P03433 (PA_I34A1) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Polymerase acidic protein

Alternative name(s):
RNA-directed RNA polymerase subunit P2

Gene names

Name:

PA

Organism

Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) [Reference proteome]

Taxonomic identifier

211044 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA negative-strand viruses › Orthomyxoviridae › Influenzavirus A › Influenza A virus › H1N1 subtype

Virus host

Aves [TaxID: 8782]
Homo sapiens (Human) [TaxID: 9606]
Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	716 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Implicated in endonuclease cleavage of capped RNA primers. Displays an elongation factor activity in viral RNA synthesis. Dispensable for viral transcription, but not replication.
Subunit structure	Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA.
Post-translational modification	Phosphorylated on serines and threonines by host kinases, including human casein kinase II By similarity.
Sequence similarities	Belongs to the influenza viruses PA family.

Ontologies

Keywords
Biological process	Host gene expression shutoff by virus Host transcription shutoff by virus Host-virus interaction Inhibition of host RNA polymerase II by virus
Coding sequence diversity	Ribosomal frameshifting
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	suppression by virus of host RNA polymerase II activity Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro uncoating of virus Traceable author statement. Source: Reactome viral entry into host cell via membrane fusion with the plasma membrane Traceable author statement. Source: Reactome viral entry into host cell via receptor-mediated endocytosis Traceable author statement. Source: Reactome viral genome maturation Traceable author statement. Source: Reactome viral genome packaging Traceable author statement. Source: Reactome viral release from host cell Traceable author statement. Source: Reactome viral transcription Traceable author statement. Source: Reactome
Cellular_component	cytosol Traceable author statement. Source: Reactome endosome lumen Traceable author statement. Source: Reactome extracellular region Traceable author statement. Source: Reactome nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Isoform PA (identifier: P03433-1)

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.

Isoform PA-X (identifier: P0CK64-1)

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.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 716

716

Polymerase acidic protein

PRO_0000078796

Experimental info

Sequence conflict

550

1

I → L in CAA24295. Ref.1

Secondary structure

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716

Helix Strand Turn

Details...

