PA_INBLE
ID PA_INBLE Reviewed; 726 AA.
AC Q9QLI9;
DT 09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 82.
DE RecName: Full=Polymerase acidic protein {ECO:0000255|HAMAP-Rule:MF_04063};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_04063};
DE AltName: Full=RNA-directed RNA polymerase subunit P2 {ECO:0000255|HAMAP-Rule:MF_04063};
GN Name=PA {ECO:0000255|HAMAP-Rule:MF_04063};
OS Influenza B virus (strain B/Lee/1940).
OC Viruses; Riboviria; Orthornavirae; Negarnaviricota; Polyploviricotina;
OC Insthoviricetes; Articulavirales; Orthomyxoviridae; Betainfluenzavirus.
OX NCBI_TaxID=518987;
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=10725418; DOI=10.1099/0022-1317-81-4-929;
RA Hiromoto Y., Saito T., Lindstrom S.E., Li Y., Nerome R., Sugita S.,
RA Shinjoh M., Nerome K.;
RT "Phylogenetic analysis of the three polymerase genes (PB1, PB2 and PA) of
RT influenza B virus.";
RL J. Gen. Virol. 81:929-937(2000).
CC -!- FUNCTION: Plays an essential role in viral RNA transcription and
CC replication by forming the heterotrimeric polymerase complex together
CC with PB1 and PB2 subunits. The complex transcribes viral mRNAs by using
CC a unique mechanism called cap-snatching. It consists in the hijacking
CC and cleavage of host capped pre-mRNAs. These short capped RNAs are then
CC used as primers for viral mRNAs. The PB2 subunit is responsible for the
CC binding of the 5' cap of cellular pre-mRNAs which are subsequently
CC cleaved after 10-13 nucleotides by the PA subunit that carries the
CC endonuclease activity. {ECO:0000255|HAMAP-Rule:MF_04063}.
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04063};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_04063};
CC -!- SUBUNIT: Influenza RNA polymerase is composed of three subunits: PB1,
CC PB2 and PA. Interacts (via C-terminus) with PB1 (via N-terminus).
CC {ECO:0000255|HAMAP-Rule:MF_04063}.
CC -!- SUBCELLULAR LOCATION: Host cytoplasm {ECO:0000255|HAMAP-Rule:MF_04063}.
CC Host nucleus {ECO:0000255|HAMAP-Rule:MF_04063}. Note=PB1 and PA are
CC transported in the host nucleus as a complex. {ECO:0000255|HAMAP-
CC Rule:MF_04063}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Ribosomal frameshifting; Named isoforms=2;
CC Name=PA;
CC IsoId=Q9QLI9-1; Sequence=Displayed;
CC Name=PA-X;
CC IsoId=Q9QLI9-2; Sequence=Not described;
CC -!- PTM: Phosphorylated on serines and threonines by host kinases,
CC including human casein kinase II. {ECO:0000255|HAMAP-Rule:MF_04063}.
CC -!- SIMILARITY: Belongs to the influenza viruses PA family.
CC {ECO:0000255|HAMAP-Rule:MF_04063}.
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DR EMBL; AF102017; AAF06886.1; -; Genomic_RNA.
DR RefSeq; NP_056659.1; NC_002206.1. [Q9QLI9-1]
DR SMR; Q9QLI9; -.
DR BindingDB; Q9QLI9; -.
DR ChEMBL; CHEMBL2028641; -.
DR GeneID; 956547; -.
DR KEGG; vg:956547; -.
DR PRO; PR:Q9QLI9; -.
DR Proteomes; UP000008158; Genome.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0075526; P:cap snatching; IEA:UniProtKB-UniRule.
DR GO; GO:0039523; P:suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-UniRule.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 3.40.91.90; -; 1.
DR HAMAP; MF_04063; INFV_PA; 1.
DR InterPro; IPR037534; INFV_PA.
DR InterPro; IPR001009; PA/PA-X.
DR InterPro; IPR038372; PA/PA-X_sf.
DR Pfam; PF00603; Flu_PA; 1.
PE 3: Inferred from homology;
KW Cap snatching; Endonuclease;
KW Eukaryotic host gene expression shutoff by virus;
KW Eukaryotic host transcription shutoff by virus; Host cytoplasm;
KW Host gene expression shutoff by virus; Host nucleus;
KW Host-virus interaction; Hydrolase;
KW Inhibition of host RNA polymerase II by virus; Manganese; Metal-binding;
KW Nuclease; Phosphoprotein; Reference proteome; Ribosomal frameshifting.
FT CHAIN 1..726
FT /note="Polymerase acidic protein"
FT /id="PRO_0000391499"
FT MOTIF 125..140
FT /note="Nuclear localization signal 1 (NLS1)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT MOTIF 183..244
FT /note="Nuclear localization signal 2 (NLS2)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 41
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 81
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 109
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 109
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 120
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 121
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
SQ SEQUENCE 726 AA; 83132 MW; DC3A3FE08DC40590 CRC64;
MDTFITKNFQ TTIIQKAKNT MAEFSEDPEL QPAVLFNICV HLEVCYVISD MNFLDEEGKT
YTALEGQGKE QNLRPQYEVI EGMPRNIAWM VQRSLAQEHG IETPRYLADL FDYKTKRFIE
VGITKGLADD YFWKKKEKLG NSMELMIFSY NQDYSLSDES SLDEEGKGRV LSRLTELQAE
LSLKNLWQVL IGEEEIEKGI DFKLGQTISK LRNISVPAGF SNFEGMRSYI DNIDPKGAIE
RNLARMSPLV SVTPKKLKWE DLRPIGPHIY NHELPEVPYN AFLLMSDELG LANMTEGKSK
KPKTLAKECL ERYSTLRDQT DPILIMKSEK ANENFLWRLW RDCVNTISNE ETGNELQKTN
YAKWATGDGL TYQKIMKEVA IDDETMYQEE PKIPNKCRVA AWVQAEMNLL STLTSKRALD
LPEIGPDVAP VEHVGSERRK YFVNEINYCK ASTVMMKYVL FHTSLLNESN ASMGKYKVIP
ITNRVVNEKG ESFDMLYGLA VKGQSHLRGD TDVVTVVTFE FSSTDPRVDS GKWPKYTVFK
IGSLFVSGRE KPVYLYCRVN GTNKIQMKWG MEARRCLLQS MQQMEAIVDQ ESSIQGYDMT
KACFKGDRVN NPKTFSIGTQ EGKLVKGSFG KALRVIFTKC LMHYVFGNAQ LEGFSAESRR
LLLLIQALKD RKGPWVFDLE GMYFGVEECI SNNPWVIQSA YWFNEWLGIE KEGSKVLESI
DEIMDE
