P06210 (POLG_POL2L) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 12 chains: Protein VP0 Alternative name(s): VP4-VP2 Protein VP4 Alternative name(s): P1A Virion protein 4 Protein VP2 Alternative name(s): P1B Virion protein 2 Protein VP3 Alternative name(s): P1C Virion protein 3 Protein VP1 Alternative name(s): P1D Virion protein 1 Picornain 2A Short name=P2A Short name=Protein 2A EC=3.4.22.29 Protein 2B Short name=P2B Protein 2C Short name=P2C EC=3.6.1.15 Protein 3A Short name=P3A Protein 3B Short name=P3B Alternative name(s): VPg Picornain 3C EC=3.4.22.28 Alternative name(s): Protease 3C Short name=P3C RNA-directed RNA polymerase 3D-POL Short name=P3D-POL EC=2.7.7.48
Organism	Poliovirus type 2 (strain Lansing) [Complete proteome]
Taxonomic identifier	12084 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Picornaviridae › Enterovirus › Enterovirus C › Human poliovirus 2
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	2207 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm By similarity. VP0 precursor is a component of immature procapsids By similarity. Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription By similarity. Protein 2B affects membrane integrity and cause an increase in membrane permeability By similarity. Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities By similarity. Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport By similarity. Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease By similarity. RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals By similarity.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. NTP + H2O = NDP + phosphate.
Subunit structure	Interacts with human PVR By similarity.
Subcellular location	Protein VP2: Virion. Host cytoplasm Potential. Protein VP3: Virion. Host cytoplasm Potential. Protein VP1: Virion. Host cytoplasm Potential. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity. Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity. Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity. Protein 3B: Virion Potential. Picornain 3C: Host cytoplasm Potential. RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side Potential. Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum By similarity.
Post-translational modification	Specific enzymatic cleavages in vivo by the viral proteases yield a variety of precursors and mature proteins. Polyprotein processing intermediates such as VP0 which is a VP4-VP2 precursor are produced. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle By similarity. VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity. Myristoylation of VP4 is required during RNA encapsidation and formation of the mature virus particle By similarity.
Sequence similarities	Belongs to the picornaviruses polyprotein family. Contains 2 peptidase C3 domains. Contains 1 RdRp catalytic domain. Contains 1 SF3 helicase domain.

Ontologies

Keywords
Biological process	Activation of host autophagy by virus Clathrin- and caveolin-independent endocytosis of virus by host Host gene expression shutoff by virus Host transcription shutoff by virus Host-virus interaction Inhibition of host IFN-mediated response initiation by virus Inhibition of host RIG-I by virus Inhibition of host innate immune response by virus Inhibition of host transcription initiation by virus Ion transport Pore-mediated penetration of viral genome into host cell Transport Viral RNA replication Viral attachment to host cell Viral immunoevasion Viral penetration into host cytoplasm Virus endocytosis by host Virus entry into host cell
Cellular component	Host cytoplasm Host cytoplasmic vesicle Host membrane Membrane Virion
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Capsid protein Helicase Hydrolase Ion channel Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase Viral ion channel
PTM	Covalent protein-RNA linkage Lipoprotein Myristate Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW induction by virus of host autophagy Inferred from electronic annotation. Source: UniProtKB-KW ion transport Inferred from electronic annotation. Source: UniProtKB-KW pore-mediated entry of viral genome into host cell Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host DNA-dependent transcription, initiation Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host RIG-I activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon production Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral attachment to host cell Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell via endocytosis Inferred from electronic annotation. Source: UniProtKB-KW viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell cytoplasmic vesicle membrane Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host By similarity

