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Protein

Polymerase acidic protein

Gene

PA

Organism
Influenza A virus (strain A/Brevig Mission/1/1918 H1N1) (Influenza A virus (strain A/South Carolina/1/1918 H1N1))
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

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

Miscellaneous

South Carolina isolate has been sequenced from formalid fixed-lung tissues of a 21-year-old male which died in 1918 at Ft. Jackson, SC. Brevig Mission isolate has been sequenced from lung tissues of an Inuit woman buried in the permafrost in a gravesite near Brevig Mission, Alaska. This sample was recovered by John Hultin, retired pathologist.

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi41Manganese 1; via tele nitrogenUniRule annotation1
Metal bindingi80Manganese 2UniRule annotation1
Metal bindingi108Manganese 1UniRule annotation1
Metal bindingi108Manganese 2UniRule annotation1
Metal bindingi119Manganese 1UniRule annotation1
Metal bindingi120Manganese 1; via carbonyl oxygenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processCap 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
LigandManganese, 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
OrganismiInfluenza A virus (strain A/Brevig Mission/1/1918 H1N1) (Influenza A virus (strain A/South Carolina/1/1918 H1N1))
Taxonomic identifieri88776 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA negative-strand virusesOrthomyxoviridaeAlphainfluenzavirus
Virus hostiAves [TaxID: 8782]
Homo sapiens (Human) [TaxID: 9606]
Sus scrofa (Pig) [TaxID: 9823]
Proteomesi
  • UP000008430 Componenti: Genome

Subcellular locationi

  • Host cytoplasm UniRule annotation
  • Host nucleus UniRule annotation
  • Note: PB1 and PA are transported in the host nucleus as a complex.UniRule annotationBy similarity

GO - Cellular componenti

Keywords - Cellular componenti

Host cytoplasm, Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003105711 – 716Polymerase acidic proteinAdd BLAST716

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiQ3HM39

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

ProteinModelPortaliQ3HM39
SMRiQ3HM39
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi124 – 139Nuclear localization signal 1 (NLS1)UniRule annotationBy similarityAdd BLAST16
Motifi184 – 247Nuclear localization signal 2 (NLS2)UniRule annotationBy similarityAdd BLAST64

Sequence similaritiesi

Belongs to the influenza viruses PA family.UniRule annotation

Phylogenomic databases

OrthoDBiVOG0900002P

Family and domain databases

Gene3Di3.40.91.90, 1 hit
HAMAPiMF_04063 INFV_PA, 1 hit
InterProiView protein in InterPro
IPR037534 INFV_PA
IPR001009 PA/PA-X
IPR038372 PA/PA-X_sf
PfamiView protein in Pfam
PF00603 Flu_PA, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform PA (identifier: Q3HM39-1) [UniParc]FASTAAdd 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 MKEYGEDLKI ETNKFAAICT HLEVCFMYSD
60 70 80 90 100
FHFINERGES IIVESGDPNA 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 PNFSSLENFR AYVDGFEPNG YIEGKLSQMS
260 270 280 290 300
KEVNARIEPF LKTTPRPLRL PDGPPCSQRS KFLLMDALKL SIEDPSHEGE
310 320 330 340 350
GIPLYDAIKC MRTFFGWKEP NVVKPHEKGI NPNYLLAWKQ VLAELQDIEN
360 370 380 390 400
EEKIPKTKNM KKTSQLKWAL GENMAPEKVD FDDCKDVSDL KQYDSDEPEL
410 420 430 440 450
RSLASWIQSE FNKACELTDS SWIELDEIGE 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):82,599
Last modified:November 8, 2005 - v1
Checksum:i21ACA43508075CFE
GO
Isoform PA-X (identifier: P0CK68-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0CK68.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:252
Mass (Da):29,378
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ208311 mRNA Translation: ABA55040.1

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Entry informationi

Entry nameiPA_I18A0
AccessioniPrimary (citable) accession number: Q3HM39
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 8, 2005
Last modified: May 23, 2018
This is version 47 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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