PA - Polymerase acidic protein - Influenza A virus (strain A/Puerto Rico/8/1934 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 annotation3 Publications

Cofactorⁱ

Mn²⁺UniRule annotation2 PublicationsNote: Binds 2 manganese ions per subunit.UniRule annotation2 Publications

Sites

Feature key	Position(s)	DescriptionActions	Length
Metal bindingⁱ	41	Manganese 1; via tele nitrogenUniRule annotationCombined sources2 Publications	1
Metal bindingⁱ	80	Manganese 2UniRule annotationCombined sources1 Publication	1
Metal bindingⁱ	108	Manganese 1UniRule annotationCombined sources1 Publication	1
Metal bindingⁱ	108	Manganese 2UniRule annotationCombined sources1 Publication	1
Metal bindingⁱ	119	Manganese 1UniRule annotationCombined sources1 Publication	1
Metal bindingⁱ	120	Manganese 1; via carbonyl oxygenUniRule annotationCombined sources2 Publications	1

GO - Molecular functionⁱ

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

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

cap snatching Source: UniProtKB-UniRule
suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity Source: UniProtKB-UniRule
transcription, DNA-templated Source: UniProtKB-UniRule
viral RNA genome replication Source: InterPro

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

Enzyme and pathway databases

BRENDAⁱ	2.7.7.48, 7479
Reactomeⁱ	R-HSA-168255, Influenza Infection R-HSA-168271, Transport of Ribonucleoproteins into the Host Nucleus R-HSA-168275, Entry of Influenza Virion into Host Cell via Endocytosis R-HSA-168288, Fusion of the Influenza Virion to the Host Cell Endosome R-HSA-168298, Release R-HSA-168302, Budding R-HSA-168303, Packaging of Eight RNA Segments R-HSA-168325, Viral Messenger RNA Synthesis R-HSA-168330, Viral RNP Complexes in the Host Cell Nucleus R-HSA-168333, NEP/NS2 Interacts with the Cellular Export Machinery R-HSA-168336, Uncoating of the Influenza Virion R-HSA-192814, vRNA Synthesis R-HSA-192823, Viral mRNA Translation R-HSA-192869, cRNA Synthesis R-HSA-192905, vRNP Assembly

BRENDAⁱ

2.7.7.48, 7479

Reactomeⁱ

R-HSA-168255, Influenza Infection
R-HSA-168271, Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168275, Entry of Influenza Virion into Host Cell via Endocytosis
R-HSA-168288, Fusion of the Influenza Virion to the Host Cell Endosome
R-HSA-168298, Release
R-HSA-168302, Budding
R-HSA-168303, Packaging of Eight RNA Segments
R-HSA-168325, Viral Messenger RNA Synthesis
R-HSA-168330, Viral RNP Complexes in the Host Cell Nucleus
R-HSA-168333, NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-168336, Uncoating of the Influenza Virion
R-HSA-192814, vRNA Synthesis
R-HSA-192823, Viral mRNA Translation
R-HSA-192869, cRNA Synthesis
R-HSA-192905, vRNP Assembly

Protein family/group databases

MEROPS protease database More...MEROPSⁱ	S62.001

MEROPSⁱ

S62.001

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/Puerto Rico/8/1934 H1N1)
Taxonomic identifierⁱ	211044 [NCBI]
Taxonomic lineageⁱ	Viruses › Riboviria › Orthornavirae › Negarnaviricota › Polyploviricotina › Insthoviricetes › Articulavirales › Orthomyxoviridae › Alphainfluenzavirus › Influenza A virus › H1N1 subtype
Virus hostⁱ	Aves [TaxID: 8782] Homo sapiens (Human) [TaxID: 9606] Sus scrofa (Pig) [TaxID: 9823]
Proteomesⁱ	UP000116373 Componentⁱ: Genome UP000170967 Componentⁱ: Genome UP000009255 Componentⁱ: Genome

Subcellular locationⁱ

Note:

PB1 and PA are transported in the host nucleus as a complex.UniRule annotation3 Publications

Keywords - Cellular componentⁱ

Host cytoplasm, Host nucleus

Pathology & Biotechⁱ

Chemistry databases

ChEMBLⁱ	CHEMBL1169598
Drug and drug target database More...DrugBankⁱ	DB13997, Baloxavir marboxil
DrugCentral More...DrugCentralⁱ	P03433

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Graphical view	Length
ChainⁱPRO_0000078796	1 – 716	Polymerase acidic proteinAdd BLAST		716