Chain

2 – 340

339

Protein VP0 Potential

PRO_0000311080

Chain

2 – 69

68

Protein VP4 Potential

PRO_0000040102

Chain

70 – 340

271

Protein VP2 Potential

PRO_0000040103

Chain

341 – 578

238

Protein VP3 Potential

PRO_0000040104

Chain

579 – 879

301

Protein VP1 Potential

PRO_0000040105

Chain

880 – 1028

149

Picornain 2A Potential

PRO_0000040106

Chain

1029 – 1125

97

Protein 2B Potential

PRO_0000040107

Chain

1126 – 1454

329

Protein 2C Potential

PRO_0000040108

Chain

1455 – 1541

87

Protein 3A Potential

PRO_0000040109

Chain

1542 – 1563

22

Protein 3B Potential

PRO_0000040110

Chain

1564 – 1746

183

Picornain 3C Potential

PRO_0000040111

Chain

1747 – 2207

461

RNA-directed RNA polymerase 3D-POL Potential

PRO_0000040112

Regions

Topological domain

2 – 1518

1517

Cytoplasmic Potential

Intramembrane

1519 – 1534

16

Potential

Topological domain

1535 – 2207

673

Cytoplasmic Potential

Domain

1230 – 1386

157

SF3 helicase

Domain

1973 – 2088

116

RdRp catalytic

Nucleotide binding

1254 – 1261

8

ATP Potential

Sites

Active site

899

1

For picornain 2A activity By similarity

Active site

917

1

For picornain 2A activity By similarity

Active site

988

1

For picornain 2A activity By similarity

Active site

1603

1

For picornain 3C activity Potential

Active site

1634

1

For picornain 3C activity Potential

Active site

1710

1

For picornain 3C activity By similarity

Site

69 – 70

2

Cleavage Potential

Site

340 – 341

2

Cleavage; by picornain 3C Potential

Site

879 – 880

2

Cleavage; by picornain 2A Potential

Site

1028 – 1029

2

Cleavage; by picornain 3C Potential

Site

1125 – 1126

2

Cleavage; by picornain 3C Potential

Site

1454 – 1455

2

Cleavage; by picornain 3C Potential

Site

1541 – 1542

2

Cleavage; by picornain 3C Potential

Site

1563 – 1564

2

Cleavage; by picornain 3C Potential

Site

1746 – 1747

2

Cleavage; by picornain 3C Potential

Amino acid modifications

Modified residue

1544

1

O-(5'-phospho-RNA)-tyrosine By similarity

Lipidation

2

1

N-myristoyl glycine; by host By similarity

Secondary structure

1

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2207

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Helix

17 – 19

3

Helix

23 – 25

3

Beta strand

26 – 29

4

Helix

36 – 38

3

Helix

51 – 54

4

Beta strand

57 – 59

3

Beta strand

63 – 65

3

Beta strand

83 – 87

5

Beta strand

90 – 96

7

Helix

103 – 105

3

Turn

113 – 115

3

Helix

126 – 128

3

Beta strand

138 – 140

3

Beta strand

147 – 151

5

Helix

153 – 155

3

Helix

159 – 167

9

Beta strand

168 – 180

13

Beta strand

187 – 197

11

Beta strand

203 – 207

5

Helix

213 – 216

4

Helix

219 – 221

3

Beta strand

226 – 228

3

Beta strand

235 – 237

3

Helix

246 – 248

3

Turn

249 – 252

4

Helix

255 – 260

6

Beta strand

261 – 267

7

Turn

268 – 270

3

Beta strand

272 – 278

7

Beta strand

282 – 287

6

Turn

289 – 291

3

Beta strand

295 – 307

13

Beta strand

315 – 331

17

Turn

348 – 351

4

Beta strand

363 – 365

3

Beta strand

379 – 382

4

Helix

384 – 387

4

Turn

399 – 403

5

Helix

405 – 408

4

Beta strand

410 – 413

4

Beta strand

422 – 427

6

Turn

429 – 431

3

Turn

433 – 437

5

Helix

439 – 444

6

Beta strand

447 – 452

6

Beta strand

454 – 460

7

Beta strand

469 – 475

7

Beta strand

477 – 479

3

Helix

485 – 488

4

Beta strand

491 – 497

7

Beta strand

499 – 501

3

Beta strand

503 – 508

6

Beta strand

513 – 520

8

Beta strand

529 – 536

8

Beta strand

546 – 556

11

Beta strand

561 – 565

5

Helix

625 – 627

3

Helix

635 – 637

3

Helix

655 – 659

5

Beta strand

663 – 671

9

Beta strand

683 – 687

5

Helix

695 – 700

6

Beta strand

703 – 725

23

Beta strand

732 – 738

7

Helix

751 – 754

4

