLAGEPSYSG
360 370 380 390 400
FEDLLRIRVE PNTSPLANTE GKIFRFGSHK WYGAGKRARK ARSCATATVA
410 420 430 440 450
GRALSVRETR QAKEHEVAGA DKAEHLKHYS PPAEGNCGWH CISAIANRMV
460 470 480 490 500
NSIFETTLPE RVRPPDDWAT DDDLANAIQI LRLPAALDRN GACTSAKYVL
510 520 530 540 550
KLEGEHWTVT VTPGMSPSLL PLECVQGCCE HKGGLGSPDA IEVSGFDPAC
560 570 580 590 600
LDWLAEVMHL PSSAIPAALA EMSGDSDRSA SPVTTVWTVS QFFARHSGGN
610 620 630 640 650
HPDQVRLGKI ISLCQVIEDC CCSQNKTNRV TPEEVAAKID LYLRGATNLE
660 670 680 690 700
ECLARLEKAR PPRVIDTSFD WDVVLPGVEA ATQTNKLPQV NQCRALVPVV
710 720 730 740 750
TQKSLDNNSV PLTAFSLANY YYRAQGDEVR HRERLTAVLS KLEEVVREEY
760 770 780 790 800
GLMPTEPGPR PTLPRGLDEL KDQMEEDLLR LANAQATSDM MAWAVEQVDL
810 820 830 840 850
KTWVKNYPRW TPPPPPPKVQ PRKTKPVKSL PERKPVPAPR RKVGPDCGSP
860 870 880 890 900
VSLGGDVPNS WEDLAVSSPL DLPTPPEPAT LSSELVIVSS PQCIFRPATP
910 920 930 940 950
LSEPAPIPAP RGTVSRPVTP LSEPIPVPAP RRKFQQVKRL SSAAAVPLHQ
960 970 980 990 1000
NEPLDLSASS QTEYEASPSA PPQSGGVLGV EGHEAEETLS EISDMSGNIK
1010 1020 1030 1040 1050
PASVSSSSSL SSVEITRPKY SAQAIIDSGG PCSGHLQGVK ETCLSVMREA
1060 1070 1080 1090 1100
CDATKLDDPA TQEWLSRMWD RVDMLTWRNT SVCQAIRTLD GRLKFLPKMI
1110 1120 1130 1140 1150
LETPPPYPCE FVMMPHTPAP SVGAESDLTI GSVATEDVPR ILEKIENVGE
1160 1170 1180 1190 1200
MANQEPSAFS EDKPVDDQLV NDPRISSRRP DESTAAPSAG TGGAGSFTDL
1210 1220 1230 1240 1250
PSSDGADADG GGPFRTAKRK AERLFDQLSR QVFDLVSHLP VFFSRLFHPG
1260 1270 1280 1290 1300
GGYSTGDWGF AAFTLLCLFL CYSYPAFGIA PLLGVFSGTS RRVRMGVFGC
1310 1320 1330 1340 1350
WLAFAVGLFK PVSDPVGAAC EFDSPECRNI LLSFELLKPW DPVRSLVVGP
1360 1370 1380 1390 1400
VGLGLAILGR LLGGARCIWH FLLRLGIVAD CILAGAYVLS QGRCKKCWGS
1410 1420 1430 1440 1450
CIRTAPNEVA FNVFPFTRAT RSSLIDLCDR FCAPKGMDPI FLATGWRGCW
1460 1470 1480 1490 1500
AGRSPIEQPS EKPIAFAQLD EKKITARTVV AQPYDPNQAV KCLRVLQAGG
1510 1520 1530 1540 1550
AMVAEAVPKV VKVSAVPFRA PFFPTGVKVD PDCRVVVDPD TFTAALRSGY
1560 1570 1580 1590 1600
STTNLVLGVG DFAQLNGLKI RQISKPSGGG PHLMAALHVA CSMALHMLTG
1610 1620 1630 1640 1650
IYVTAVGSCG TGTNDPWCAN PFAVPGYGPG SLCTSRLCIS QHGLTLPLTA
