Reviewed, UniProtKB/Swiss-Prot O91734 (POLG_EC01F)

Names and origin

Protein names	Recommended name:     Genome polyprotein Cleaved into the following 12 chains:     1- Recommended name:             Protein VP0         Alternative name(s):             VP4-VP2     2- Recommended name:             Protein VP4         Alternative name(s):             Virion protein 4             P1A     3- Recommended name:             Protein VP2         Alternative name(s):             Virion protein 2             P1B     4- Recommended name:             Protein VP3         Alternative name(s):             Virion protein 3             P1C     5- Recommended name:             Protein VP1         Alternative name(s):             Virion protein 1             P1D     6- Recommended name:             Picornain 2A                 Short name=Protein 2A                 Short name=P2A               EC=3.4.22.29     7- Recommended name:             Protein 2B                 Short name=P2B     8- Recommended name:             Protein 2C                 Short name=P2C               EC=3.6.1.15     9- Recommended name:             Protein 3A                 Short name=P3A     10- Recommended name:             Protein 3B                 Short name=P3B         Alternative name(s):             VPg     11- Recommended name:             Picornain 3C               EC=3.4.22.28         Alternative name(s):             Protease 3C               Short name=P3C     12- Recommended name:             RNA-directed RNA polymerase 3D-POL                 Short name=P3D-POL               EC=2.7.7.48
Organism	Echovirus 1 (strain Human/Egypt/Farouk/1951) (E-1) [Complete proteome]
Taxonomic identifier	103908 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Picornaviridae › Enterovirus › Human enterovirus B
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	2184 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 By similarity. Capsid proteins interact with host alpha-2/beta-1 integrin heterodimer to provide virion attachment target cell. 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	Capsid proteins interact with host integrin ITGA2/ITGB1 heterodimer.
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	Host-virus interaction RNA replication
Cellular component	Capsid protein Host cytoplasm Host cytoplasmic vesicle Host membrane Membrane Virion
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
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 interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: InterPro transcription, RNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	host cell cytoplasm 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 – 330