Post-translational modificationⁱ

Phosphorylated on serines and threonines by host kinases, including human casein kinase II.UniRule annotation1 Publication

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 annotation1 Publication

Binary interactionsⁱ

Hide details

P03433

With	#Exp.	IntAct
M [P03485]	2	EBI-2547616,EBI-2547543
NP [P03466]	3	EBI-2547616,EBI-2547640
PB1 [P03431]	6	EBI-2547616,EBI-2547514

Protein-protein interaction databases

Database of interacting proteins More...DIPⁱ	DIP-43996N
IntActⁱ	P03433, 57 interactors
Molecular INTeraction database More...MINTⁱ	P03433

Chemistry databases

BindingDBⁱ

P03433

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Helixⁱ	1 – 8	Combined sources	8
Helixⁱ	11 – 23	Combined sources	13
Turnⁱ	28 – 30	Combined sources	3
Helixⁱ	32 – 50	Combined sources	19
Turnⁱ	73 – 75	Combined sources	3
Beta strandⁱ	76 – 78	Combined sources	3
Helixⁱ	84 – 98	Combined sources	15
Beta strandⁱ	108 – 111	Combined sources	4
Turnⁱ	112 – 115	Combined sources	4
Beta strandⁱ	116 – 125	Combined sources	10
Helixⁱ	127 – 138	Combined sources	12
Beta strandⁱ	141 – 149	Combined sources	9
Beta strandⁱ	154 – 156	Combined sources	3
Helixⁱ	157 – 159	Combined sources	3
Helixⁱ	165 – 184	Combined sources	20
Helixⁱ	188 – 194	Combined sources	7
Beta strandⁱ	273 – 275	Combined sources	3
Beta strandⁱ	290 – 294	Combined sources	5
Turnⁱ	298 – 301	Combined sources	4
Helixⁱ	303 – 311	Combined sources	9
Beta strandⁱ	317 – 324	Combined sources	8
Beta strandⁱ	327 – 329	Combined sources	3
Helixⁱ	331 – 345	Combined sources	15
Helixⁱ	364 – 369	Combined sources	6
Helixⁱ	406 – 414	Combined sources	9
Beta strandⁱ	419 – 421	Combined sources	3
Helixⁱ	437 – 450	Combined sources	14
Beta strandⁱ	451 – 453	Combined sources	3
Helixⁱ	454 – 474	Combined sources	21
Beta strandⁱ	477 – 479	Combined sources	3
Beta strandⁱ	481 – 490	Combined sources	10
Beta strandⁱ	496 – 506	Combined sources	11
Beta strandⁱ	517 – 526	Combined sources	10
Helixⁱ	530 – 532	Combined sources	3
Turnⁱ	534 – 539	Combined sources	6
Beta strandⁱ	541 – 548	Combined sources	8
Beta strandⁱ	559 – 571	Combined sources	13
Helixⁱ	572 – 579	Combined sources	8
Helixⁱ	580 – 582	Combined sources	3
Helixⁱ	583 – 602	Combined sources	20
Helixⁱ	608 – 613	Combined sources	6
Beta strandⁱ	619 – 624	Combined sources	6
Beta strandⁱ	627 – 631	Combined sources	5
Helixⁱ	633 – 649	Combined sources	17
Helixⁱ	653 – 674	Combined sources	22
Helixⁱ	686 – 691	Combined sources	6
Helixⁱ	698 – 714	Combined sources	17

Show more details

3D structure databases

SMRⁱ	P03433
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Miscellaneous databases

EvolutionaryTraceⁱ	P03433

EvolutionaryTraceⁱ

P03433

Family & Domainsⁱ

Motif

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Motifⁱ	124 – 139	Nuclear localization signal 1 (NLS1)UniRule annotation1 PublicationAdd BLAST		16
Motifⁱ	184 – 247	Nuclear localization signal 2 (NLS2)UniRule annotation1 PublicationAdd BLAST		64