1660 1670 1680 1690 1700
LVAGFGIQEI ALVVLIFVSI GGMAHRLSCK ADMLCILLAI ASYVWVPLTW
1710 1720 1730 1740 1750
LLCVFPCWLR CFSLHPLTIL WLVFFLISVN MPSGILAMVL LVSLWLLGRY
1760 1770 1780 1790 1800
TNVAGLVTPY DIHHYTSGPR GVAALATAPD GTYLAAVRRA ALTGRTMLFT
1810 1820 1830 1840 1850
PSQLGSLLEG AFRTRKPSLN TVNVIGSSMG SGGVFTIDGK VKCVTAAHVL
1860 1870 1880 1890 1900
TGNSARVSGV GFNQMLDFDV KGDFAIADCP NWQGAAPKAQ FCADGWTGRA
1910 1920 1930 1940 1950
YWLTSSGVEP GVIGKGFAFC FTACGDSGSP VITEAGELVG VHTGSNKQGG
1960 1970 1980 1990 2000
GIVTRPSGQF CNVAPIKLSE LSEFFAGPKV PLGDVKVGSH IIKDISEVPS
2010 2020 2030 2040 2050
DLCALLAAKP ELEGGLSTVQ LLCVFFLLWR MMGHAWTPLV AVSFFILNEV
2060 2070 2080 2090 2100
LPAVLVRSVF SFGMFVLSWL TPWSAQILMI RLLTAALNRN RWSLAFFSLG
2110 2120 2130 2140 2150
AVTGFVADLA ATQGHPLQAV MNLSTYAFLP RMMVVTSPVP VITCGVVHLL
2160 2170 2180 2190 2200
AIILYLFKYR GLHQILVGDG VFSAAFFLRY FAEGKLREGV SQSCGMNHES
2210 2220 2230 2240 2250
LTGALAMRLN DEDLDFLMKW TDFKCFVSAS NMRNAAGQFI EAAYAKALRV
2260 2270 2280 2290 2300
ELAQLVQVDK VRGVLAKLEA FADTVAPQLS PGDIVVALGH TPVGSIFDLK
2310 2320 2330 2340 2350
VGSTKHTLQA IETRVLAGSK MTVARVVDPT PTPPPAPVPI PLPPKVLENG
2360 2370 2380 2390 2400
PNAWGDEDRL NKKKRRRMEA LGIYVMGGKK YQKFWDKNSG DVFYEEVHNN
2410 2420 2430 2440 2450
TDEWECLRVG DPADFDPEKG TLCGHVTIEN KAYHVYISPS GKKFLVPVNP
2460 2470 2480 2490 2500
ENGRVQWEAA KLSMEQALGM MNVDGELTAK ELEKLKRIID KLQGLTKEQC
2510 2520 2530 2540 2550
LNCLLAASGL TRCGRGGLVV TETAVKIVKF HNRTFTLGPV NLKVASEVEL
2560 2570 2580 2590 2600
KDAVEHNQHP VARPIDGGVV LLRSAVPSLI DVLISGADAS PKLLAHHGPG
2610 2620 2630 2640 2650
NTGIDGTLWD FESEATKEEV ALSAQIIQAC DIRRGDAPKI GLPYKLYPVR
2660 2670 2680 2690 2700
GNPERVKGVL QNTRFGDIPY KTPSDTGSPV HAAACLTPNA TPVTDGRSVL
2710 2720 2730 2740 2750
ATTMPPGFEL YVPTIPASVL DYLDSRPDCP KQLTEHGCED AALKDLSKYD
2760 2770 2780 2790 2800
LSTQGFVLPG VLRLVRKYLF AHVGKCPPVH RPSTYPAKNS MAGINGNRFP
2810 2820 2830 2840 2850
TKDIQSVPEI DVLCAQAVRE NWQTVTPCTL KKQYCGKKKT RTILGTNNFI
2860 2870 2880 2890 2900
ALAHRAALSG VTQGFMKKAF NSPIALGKNK FKELQTSVLG RCLEADLASC