329

Protein VP0 Potential

PRO_0000311053

Chain

2 – 69

68

Protein VP4 Potential

PRO_0000039648

Chain

70 – 330

261

Protein VP2 Potential

PRO_0000039649

Chain

331 – 569

239

Protein VP3 Potential

PRO_0000039650

Chain

570 – 850

281

Protein VP1 Potential

PRO_0000039651

Chain

851 – 1000

150

Picornain 2A Potential

PRO_0000039652

Chain

1001 – 1099

99

Protein 2B Potential

PRO_0000039653

Chain

1100 – 1428

329

Protein 2C Potential

PRO_0000039654

Chain

1429 – 1517

89

Protein 3A Potential

PRO_0000039655

Chain

1518 – 1539

22

Protein 3B Potential

PRO_0000039656

Chain

1540 – 1722

183

Picornain 3C Potential

PRO_0000039657

Chain

1723 – 2184

462

RNA-directed RNA polymerase 3D-POL Potential

PRO_0000039658

Regions

Topological domain

2 – 1494

1493

Cytoplasmic Potential

Topological domain

1495 – 1510

16

In membrane Potential

Topological domain

1511 – 2184

674

Cytoplasmic Potential

Domain

1204 – 1360

157

SF3 helicase

Domain

1949 – 2065

117

RdRp catalytic

Nucleotide binding

1228 – 1235

8

ATP Potential

Sites

Active site

871

1

For picornain 2A activity By similarity

Active site

889

1

For picornain 2A activity By similarity

Active site

960

1

For picornain 2A activity By similarity

Active site

1579

1

For picornain 3C activity Potential

Active site

1610

1

For picornain 3C activity Potential

Active site

1686

1

For picornain 3C activity By similarity

Site

69 – 70

2

Cleavage Potential

Site

330 – 331

2

Cleavage; by picornain 3C Potential

Site

850 – 851

2

Cleavage; by picornain 2A Potential

Site

1000 – 1001

2

Cleavage; by picornain 3C Potential

Site

1099 – 1100

2

Cleavage; by picornain 3C Potential

Site

1428 – 1429

2

Cleavage; by picornain 3C Potential

Site

1517 – 1518

2

Cleavage; by picornain 3C Potential

Site

1539 – 1540

2

Cleavage; by picornain 3C Potential

Site

1722 – 1723

2

Cleavage; by picornain 3C Potential

Amino acid modifications

Modified residue

1520

1

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

Lipidation

2

1

N-myristoyl glycine; by host

Experimental info

Sequence conflict

69

1

N → M in CAA61710. Ref.2

Sequence conflict

238

1

A → R in CAA61710. Ref.2

Sequence conflict

611

1

A → V in AAD17718. Ref.3

Sequence conflict

645

1

Y → F in AAD17718. Ref.3

Sequence conflict

724

1

V → I in AAD17718. Ref.3

Sequence conflict

774

1

A → T in AAD17718. Ref.3

Secondary structure

1

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2184

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Beta strand

26 – 29

4

Beta strand

33 – 35

3

Helix

36 – 38

3

Helix

51 – 54

4

Beta strand

57 – 59

3

Beta strand

83 – 86

4

Beta strand

91 – 96

6

Helix

103 – 105

3

Turn

113 – 115

3

Helix

126 – 128

3

Beta strand

138 – 140

3

Beta strand

147 – 151

5

Helix

153 – 157

5

Helix

159 – 167

9

Beta strand

168 – 180

13

Beta strand

188 – 197

10

Beta strand

203 – 205

3

Helix

212 – 214

3

Beta strand

225 – 228

4

Helix

239 – 241

3

Turn

242 – 245

4

Helix

248 – 253

6

Beta strand

254 – 260

7

Turn

261 – 263

3

Beta strand

265 – 271

7

Beta strand

276 – 280

5

Turn

282 – 284

3

Beta strand

288 – 299

12

Beta strand

308 – 324

17

Turn

338 – 341

4

Beta strand

353 – 355

3

Helix

374 – 377

4

Helix

390 – 393

4

Helix

397 – 399

3

Beta strand

400 – 405

6

Beta strand

412 – 417

6

Turn

420 – 422

3

Helix

424 – 427

4

Helix

430 – 435

6

Beta strand

438 – 443

6

Beta strand

445 – 453

9

Beta strand

460 – 466

7

Helix

476 – 481

6

Beta strand

482 – 488

7

Beta strand

490 – 492

3

Beta strand

494 – 499

6

Beta strand

504 – 506

3

Beta strand

508 – 511

4

Helix

514 – 516

3

Beta strand

520 – 527

8

Beta strand

537 – 547

11

Beta strand

552 – 556

5

Helix

603 – 605

3

Helix

613 – 615

3

Helix

633 – 637

5

Beta strand

641 – 650

10

Helix

656 – 658

3

Beta strand

659 – 663

