PA - Polymerase acidic protein - Influenza A virus (strain A/Malaysia:Malaya/302/1954 H1N1)

Functionⁱ

Plays an essential role in viral RNA transcription and replication by forming the heterotrimeric polymerase complex together with PB1 and PB2 subunits. The complex transcribes viral mRNAs by using a unique mechanism called cap-snatching. It consists in the hijacking and cleavage of host capped pre-mRNAs. These short capped RNAs are then used as primers for viral mRNAs. The PB2 subunit is responsible for the binding of the 5' cap of cellular pre-mRNAs which are subsequently cleaved after 10-13 nucleotides by the PA subunit that carries the endonuclease activity.UniRule annotation

Cofactorⁱ

Mn²⁺UniRule annotationNote: Binds 2 manganese ions per subunit.UniRule annotation

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	41	Manganese 1; via tele nitrogenUniRule annotation	1
Metal bindingⁱ	80	Manganese 2UniRule annotation	1
Metal bindingⁱ	108	Manganese 1UniRule annotation	1
Metal bindingⁱ	108	Manganese 2UniRule annotation	1
Metal bindingⁱ	119	Manganese 1UniRule annotation	1
Metal bindingⁱ	120	Manganese 1; via carbonyl oxygenUniRule annotation	1

GO - Molecular functionⁱ

endonuclease activity Source: UniProtKB-KW
metal ion binding Source: UniProtKB-KW
RNA binding Source: InterPro

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

cap snatching Source: UniProtKB-KW
suppression by virus of host RNA polymerase II activity Source: UniProtKB-KW
viral RNA genome replication Source: InterPro

View the complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Endonuclease, Hydrolase, Nuclease
Biological process	Cap snatching, Eukaryotic host gene expression shutoff by virus, Eukaryotic host transcription shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Inhibition of host RNA polymerase II by virus
Ligand	Manganese, Metal-binding

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Polymerase acidic proteinUniRule annotation (EC:3.1.-.-UniRule annotation) Alternative name(s): RNA-directed RNA polymerase subunit P2UniRule annotation
Gene namesⁱ	Name:PAUniRule annotation
Organismⁱ	Influenza A virus (strain A/Malaysia:Malaya/302/1954 H1N1)
Taxonomic identifierⁱ	425566 [NCBI]
Taxonomic lineageⁱ	Viruses › ssRNA viruses › ssRNA negative-strand viruses › Orthomyxoviridae › Influenzavirus A › Influenza A virus › H1N1 subtype
Virus hostⁱ	Aves [TaxID: 8782] Homo sapiens (Human) [TaxID: 9606] Sus scrofa (Pig) [TaxID: 9823]
Proteomesⁱ	UP000008219 Componentⁱ: Genome

Subcellular locationⁱ

Host cytoplasm
UniRule annotation
Manual assertion according to rulesⁱ
- HAMAP-Rule:MF_04063
Host nucleus
UniRule annotation
Manual assertion according to rulesⁱ
- HAMAP-Rule:MF_04063

Note:

PB1 and PA are transported in the host nucleus as a complex.UniRule annotationBy similarity

GO - Cellular componentⁱ

host cell cytoplasm Source: UniProtKB-SubCell
host cell nucleus Source: UniProtKB-SubCell

View the complete GO annotation on QuickGO ...

Keywords - Cellular componentⁱ

Host cytoplasm, Host nucleus

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
ChainⁱPRO_0000373002	1 – 716	Polymerase acidic proteinAdd BLAST		716

Post-translational modificationⁱ

Phosphorylated on serines and threonines by host kinases, including human casein kinase II.UniRule annotationBy similarity

Keywords - PTMⁱ

Phosphoprotein

Interactionⁱ

Subunit structureⁱ

Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA. Interacts (via C-terminus) with PB1 (via N-terminus).UniRule annotationBy similarity

Structureⁱ

3D structure databases

SMRⁱ	A4K150.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Family & Domainsⁱ

Motif

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Motifⁱ	124 – 139	Nuclear localization signal 1 (NLS1)UniRule annotationBy similarityAdd BLAST		16
Motifⁱ	184 – 247	Nuclear localization signal 2 (NLS2)UniRule annotationBy similarityAdd BLAST		64

Sequence similaritiesⁱ

Belongs to the influenza viruses PA family.UniRule annotation

Phylogenomic databases

Database of Orthologous Groups More...OrthoDBⁱ	VOG0900002P.