2910 2920 2930 2940 2950
DRSTPAIVRW FAANLLYELA CAEEHLPSYV LNCCHDLLVT QSGAVTKRGG
2960 2970 2980 2990 3000
LSSGDPITSV SNTIYSLVIY AQHMVLSYFK SGHPHGLLFL QDQLKFEDML
3010 3020 3030 3040 3050
KVQPLIVYSD DLVLYAESPT MPNYHWWVEH LNLMLGFQTD PKKTAITDSP
3060 3070 3080 3090 3100
SFLGCRIING RQLVPNRDRI LAALAYHMKA SNVSEYYASA AAILMDSCAC
3110 3120 3130 3140 3150
LEYDPEWFEE LVVGIAQCAR KDGYSFPGTP FFMSMWEKLR SNYEGKKSRV
3160 3170 3180 3190 3200
CGYCGAPAPY ATACGLDVCI YHTHFHQHCP VTIWCGHPAG SGSCSECKSP
3210 3220 3230 3240 3250
VGKGTSPLDE VLEQVPYKPP RTVIMHVEQG LTPLDPGRYQ TRRGLVSVRR
3260 3270 3280 3290 3300
GIRGNEVELP DGDYASTALL PTCKEINMVA VASNVLRSRF IIGPPGAGKT
3310 3320 3330 3340 3350
YWLLQQVQDG DVIYTPTHQT MLDMIRALGT CRFNVPAGTT LQFPVPSRTG
3360 3370 3380 3390 3400
PWVRILAGGW CPGKNSFLDE AAYCNHLDVL RLLSKTTLTC LGDFKQLHPV
3410 3420 3430 3440 3450
GFDSHCYVFD IMPQTQLKTI WRFGQNICDA IQPDYRDKLM SMVNTTRVTY
3460 3470 3480 3490 3500
VEKPVRYGQV LTPYHRDRED DAITIDSSQG ATFDVVTLHL PTKDSLNRQR
3510 3520 3530 3540 3550
ALVAITRARH AIFVYDPHRQ LQGLFDLPAK GTPVNLAVHR DGQLIVLDRN
3560 3570 3580 3590 3600
NKECTVAQAL GNGDKFRATD KRVVDSLRAI CADLEGSSSP LPKVAHNLGF
3610 3620 3630 3640 3650
YFSPDLTQFA KLPVELAPHW PVVTTQNNEK WPDRLVASLR PIHKYSRACI
3660 3670 3680 3690 3700
GAGYMVGPSV FLGTPGVVSY YLTKFVKGEA QLLPETVFST GRIEVDCREY
3710 3720 3730 3740 3750
LDDREREVAA SLPHAFIGDV KGTTVGGCHH VTSRYLPRVL PKESVAVVGV
3760 3770 3780 3790 3800
SSPGKAAKAL CTLTDVYLPD LEAYLHPETQ SKCWKMMLDF KEVRLMVWRD
3810 3820 3830 3840 3850
KTAYFQLEGR YFTWYQLASY ASYIRVPVNS TVYLDPCMGP ALCNRRVVGS
3860 3870 3880 3890 3900
THWGADLAVT PYDYGAKIIL SSAYHGEMPP GYKILACAEF SLDDPVRYKH
3910 3920 3930 3940 3950
TWGFESDTAY LYEFTGNGED WEDYNDAFRA RQEGKIYKAT ATSLKFHFPP
3960
GPVIEPTLGL N
Note: Produced by -1 ribosomal frameshifting at the 1a-1b genes boundary.
Length:3,961
Mass (Da):432,802
Last modified:August 10, 2010 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i111B73F5926C9DB0
GO
Isoform Replicase polyprotein 1a (identifier: Q9YN02-2) [UniParc]FASTAAdd to basket
Also known as: pp1a, ORF1a polyprotein

