PA_INCJH
ID PA_INCJH Reviewed; 709 AA.
AC Q9IMP5;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 14-APR-2009, sequence version 3.
DT 03-AUG-2022, entry version 70.
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}; Synonyms=P3;
OS Influenza C virus (strain C/Johannesburg/1/1966).
OC Viruses; Riboviria; Orthornavirae; Negarnaviricota; Polyploviricotina;
OC Insthoviricetes; Articulavirales; Orthomyxoviridae; Gammainfluenzavirus.
OX NCBI_TaxID=100673;
OH NCBI_TaxID=9606; Homo sapiens (Human).
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND SEQUENCE REVISION TO 11.
RA Crescenzo-Chaigne B.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2-709.
RX PubMed=10600605; DOI=10.1006/viro.1999.0059;
RA Crescenzo-Chaigne B., Naffakh N., van der Werf S.;
RT "Comparative analysis of the ability of the polymerase complexes of
RT influenza viruses type A, B and C to assemble into functional RNPs that
RT allow expression and replication of heterotypic model RNA templates in
RT vivo.";
RL Virology 265:342-353(1999).
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=Q9IMP5-1; Sequence=Displayed;
CC Name=PA-X;
CC IsoId=Q9IMP5-2; 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; AF170574; AAF89737.2; -; Genomic_RNA.
DR PDB; 5D98; X-ray; 3.90 A; A/D=1-709.
DR PDB; 5D9A; X-ray; 4.30 A; A/D/G/J=1-709.
DR PDB; 6F5P; X-ray; 4.14 A; A/D=1-709.
DR PDB; 6XZD; EM; 3.40 A; AP1/DP1=1-709.
DR PDB; 6XZG; EM; 3.80 A; AP1/DP1=1-709.
DR PDB; 6XZP; EM; 3.30 A; AP1/DP1=1-709.
DR PDB; 6XZQ; EM; 3.60 A; A/D=1-709.
DR PDB; 6XZR; EM; 3.30 A; AP1/DP1=1-709.
DR PDB; 6Y0C; EM; 3.20 A; A=1-709.
DR PDBsum; 5D98; -.
DR PDBsum; 5D9A; -.
DR PDBsum; 6F5P; -.
DR PDBsum; 6XZD; -.
DR PDBsum; 6XZG; -.
DR PDBsum; 6XZP; -.
DR PDBsum; 6XZQ; -.
DR PDBsum; 6XZR; -.
DR PDBsum; 6Y0C; -.
DR SMR; Q9IMP5; -.
DR DIP; DIP-61786N; -.
DR IntAct; Q9IMP5; 2.
DR Proteomes; UP000138885; 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 1: Evidence at protein level;
KW 3D-structure; 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..709
FT /note="Polymerase acidic protein"
FT /id="PRO_0000269901"
FT MOTIF 109..124
FT /note="Nuclear localization signal 1 (NLS1)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT MOTIF 166..228
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 65
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 93
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 93
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 104
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
FT BINDING 105
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04063"
SQ SEQUENCE 709 AA; 81912 MW; 9B402DD4E3F74CB8 CRC64;
MSKTFAEIAE AFLEPEAVRI AKEAVEEYGD HERKIIQIGI HFQVCCMFCD EYLSTNGSDR
FVLIEGRKRG TAVSLQNELC KSYDLEPLPF LCDIFDREEK QFVEIGITRK ADDSYFQSKF
GKLGNSCKIF VFSYDGRLDK NCEGPMEEQK LRIFSFLATA ADFLRKENMF NEIFLPDNEE
TIIEMKKGKT FLELRDESVP LPFQTYEQMK DYCEKFKGNP RELASKVSQM QSNIKLPIKH
YEQNKFRQIR LPKGPMAPYT HKFLMEEAWM FTKISDPERS RAGEILIDFF KKGNLSAIRP
KDKPLQGKYP IHYKNLWNQI KAAIADRTMV INENDHSEFL GGIGRASKKI PEISLTQDVI
TTEGLKQSEN KLPEPRSFPR WFNAEWMWAI KDSDLTGWVP MAEYPPADNE LEDYAEHLNK
TMEGVLQGTN CAREMGKCIL TVGALMTECR LFPGKIKVVP IYARSKERKS MQEGLPVPSE
MDCLFGICVK SKSHLNKDDG MYTIITFEFS IREPNLEKHQ KYTVFEAGHT TVRMKKGESV
IGREVPLYLY CRTTALSKIK NDWLSKARRC FITTMDTVET ICLRESAKAE ENLVEKTLNE
KQMWIGKKNG ELIAQPLREA LRVQLVQQFY FCIYNDSQLE GFCNEQKKIL MALEGDKKNK
SSFGFNPEGL LEKIEECLIN NPMCLFMAQR LNELVIEASK RGAKFFKTD