Beta strand

756 – 758

3

Beta strand

760 – 764

5

Beta strand

770 – 774

5

Beta strand

779 – 785

7

Turn

800 – 803

4

Beta strand

812 – 815

4

Beta strand

817 – 822

6

Beta strand

831 – 849

19

Beta strand

859 – 862

4

Sequences

	Sequence		Length	Mass (Da)
	P06210 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 2B1E2070B7D44F99	FASTA	2,207	245,831
	10 20 30 40 50 60 MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYRDSASNA ASKQDFAQDP SKFTEPIKDV 70 80 90 100 110 120 LIKTAPTLNS PNIEACGYSD RVMQLTLGNS TITTQEAANS VVAYGRWPEY IKDSEANPVD 130 140 150 160 170 180 QPTEPDVAAC RFYTLDTVTW RKESRGWWWK LPDALKDMGL FGQNMFYHYL GRAGYTVHVQ 190 200 210 220 230 240 CNASKFHQGA LGVFAVPEMC LAGDSTTHMF TKYENANPGE KGGEFKGSFT LDTNATNPAR 250 260 270 280 290 300 NFCPVDYLFG SGVLAGNAFV YPHQIINLRT NNCATLVLPY VNSLSIDSMT KHNNWGIAIL 310 320 330 340 350 360 PLAPLDFATE SSTEIPITLT IAPMCCEFNG LRNITVPRTQ GLPVLNTPGS NQYLTADNYQ 370 380 390 400 410 420 SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT 430 440 450 460 470 480 PILCLSLSPA SDPRLAHTML GEILNYYTHW AGSLKFTFLF CGSMMATGKL LVSYAPPGAE 490 500 510 520 530 540 APKSRKEAML GTHVIWDIGL QSSCTMVVPW ISNTTYRQTI NDSFTEGGYI SMFYQTRVVV 550 560 570 580 590 600 PLSTPRKMDI LGFVSACNDF SVRLLRDTTH ISQEAMPQGL GDLIEGVVEG VTRNALTPLT 610 620 630 640 650 660 PANNLPDTQS SGPAHSKETP ALTAVETGAT NPLVPSDTVQ TRHVIQKRTR SESTVESFFA 670 680 690 700 710 720 RGACVAIIEV DNDAPTKRAS KLFSVWKITY KDTVQLRRKL EFFTYSRFDM EFTFVVTSNY 730 740 750 760 770 780 TDANNGHALN QVYQIMYIPP GAPIPGKWND YTWQTSSNPS VFYTYGAPPA RISVPYVGIA 790 800 810 820 830 840 NAYSHFYDGF AKVPLAGQAS TEGDSLYGAA SLNDFGSLAV RVVNDHNPTK LTSKIRVYMK 850 860 870 880 890 900 PKHVRVWCPR PPRAVPYYGP GVDYKDGLAP LPGKGLTTYG FGHQNKAVYT AGYKICNYHL 910 920 930 940 950 960 ATQEDLQNAV NIMWIRDLLV VESKAQGIDS IARCNCHTGV YYCESRRKYY PVSFTGPTFQ 970 980 990 1000 1010 1020 YMEANEYYPA RYQSHMLIGH GFASPGDCGG ILRCQHGVIG IITAGGEGLV AFSDIRDLYA 1030 1040 1050 1060 1070 1080 YEEEAMEQGV SNYIESLGAA FGSGFTQQIG NKISELTSMV TSTITEKLLK NLIKIISSLV 1090 1100 1110 1120 1130 1140 IITRNYEDTT TVLATLALLG CDASPWQWLK KKACDILEIP YIMRQGDSWL KKFTEACNAA 1150 1160 1170 1180 1190 1200 KGLEWVSNKI SKFIDWLKEK IIPQARDKLE FVTKLKQLEM LENQIATIHQ SCPSQEHQEI 1210 1220 1230 1240 1250 1260 LFNNVRWLSI QSKRFAPLYA VEAKRIQKLE HTINNYVQFK SKHRIEPVCL LVHGSPGTGK 1270 1280 1290 1300 1310 1320 SVATNLIARA IAEKENTSTY SLPPDPSHFD GYKQQGVVIM DDLNQNPDGA DMKLFCQMVS 1330 1340 1350 1360 1370 1380 TVEFIPPMAS LEEKGILFTS NYVLASTNSS RITPPTVAHS DALARRFAFD MDIQIMSEYS 1390 1400 1410 1420 1430 1440 RDGKLNMAMA TEMCKNCHHP ANFKRCCPLV CGKAIQLMDK SSRVRYSIDQ ITTMIINERN 1450 1460 1470 1480 1490 1500 RRSSIGNCME ALFQGPLQYK DLKIDIKTTP PPECINDLLQ AVDSQEVRDY CEKKGWIVDI 1510 1520 1530 1540 1550 1560 TSQVQTERNI NRAMTILQAV TTFAAVAGVV YVMYKLFAGH QGAYTGLPNK RPNVPTIRTA 1570 1580 1590 1600 1610 1620 KVQGPGFDYA VAMAKRNILT ATTIKGEFTM LGVHDNVAIL PTHASPGETI VIDGKEVEVL 1630 1640 1650 1660 1670 1680 DAKALEDQAG TNLEITIVTL KRNEKFRDIR PHIPTQITET NDGVLIVNTS KYPNMYVPVG 1690 1700 1710 1720 1730 1740 AVTEQGYLNL SGRQTARTLM YNFPTRAGQC GGVITCTGKV IGMHVGGNGS HGFAAALKRS 1750 1760 1770 1780 1790 1800 YFTQSQGEIQ WMRPSKEVGY PVINAPSKTK LEPSAFHYVF EGVKEPAVLT KSDPRLKTDF 1810 1820 1830 1840 1850 1860 EEAIFSKYVG NKITEVDEYM KEAVDHYAGQ LMSLDINTEQ MCLEDAMYGT DGLEALDLST 1870 1880 1890 1900 1910 1920 SAGYPYVAMG KKKRDILNKQ TRDTKEMQRL LDTYGINLPL VTYVKDELRS KTKVEQGKSR 1930 1940 1950 1960 1970 1980 LIEASSLNDS VAMRMAFGNL YAAFHKNPGV VTGSAVGCDP DLFWSKIPVL MEEKLFAFDY 1990 2000 2010 2020 2030 2040 TGYDASLSPA WFEALKMVLE KIGFGDRVDY IDYLNHSHHL YKNKTYCVKG GMPSGCSGTS 2050 2060 2070 2080 2090 2100 IFNSMINNLI IRTLLLKTYK GIDLDHLKMI AYGDDVIASY PHEVDASLLA QSGKDYGLTM 2110 2120 2130 2140 2150 2160 TPADKSATFE TVTWENVTFL KRFFRADEKY PFLVHPVMPM KEIHESIRWT KDPRNTQDHV 2170 2180 2190 2200 RSLCLLAWHN GEEEYNKFLA KIRSVPIGRA LLLPEYSTLY RRWLDSF