The sequence of this isoform differs from the canonical sequence as follows:
     2504-3961: Missing.

Note: Produced by conventional translation.Curated
Show »
Length:2,503
Mass (Da):271,602
Checksum:i91175307A4EAB65C
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAC64692 differs from that shown. Reason: Erroneous initiation.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0328902504 – 3961Missing in isoform Replicase polyprotein 1a. CuratedAdd BLAST1458

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AF046869 Genomic RNA Translation: AAC64691.1
AF046869 Genomic RNA Translation: AAC64692.1 Different initiation.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF046869 Genomic RNA Translation: AAC64691.1
AF046869 Genomic RNA Translation: AAC64692.1 Different initiation.

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5EYIX-ray2.16A/B3586-3808[»]
5YLXX-ray2.20C2703-2711[»]
SMRiQ9YN02
ModBaseiSearch...
PDBe-KBiSearch...

Proteomic databases

PRIDEiQ9YN02

Family and domain databases

CDDicd21410, 1B_av_Nsp10-like, 1 hit
cd21160, NendoU_av_Nsp11-like, 1 hit
cd21166, NTD_av_Nsp11-like, 1 hit
cd21405, ZBD_av_Nsp10-like, 1 hit
Gene3Di1.20.58.950, 1 hit
2.40.10.10, 2 hits
3.30.40.20, 1 hit
3.90.70.60, 1 hit
3.90.70.70, 1 hit
InterProiView protein in InterPro
IPR027351, (+)RNA_virus_helicase_core_dom
IPR031932, Arteri_nsp7a
IPR038451, Arteri_nsp7a_sf
IPR008743, Arterivirus_Nsp2_C33
IPR023338, Arterivirus_NSP4_peptidase
IPR008741, AV_PCPalpha
IPR038155, AV_PCPalpha_sf
IPR025773, AV_PCPbeta
IPR038154, AV_PCPbeta_sf
IPR023183, Chymotrypsin-like_C
IPR043502, DNA/RNA_pol_sf
IPR008760, EAV_peptidase_S32
IPR037227, EndoU-like
IPR043609, NendoU_nidovirus
IPR044348, NSP10_1B_Av
IPR027355, NSP10_Av_ZBD
IPR044320, NSP11_Av_N
IPR044314, NSP11_NendoU_Av
IPR032855, NSP2-B_epitope
IPR027417, P-loop_NTPase
IPR032785, Pdase_C33_assoc
IPR009003, Peptidase_S1_PA
IPR043504, Peptidase_S1_PA_chymotrypsin
IPR001205, RNA-dir_pol_C
IPR007094, RNA-dir_pol_PSvirus
PfamiView protein in Pfam
PF16749, Arteri_nsp7a, 1 hit
PF19215, CoV_NSP15_C, 1 hit
PF14757, NSP2-B_epitope, 1 hit
PF14756, Pdase_C33_assoc, 1 hit
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
SUPFAMiSSF142877, SSF142877, 1 hit
SSF50494, SSF50494, 1 hit
SSF52540, SSF52540, 2 hits
SSF56672, SSF56672, 1 hit
PROSITEiView protein in PROSITE
PS51538, AV_CP, 1 hit
PS51961, AV_NSP11N_COV_NSP15M, 1 hit
PS51493, AV_NSP4_PRO, 1 hit
PS51539, AV_PCP_ALPHA, 1 hit
PS51540, AV_PCP_BETA, 1 hit
PS51652, AV_ZBD, 1 hit
PS51958, NENDOU, 1 hit
PS51947, NIRAN, 1 hit
PS51657, PSRV_HELICASE, 1 hit
PS50507, RDRP_SSRNA_POS, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRPOA_PRRS1
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9YN02
Secondary accession number(s): Q9YN01
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 12, 2005
Last sequence update: August 10, 2010
Last modified: June 2, 2021
This is version 130 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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