Beta strand

273 – 275

3

Beta strand

290 – 294

5

Turn

298 – 301

4

Helix

303 – 311

9

Beta strand

317 – 324

8

Beta strand

327 – 329

3

Helix

331 – 345

15

Helix

364 – 369

6

Helix

406 – 414

9

Beta strand

419 – 421

3

Helix

437 – 450

14

Beta strand

451 – 453

3

Helix

454 – 474

21

Beta strand

477 – 479

3

Beta strand

481 – 490

10

Beta strand

496 – 506

11

Beta strand

517 – 526

10

Helix

530 – 532

3

Turn

534 – 539

6

Beta strand

541 – 548

8

Beta strand

559 – 571

13

Helix

572 – 579

8

Helix

580 – 582

3

Helix

583 – 602

20

Helix

608 – 613

6

Beta strand

619 – 624

6

Beta strand

627 – 631

5

Helix

633 – 649

17

Helix

653 – 674

22

Helix

686 – 691

6

Helix

698 – 714

17

Sequences

	Sequence		Length	Mass (Da)
	Isoform PA [UniParc]. Last modified October 2, 2007. Version 2. Checksum: 8829F53525814394	FASTA	716	82,588
	10 20 30 40 50 60 MEDFVRQCFN PMIVELAEKT MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINEQGES 70 80 90 100 110 120 IIVELGDPNA LLKHRFEIIE GRDRTMAWTV VNSICNTTGA EKPKFLPDLY DYKENRFIEI 130 140 150 160 170 180 GVTRREVHIY YLEKANKIKS EKTHIHIFSF TGEEMATKAD YTLDEESRAR IKTRLFTIRQ 190 200 210 220 230 240 EMASRGLWDS FRQSERGEET IEERFEITGT MRKLADQSLP PNFSSLENFR AYVDGFEPNG 250 260 270 280 290 300 YIEGKLSQMS KEVNARIEPF LKTTPRPLRL PNGPPCSQRS KFLLMDALKL SIEDPSHEGE 310 320 330 340 350 360 GIPLYDAIKC MRTFFGWKEP NVVKPHEKGI NPNYLLSWKQ VLAELQDIEN EEKIPKTKNM 370 380 390 400 410 420 KKTSQLKWAL GENMAPEKVD FDDCKDVGDL KQYDSDEPEL RSLASWIQNE FNKACELTDS 430 440 450 460 470 480 SWIELDEIGE DVAPIEHIAS MRRNYFTSEV SHCRATEYIM KGVYINTALL NASCAAMDDF 490 500 510 520 530 540 QLIPMISKCR TKEGRRKTNL YGFIIKGRSH LRNDTDVVNF VSMEFSLTDP RLEPHKWEKY 550 560 570 580 590 600 CVLEIGDMLI RSAIGQVSRP MFLYVRTNGT SKIKMKWGME MRRCLLQSLQ QIESMIEAES 610 620 630 640 650 660 SVKEKDMTKE FFENKSETWP IGESPKGVEE SSIGKVCRTL LAKSVFNSLY ASPQLEGFSA 670 680 690 700 710 ESRKLLLIVQ ALRDNLEPGT FDLGGLYEAI EECLINDPWV LLNASWFNSF LTHALS
	Isoform PA-X [UniParc]. See P0CK64.		–	–

References

[1]	"Nucleotide sequences of influenza virus segments 1 and 3 reveal mosaic structure of a small viral RNA segment." Fields S., Winter G. Cell 28:303-313(1982) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Plasmid-only rescue of influenza A virus vaccine candidates." Schickli J.H., Flandorfer A., Nakaya T., Martinez-Sobrido L., Garcia-Sastre A., Palese P. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 356:1965-1973(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Efficient generation and growth of influenza virus A/PR/8/34 from eight cDNA fragments." de Wit E., Spronken M.I.J., Bestebroer T.M., Rimmelzwaan G.F., Osterhaus A.D.M.E., Fouchier R.A.M. Virus Res. 103:155-161(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], REVERSE GENETICS.
[4]	"The NIAID influenza genome sequencing project." Ghedin E., Spiro D., Miller N., Zaborsky J., Feldblyum T., Subbu V., Shumway M., Sparenborg J., Groveman L., Halpin R., Sitz J., Koo H., Salzberg S.L., Webster R.G., Hoffmann E., Krauss S., Naeve C., Bao Y. , Bolotov P., Dernovoy D., Kiryutin B., Lipman D.J., Tatusova T. Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[5]	"The structural basis for an essential subunit interaction in influenza virus RNA polymerase." Obayashi E., Yoshida H., Kawai F., Shibayama N., Kawaguchi A., Nagata K., Tame J.R., Park S.Y. Nature 454:1127-1131(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 239-716.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V01106 Genomic RNA. Translation: CAA24295.1.
AF389117 Genomic RNA. Translation: AAM75157.1.
EF467820 Genomic RNA. Translation: ABO21708.1.
CY009449 Genomic RNA. Translation: ABD77682.1.

RefSeq

NP_040986.1. NC_002022.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2ZNL	X-ray	2.30	A	239-716	[»]

ProteinModelPortal

P03433.

SMR

P03433. Positions 257-715.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-43996N.

IntAct

P03433. 30 interactions.

MINT

MINT-3375052.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

956535.

Enzyme and pathway databases

Reactome

REACT_116125. Disease.

Family and domain databases

InterPro

IPR001009. RNA-dir_pol_influenzavirus.
[Graphical view]

Pfam

PF00603. Flu_PA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChEMBL

CHEMBL1169598.

EvolutionaryTrace

P03433.

Entry information

Entry name

PA_I34A1

Accession

Primary (citable) accession number: P03433
Secondary accession number(s): A4GXH3, Q20N31, Q8JUU6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	October 2, 2007
Last modified:	April 3, 2013
This is version 77 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program