Sequence similaritiesⁱ

Belongs to the influenza viruses PA family.UniRule annotation

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

Isoform PA (identifier: P03433-1) [UniParc]FASTA Add to basket

This isoform has been chosen as the 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
MEDFVRQCFN PMIVELAEKT MKEYGEDLKI ETNKFAAICT HLEVCFMYSD 
        60         70         80         90        100
FHFINEQGES IIVELGDPNA 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 MRKLADQSLP PNFSSLENFR AYVDGFEPNG YIEGKLSQMS 
       260        270        280        290        300
KEVNARIEPF LKTTPRPLRL PNGPPCSQRS KFLLMDALKL SIEDPSHEGE 
       310        320        330        340        350
GIPLYDAIKC MRTFFGWKEP NVVKPHEKGI NPNYLLSWKQ VLAELQDIEN 
       360        370        380        390        400
EEKIPKTKNM KKTSQLKWAL GENMAPEKVD FDDCKDVGDL KQYDSDEPEL 
       410        420        430        440        450
RSLASWIQNE FNKACELTDS SWIELDEIGE DVAPIEHIAS MRRNYFTSEV 
       460        470        480        490        500
SHCRATEYIM KGVYINTALL NASCAAMDDF QLIPMISKCR TKEGRRKTNL 
       510        520        530        540        550
YGFIIKGRSH LRNDTDVVNF VSMEFSLTDP RLEPHKWEKY CVLEIGDMLI 
       560        570        580        590        600
RSAIGQVSRP MFLYVRTNGT SKIKMKWGME MRRCLLQSLQ QIESMIEAES 
       610        620        630        640        650
SVKEKDMTKE FFENKSETWP IGESPKGVEE SSIGKVCRTL LAKSVFNSLY 
       660        670        680        690        700
ASPQLEGFSA ESRKLLLIVQ ALRDNLEPGT FDLGGLYEAI EECLINDPWV 
       710 
LLNASWFNSF LTHALS

Length:716

Mass (Da):82,588

Last modified:October 2, 2007 - v2

Checksum:ⁱ8829F53525814394

GO

Isoform PA-X (identifier: P0CK64-1) [UniParc]FASTA Add to basket

The sequence of this isoform can be found in the external entry P0CK64.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Length:252

Mass (Da):29,423

GO

Experimental Info

Feature key	Position(s)	DescriptionActions	Graphical view	Length
Sequence conflictⁱ	550	I → L in CAA24295 (PubMed:7060132).		1

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	V01106 Genomic RNA Translation: CAA24295.1 AF389117 Genomic RNA Translation: AAM75157.1 EF467820 Genomic RNA Translation: ABO21708.1 CY009449 Genomic RNA Translation: ABD77682.1
NCBI Reference Sequences More...RefSeqⁱ	NP_040986.1, NC_002022.1

Genome annotation databases

GeneIDⁱ	956535
KEGGⁱ	vg:956535

Keywords - Coding sequence diversityⁱ

Ribosomal frameshifting

Protein	Similar proteins		Species	Score	Length	Source
P03433	Polymerase acidic protein		Influenza A virus (A/Puerto Rico/8-CV10/1934(H1N1))		716	UniRef100_P03433
Polymerase acidic protein		Influenza A virus (A/Puerto Rico/8-SV1/1934(H1N1))		716
Polymerase acidic protein		9INFA		716
Polymerase acidic protein		Influenza A virus (A/guineafowl/Hong Kong/WF10_CIP046_RGAO032/1999(H9N1))		716
Polymerase acidic protein		Influenza A virus (A/reassortant/IVR-148(Brisbane/59/2007 x Texas/1/1977)(H1N1))		716
+116

Protein	Similar proteins		Species	Score	Length	Source
P03433	Polymerase acidic protein		I57A0		716	UniRef90_P03433
Polymerase acidic protein		I02A4		716
Polymerase acidic protein		I86A3		716
Polymerase acidic protein		I77A4		716
Polymerase acidic protein		I71A1		716
+57244

Protein	Similar proteins		Species	Score	Length	Source
P03433	Polymerase acidic protein		I57A1		716	UniRef50_P03433
Polymerase acidic protein		I02A1		716
Polymerase acidic protein		I36A0		716
Polymerase acidic protein		I86A3		716
Polymerase acidic protein		I67A0		716
+57499

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	V01106 Genomic RNA Translation: CAA24295.1 AF389117 Genomic RNA Translation: AAM75157.1 EF467820 Genomic RNA Translation: ABO21708.1 CY009449 Genomic RNA Translation: ABD77682.1
RefSeqⁱ	NP_040986.1, NC_002022.1