5

Helix

666 – 668

3

Helix

671 – 676

6

Beta strand

679 – 696

18

Turn

700 – 703

4

Beta strand

710 – 716

7

Helix

729 – 732

4

Beta strand

734 – 736

3

Beta strand

738 – 742

5

Beta strand

748 – 752

5

Beta strand

757 – 763

7

Beta strand

767 – 770

4

Turn

771 – 773

3

Beta strand

774 – 778

5

Helix

779 – 781

3

Beta strand

787 – 792

6

Beta strand

801 – 819

19

Beta strand

830 – 832

3

Sequences

	Sequence		Length	Mass (Da)
	O91734-1 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: CBBB937D0AC18EA9	FASTA	2,184	244,004
	10 20 30 40 50 60 MGAQVSTQKT GAHETSLSAT GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPMKDV 70 80 90 100 110 120 MIKTLPALNS PTVEECGYSD RVRSITLGNS TITTQECANV VVGYGEWPEY LSDNEATAED 130 140 150 160 170 180 QPTQPDVATC RFYTLDSVQW ENGSPGWWWK FPDALRDMGL FGQNMYYHYL GRAGYTIHVQ 190 200 210 220 230 240 CNASKFHQGC ILVVCVPEAE MGSAQTSGVV NYEHISKGEI ASRFTTTTTA EDHGVQAAVW 250 260 270 280 290 300 NAGMGVGVGN LTIFPHQWIN LRTNNSATIV MPYVNSVPMD NMYRHHNFTL MIIPFVPLDF 310 320 330 340 350 360 SAGASTYVPI TVTVAPMCAE YNGLRLAGHQ GLPTMNTPGS NQFLTSDDFQ SPSAMPQFDV 370 380 390 400 410 420 TPEMHIPGEV RNLMEIAEVD SVMPINNDSA AKVSSMEAYR VELSTNTNAG TQVFGFQLNP 430 440 450 460 470 480 GAESVMNRTL MGEILNYYAH WSGSIKITFV FCGSAMTTGK FLLSYAPPGA GAPKTRKDAM 490 500 510 520 530 540 LGTHVVWDVG LQSSCVLCIP WISQTHYRFV EKDPYTNAGF VTCWYQTSVV SPASNQPKCY 550 560 570 580 590 600 MMCMVSACND FSVRMLRDTK FIEQTSFYQG DVQNAVEGAM VRVADTVQTS ATNSERVPNL 610 620 630 640 650 660 TAVETGHTSQ AVPGDTMQTR HVINNHVRSE STIENFLARS ACVFYLEYKT GTKEDSNSFN 670 680 690 700 710 720 NWVITTRRVA QLRRKLEMFT YLRFDMEITV VITSSQDQST SQNQNAPVLT HQIMYVPPGG 730 740 750 760 770 780 PIPVSVDDYS WQTSTNPSIF WTEGNAPARM SIPFISIGNA YSNFYDGWSH FSQAGVYGFT 790 800 810 820 830 840 TLNNMGQLFF RHVNKPNPAA ITSVARIYFK PKHVRAWVPR PPRLCPYINS TNVNFEPKPV 850 860 870 880 890 900 TEVRTNIITT GAFGQQSGAV YVGNYRVVNR HLATHIDWQN CVWEDYNRDL LVSTTTAHGC 910 920 930 940 950 960 DTIARCQCTT GVYFCLSRNK HYPVSFEGPG LVEVQESEYY PKRYQSHVLL AAGFSEPGDC 970 980 990 1000 1010 1020 GGILRCEHGV IGIVTMGGEG VVGFADVRDL LWLEDDAMEQ GVKDYVEQLG NAFGSGFTNQ 1030 1040 1050 1060 1070 1080 ICEQVNLLKE SLVGQDSILE KSLKALVKII SALVIVVRNH DDLITVTATL ALIGCTSSPW 1090 1100 1110 1120 1130 1140 RWLKQKVSQY YGIPMAERQN NGWLKKFTEM TNACKGMEWI AIKIQKFIEW LKVKILPEVK 1150 1160 1170 1180 1190 1200 EKHEFLNRLK QLPLLESQIA TIEQSAPSQG DQEQLFSNVQ YFAHYCRKYA PLYAAEAKRV 1210 1220 1230 1240 1250 1260 FSLEKKMSNY IQFKSKCRIE PVCLLLHGSP GAGKSVATNL IGRSLAEKLN SSVYSLPPDP 1270 1280 1290 1300 1310 1320 DHFDGYKQQA VVIMDDLCQN PDGKDVSLFC QMVSSVDFVP PMAALEEKGI LFTSPFVLAS 1330 1340 1350 1360 1370 1380 TNAGSINAPT VSDSRALARR FHFDMNIEVI SMYSQNGKIN MPMSVKTCDE DCCPVNFKKC 1390 1400 1410 1420 1430 1440 CPLVCGKAIQ FIDRKTQVRY SLDMLVTEMF REYNHRHSVG ATLEALFQGP PVYREIKISV 1450 1460 1470 1480 1490 1500 APETPPPPAI ADLLKSVDSE AVREYCKEKG WLVPEISSTL QIEKHVSRAF ICLQALTTFV 1510 1520 1530 1540 1550 1560 SVAGIIYIIY KLFAGFQGAY TGMPNQKPKV PTLRQAKVQG PAFEFAVAMM KRNASTVKTE 1570 1580 1590 1600 1610 1620 YGEFTMLGIY DRWAVLPRHA KPGPTILMND QEVGVLDAKE LVDKDGTNLE LTLLKLNRNE 1630 1640 1650 1660 1670 1680 KFRDIRGFLA REEAEVNEAV LAINTSKFPN MYIPVGQVTD YGFLNLGGTP TKRMLMYNFP 1690 1700 1710 1720 1730 1740 TRAGQCGGVL MSTGKVLGIH VGGNGHQGFS AALLRHYFNE EQGEIEFIES SKDAGFPVIN 1750 1760 1770 1780 1790 1800 TPSKTKLEPS VFHQVFEGNK EPAVLRNGDP RLKVNFEEAI FSKYIGNVNT HVDEYMQEAV 1810 1820 1830 1840 1850 1860 DHYAGQLATL DISTEPMKLE DAVYGTEGLE ALDLTTSAGY PYVALGIKKR DILSKKTKDL 1870 1880 1890 1900 1910 1920 TKLKECMDKY GLNLPMVTYV KDELRSAEKV AKGKSRLIEA SSLNDSVAMR QTFGNLYKTF 1930 1940 1950 1960 1970 1980 HLNPGIVTGS AVGCDPDVFW SKIPVMLDGH LIAFDYSGYD ASLSPVWFAC LKLLLEKLGY 1990 2000 2010 2020 2030 2040 TNKETNYIDY LCNSHHLYRD KHYFVRGGMP SGCSGTSIFN SMINNIIIRT LMLKVYKGID 2050 2060 2070 2080 2090 2100 LDQFRMIAYG DDVIASYPWP IDASLLAEAG KDYGLIMTPA DKGECFNEVT WTNVTFLKRY 2110 2120 2130 2140 2150 2160 FRADEQYPFL VHPVMPMKDI HESIRWTKDP KNTQDHVRSL CLLAWHNGEH EYEEFIRKIR 2170 2180 SVPVGRCLTL PAFSTLRRKW LDSF