OrthoDBⁱ

VOG0900002P.

Family and domain databases

Gene3Dⁱ	3.40.91.90. 1 hit.
HAMAPⁱ	MF_04063. INFV_PA. 1 hit.
InterProⁱ	View protein in InterPro IPR037534. INFV_PA. IPR001009. PA/PA-X. IPR038372. PA/PA-X_sf.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF00603. Flu_PA. 1 hit.

Sequences (2)ⁱ

Sequence statusⁱ: Complete.

This entry describes 2 isoformsⁱ produced by ribosomal frameshifting. Align Add to basket Added to basket

Isoform PA (identifier: A4K150-1) [UniParc]FASTA Add to basket

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.

« Hide

        10         20         30         40         50
MEDFVRQCFN PMIVELAEKA MKEYGENLKI ETNKFAAICT HLEVCFMYSD 
        60         70         80         90        100
FHFINEQGES IIVELDDPNA LLKHRFEIIE GRDRTMAWTV VNSICNTTGA 
       110        120        130        140        150
EKPKFLPDLY DYKENRFIEI GVTRREVHIY YLEKANKIKS EKTHIHIFSF 
       160        170        180        190        200
TGEEMATKAD YTLDEESRAR IKTRLFTIRQ EMASRGLWDS FRQSERGEET 
       210        220        230        240        250
IEERFEITGT MRRLADQSLP PNFSCLENFR AYVDGFEPNG YIEGKLSQMS 
       260        270        280        290        300
KEVNARIEPF LKTTPRPIRL PDGPPCSQRS KFLLMDALKL SIEDPSHEGE 
       310        320        330        340        350
GIPLYDAIKC MRTFFGWKEP YVVKPHEKGI NPNYLLSWKQ VLAELQDIEN 
       360        370        380        390        400
EEKIPRTKNM KKTSQLKWAL GENMAPEKVD FDDCKDISDL KQYDSDEPEL 
       410        420        430        440        450
RSLSSWIQNE FNKACELTDS IWIELDEIGE DVAPIEHIAS MRRNYFTAEV 
       460        470        480        490        500
SHCRATEYIM KGVYINTALL NASCAAMDDF QLIPMISKCR TKEGRRKTNL 
       510        520        530        540        550
YGFIIKGRSH LRNDTDVVNF VSMEFSLTDP RLEPHKWEKY CVLEIGDMLL 
       560        570        580        590        600
RSAIGQVSRP MFLYVRTNGT SKIKMKWGME MRRCLLQSLQ QIESMIEAES 
       610        620        630        640        650
SVKEKDMTKE FFENKSETWP IGESPKGVEE GSIGKVCRTL LAKSVFNSLY 
       660        670        680        690        700
ASPQLEGFSA ESRKLLLIVQ ALRDNLEPGT FDLGGLYEAI EECLINDPWV 
       710 
LLNASWFNSF LTHALR

Length:716

Mass (Da):82,847

Last modified:May 1, 2007 - v1

Checksum:ⁱ1DD9DD8F1CBBBCC3

GO

Isoform PA-X (identifier: P0DJS7-1) [UniParc]FASTA Add to basket

The sequence of this isoform can be found in the external entry P0DJS7.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Length:252

Mass (Da):29,454

GO

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	CY021058 Viral cRNA. Translation: ABO52287.1.

Select the link destinations:
EMBLⁱ
GenBankⁱ
DDBJⁱ

Links Updated

CY021058 Viral cRNA. Translation: ABO52287.1.

Keywords - Coding sequence diversityⁱ

Ribosomal frameshifting

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
A4K150	R9WNC8 Q288T4	Influenza A virus (A/Malaysia/JY2/1954(H1N1)) Influenza A virus (A/Malaysia/1954(H1N1))	716	UniRef100_A4K150	Cluster: Polymerase acidic protein	3