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 entry	Method	Resolution (Å)	Chain	Positions	PDBsum
	2ZNL	X-ray	2.30	A	239-716	[»]
	4YYL	X-ray	1.91	A	1-50	[»]
				A	73-197	[»]
	4ZHZ	X-ray	2.50	A	1-50	[»]
				A	73-197	[»]
	4ZI0	X-ray	1.80	A	1-50	[»]
				A	73-197	[»]
	4ZQQ	X-ray	1.80	A	1-50	[»]
				A	73-197	[»]
	5FDD	X-ray	2.51	A	1-50	[»]
				A	73-197	[»]
	5FDG	X-ray	2.10	A	1-50	[»]
				A	73-197	[»]
	5I13	X-ray	2.15	A	1-50	[»]
				A	73-197	[»]
	5JHT	X-ray	1.75	A	1-50	[»]
				A	73-197	[»]
	5JHV	X-ray	2.75	A/B	1-50	[»]
				A/B	73-197	[»]
SMRⁱ	P03433
ModBaseⁱ	Search...
PDBe-KBⁱ	Search...

Protein-protein interaction databases

DIPⁱ	DIP-43996N
IntActⁱ	P03433, 57 interactors
MINTⁱ	P03433

Chemistry databases

BindingDBⁱ	P03433
ChEMBLⁱ	CHEMBL1169598
DrugBankⁱ	DB13997, Baloxavir marboxil
DrugCentralⁱ	P03433

Protein family/group databases

MEROPSⁱ	S62.001

MEROPSⁱ

S62.001

Genome annotation databases

GeneIDⁱ	956535
KEGGⁱ	vg:956535

Enzyme and pathway databases

BRENDAⁱ	2.7.7.48, 7479
Reactomeⁱ	R-HSA-168255, Influenza Infection R-HSA-168271, Transport of Ribonucleoproteins into the Host Nucleus R-HSA-168275, Entry of Influenza Virion into Host Cell via Endocytosis R-HSA-168288, Fusion of the Influenza Virion to the Host Cell Endosome R-HSA-168298, Release R-HSA-168302, Budding R-HSA-168303, Packaging of Eight RNA Segments R-HSA-168325, Viral Messenger RNA Synthesis R-HSA-168330, Viral RNP Complexes in the Host Cell Nucleus R-HSA-168333, NEP/NS2 Interacts with the Cellular Export Machinery R-HSA-168336, Uncoating of the Influenza Virion R-HSA-192814, vRNA Synthesis R-HSA-192823, Viral mRNA Translation R-HSA-192869, cRNA Synthesis R-HSA-192905, vRNP Assembly

BRENDAⁱ

2.7.7.48, 7479

Reactomeⁱ

R-HSA-168255, Influenza Infection
R-HSA-168271, Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168275, Entry of Influenza Virion into Host Cell via Endocytosis
R-HSA-168288, Fusion of the Influenza Virion to the Host Cell Endosome
R-HSA-168298, Release
R-HSA-168302, Budding
R-HSA-168303, Packaging of Eight RNA Segments
R-HSA-168325, Viral Messenger RNA Synthesis
R-HSA-168330, Viral RNP Complexes in the Host Cell Nucleus
R-HSA-168333, NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-168336, Uncoating of the Influenza Virion
R-HSA-192814, vRNA Synthesis
R-HSA-192823, Viral mRNA Translation
R-HSA-192869, cRNA Synthesis
R-HSA-192905, vRNP Assembly

Miscellaneous databases

EvolutionaryTraceⁱ	P03433

EvolutionaryTraceⁱ

P03433

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
Pfamⁱ	View protein in Pfam PF00603, Flu_PA, 1 hit
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	PA_I34A1
Accessionⁱ	P03433Primary (citable) accession number: P03433 Secondary accession number(s): A4GXH3, Q20N31, Q8JUU6
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
	Last sequence update:	October 2, 2007
	Last modified:	February 23, 2022
	This is version 131 of the entry and version 2 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Viral Protein Annotation Program

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Supporting data

UniProtKB - P03433 (PA_I34A1)

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Polymerase acidic protein

PA

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<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

GO - Biological processi

Enzyme and pathway databases

Protein family/group databases

<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

Keywords - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Chemistry databases

<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

Keywords - PTMi

<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

P03433

Protein-protein interaction databases

Chemistry databases

<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

3D structure databases

Miscellaneous 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

Family and domain databases

Experimental Info

Sequence databases

Genome annotation databases

Keywords - Coding sequence diversityi

<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

Protein-protein interaction databases

Chemistry databases

Protein family/group databases

Genome annotation databases

Enzyme and pathway databases

Miscellaneous 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

Keywords - Technical termi

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Functionⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Keywords - Cellular componentⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Keywords - PTMⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Keywords - Coding sequence diversityⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