Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Polymerase acidic protein

Gene

PA

Organism
Influenza A virus (strain A/USA:Texas/UR06-0195/2007 H1N1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 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/USA:Texas/UR06-0195/2007 H1N1)
Taxonomic identifieri455880 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA negative-strand virusesOrthomyxoviridaeInfluenzavirus A
Virus hostiAves [TaxID: 8782]
Homo sapiens (Human) [TaxID: 9606]
Sus scrofa (Pig) [TaxID: 9823]

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_00003729951 – 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

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

SMRiA8C8K1.
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

Family and domain databases

HAMAPiMF_04063. INFV_PA. 1 hit.
InterProiView protein in InterPro
IPR001009. RNA-dir_pol_influenzavirus.
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: A8C8K1-1) [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
FHFINEQGES IIVEPEDPNA 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 PNFSCIENFR AYVDGFEPNG YIEGKLSQMS
260 270 280 290 300
KEVNARIEPF LKTTPRPIRL PNGPPCFQRS KFLLMDSLKL SIEDPNHEGE
310 320 330 340 350
GIPLYDAIKC MRTFFGWKEP TVVKPHEKGI NPNYLLSWKQ VLEELQDIES
360 370 380 390 400
EEKIPRTKNM KKTSQLKWAL GENMAPEKVD FDDCKDVSDL KQYDSDEPEL
410 420 430 440 450
RSFSSWIQNE FNKACELTDS IWIELDEIGE DVAPIEHIAS MRRNYFTAEV
460 470 480 490 500
SHCRATEYIM KGVYINTALL NASCAAMDDF QLIPMISKCR TKEGRRKTNL
510 520 530 540 550
YGFIIKGRSH LRNDTDVVNF VSMEFSLTDP RLEPHKWERY CVLEIGDMLL
560 570 580 590 600
RSAIGQVSRP MFLYVRTNGT SKIKMKWGME MRRCLLQSLQ QIESMIEAES
610 620 630 640 650
SVKEKDMTKE FFENRSETWP IGESPEGVEE GSIGKVCRTL LAKSVFNSLY
660 670 680 690 700
ASPQLEGFSA ESRKLLLIVQ ALRDNLEPGT FDLGGLYEAI EECLINDPWV
710
LLNASWFNSF LTHALR
Length:716
Mass (Da):82,994
Last modified:November 13, 2007 - v1
Checksum:i6B8B6B4597C358BA
GO
Isoform PA-X (identifier: P0DJW6-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0DJW6.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:252
Mass (Da):29,339
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CY026216 Viral cRNA. Translation: ABV45933.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CY026216 Viral cRNA. Translation: ABV45933.1.

3D structure databases

SMRiA8C8K1.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

HAMAPiMF_04063. INFV_PA. 1 hit.
InterProiView protein in InterPro
IPR001009. RNA-dir_pol_influenzavirus.
PfamiView protein in Pfam
PF00603. Flu_PA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPA_I07A0
AccessioniPrimary (citable) accession number: A8C8K1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 5, 2009
Last sequence update: November 13, 2007
Last modified: June 7, 2017
This is version 32 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.