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
A4K150	P03433 I6S6F2 F0TTS3 C3PQG3 B4UPB3 A0A1D8EMV6 J7GS12 C7S277 C7S1X8 I6S677 +47474	Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) Influenza A virus (A/reassortant/X-139(X-31B x New Caledonia/20/1999)(H1N1)) Influenza A virus (A/Puerto Rico/8-CV10/1934(H1N1)) Influenza A virus (A/Puerto Rico/8-SV1/1934(H1N1)) Influenza A virus (A/guineafowl/Hong Kong/WF10_CIP046_RGAO032/1999(H9N1)) Influenza A virus (A/reassortant/IVR-148(Brisbane/59/2007 x Texas/1/1977)(H1N1)) Influenza A virus (A/Nymc X-161B(Puerto Rico/8/1934-Wisconsin/67/2005)(H3N2)) Influenza A virus (A/Puerto Rico/8-1/1934(H1N1)) Influenza A virus (A/reassortant/X-121(Shangdong/9/1993 x Puerto Rico/8/1934)(H3N2)) Influenza A virus (A/Puerto Rico/8-KV7/1934(H1N1)) And more	716	UniRef90_P03433	Cluster: Polymerase acidic protein	47,485

Protein	Similar proteins	Organisms	Length	Cluster ID	Cluster name	Size
A4K150	P03433 I6S6F2 F0TTS3 C3PQG3 B4UPB3 A0A1D8EMV6 J7GS12 C7S277 C7S1X8 I6S677 +47521	Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) Influenza A virus (A/reassortant/X-139(X-31B x New Caledonia/20/1999)(H1N1)) Influenza A virus (A/Puerto Rico/8-CV10/1934(H1N1)) Influenza A virus (A/Puerto Rico/8-SV1/1934(H1N1)) Influenza A virus (A/guineafowl/Hong Kong/WF10_CIP046_RGAO032/1999(H9N1)) Influenza A virus (A/reassortant/IVR-148(Brisbane/59/2007 x Texas/1/1977)(H1N1)) Influenza A virus (A/Nymc X-161B(Puerto Rico/8/1934-Wisconsin/67/2005)(H3N2)) Influenza A virus (A/Puerto Rico/8-1/1934(H1N1)) Influenza A virus (A/reassortant/X-121(Shangdong/9/1993 x Puerto Rico/8/1934)(H3N2)) Influenza A virus (A/Puerto Rico/8-KV7/1934(H1N1)) And more	716	UniRef50_P03433	Cluster: Polymerase acidic protein	47,532

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	CY021058 Viral cRNA. Translation: ABO52287.1.

Select the link destinations:
EMBLⁱ
GenBankⁱ
DDBJⁱ

Links Updated

CY021058 Viral cRNA. Translation: ABO52287.1.

3D structure databases

SMRⁱ	A4K150.
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Phylogenomic databases

Database of Orthologous Groups More...OrthoDBⁱ	VOG0900002P.

OrthoDBⁱ

VOG0900002P.

Family and domain databases

Gene3Dⁱ	3.40.91.90. 1 hit.
HAMAPⁱ	MF_04063. INFV_PA. 1 hit.
InterProⁱ	View protein in InterPro IPR037534. INFV_PA. IPR001009. PA/PA-X. IPR038372. PA/PA-X_sf.
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF00603. Flu_PA. 1 hit.
ProtoNetⁱ	Search...

Entry informationⁱ

Entry nameⁱ	PA_I54A2
Accessionⁱ	A4K150Primary (citable) accession number: A4K150
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	May 5, 2009
	Last sequence update:	May 1, 2007
	Last modified:	March 28, 2018
	This is version 37 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Viral Protein Annotation Program

Miscellaneousⁱ

Keywords - Technical termⁱ

Complete proteome

UniProtKB

UniParc

Help

UniRef

Proteomes

Annotation systems

Supporting data

UniProtKB - A4K150 (PA_I54A2)

Your basket is currently empty. i <p>When browsing through different UniProt proteins, you can use the ‘basket’ to save them, so that you can back to find or analyse them later.<p><a href='/help/basket' target='_top'>More...</a></p>

Polymerase acidic protein

PA

Select a section on the left to see content.

<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

Sites

<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

<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 - Biological processi

<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 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

<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 - Cellular componenti

<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

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<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

3D structure databases

<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

Motif

<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

Phylogenomic databases

Family and domain databases

Sequence databases

<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

3D structure databases

Protocols and materials databases

Phylogenomic databases

Family and domain databases

<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 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

Your basket is currently empty. ⁱ

Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

GO - Cellular componentⁱ

PTM / Processingⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