References

[1]	"Mapping of sequences required for mouse neurovirulence of poliovirus type 2 Lansing." la Monica N., Meriam C., Racaniello V.R. J. Virol. 57:515-525(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
+	Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M12197 Genomic RNA. Translation: AAA46912.1.

PIR

GNNY5P. A29507.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EAH	X-ray	2.90	1	579-878	[»]
			2	70-339	[»]
			3	341-577	[»]
			4	2-68	[»]
3EPF	electron microscopy	9.00	1	602-879	[»]
			2	81-340	[»]
			3	341-575	[»]
			4	2-69	[»]

ProteinModelPortal

P06210.

SMR

P06210. Positions 2-575, 602-1028, 1455-1513, 1564-2207.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

4.10.80.10. 2 hits.

InterPro

IPR003593. AAA+_ATPase.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR014838. P3A.
IPR000081. Peptidase_C3.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]

Pfam

PF08727. P3A. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF02226. Pico_P1A. 1 hit.
PF00947. Pico_P2A. 1 hit.
PF01552. Pico_P2B. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 3 hits.
PF00910. RNA_helicase. 1 hit.
[Graphical view]

ProDom

PD001306. Peptidase_C3. 1 hit.
PD649346. Pico_P2B. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00382. AAA. 1 hit.
[Graphical view]

SUPFAM

SSF89043. P3A. 1 hit.
SSF50494. Pept_Ser_Cys. 2 hits.

PROSITE

PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P06210.

Entry information

Entry name

POLG_POL2L

Accession

Primary (citable) accession number: P06210

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 137 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program