References

[1]	"Receptor interactions, infectious cDNA, and nucleotide sequences of echovirus 1/8." Bergelson J.M. Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"The major echovirus group is genetically coherent and related to coxsackie B viruses." Huttunen P., Santti J., Pulli T., Hyypiae T. J. Gen. Virol. 77:715-725(1996) [PubMed: 8627260] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 69-330.
[3]	"Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification." Oberste M.S., Maher K., Kilpatrick D.R., Pallansch M.A. J. Virol. 73:1941-1948(1999) [PubMed: 9971773] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 570-853.
[4]	"Infection by echoviruses 1 and 8 depends on the alpha 2 subunit of human VLA-2." Bergelson J.M., St John N., Kawaguchi S., Chan M., Stubdal H., Modlin J., Finberg R.W. J. Virol. 67:6847-6852(1993) [PubMed: 8411387] [Abstract] Cited for: INTERACTION WITH HUMAN ITGA2/ITGB1 INTEGRIN.
[5]	"Structure determination of echovirus 1." Filman D.J., Wien M.W., Cunningham J.A., Bergelson J.M., Hogle J.M. Acta Crystallogr. D 54:1261-1272(1998) [PubMed: 10089503] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.55 ANGSTROMS) OF 1-850.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF029859 Genomic RNA. Translation: AAC63944.2.
X89531 Genomic RNA. Translation: CAA61710.1.
AF081314 Genomic RNA. Translation: AAD17718.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EV1	X-ray	3.55	1	570-850	[»]
			2	77-330	[»]
			3	331-569	[»]
			4	2-69	[»]

SMR

O91734. Positions 329-600, 851-1000, 1540-2184.

ModBase

Search...

Protein family/group databases

MEROPS

C03.011.
C03.020.

Family and domain databases

InterPro

IPR003593. ATPase_AAA+_core.
IPR004004. Helicase/Pol/Pept_Calicivir.
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_picornavirus.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Ser/Cys_Pept_Trypsin-like.
[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]

PRINTS

PR00918. CALICVIRUSNS.

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]

PROSITE

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

ProtoNet

Search...

Entry information

Entry name

POLG_EC01F

Accession

Primary (citable) accession number: O91734
Secondary accession number(s): Q66795, Q9YID6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	January 23, 2007
Last modified:	January 19, 2010
This is version 98 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)