Reviewed, UniProtKB/Swiss-Prot P29813 (POLG_EC11G)

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 11 (strain Gregory) [Complete proteome]
Taxonomic identifier	31705 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Picornaviridae › Enterovirus
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	2195 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 CD55 to provide virion attachment to 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 CD55.
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 Cytoplasm Cytoplasmic vesicle 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	cytoplasmic vesicle Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW
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 – 331

330

Protein VP0 Potential

PRO_0000311058

Chain

2 – 69

68

Protein VP4 Potential

PRO_0000039703

Chain

70 – 331

262

Protein VP2 Potential

PRO_0000039704

Chain

332 – 569

238

Protein VP3 Potential

PRO_0000039705

Chain

570 – 861

292

Protein VP1 Potential

PRO_0000039706

Chain

862 – 1011

150

Picornain 2A Potential

PRO_0000039707

Chain

1012 – 1110

99

Protein 2B Potential

PRO_0000039708

Chain

1111 – 1439

329

Protein 2C Potential

PRO_0000039709

Chain

1440 – 1528

89

Protein 3A Potential

PRO_0000039710

Chain

1529 – 1550

22

Protein 3B Potential

PRO_0000039711

Chain

1551 – 1733

183

Picornain 3C Potential

PRO_0000039712

Chain

1734 – 2195

462

RNA-directed RNA polymerase 3D-POL Potential

PRO_0000039713

Regions

Topological domain

2 – 1505

1504

Cytoplasmic Potential

Topological domain

1506 – 1521

16

In membrane Potential

Topological domain

1522 – 2195

674

Cytoplasmic Potential

Domain

1215 – 1371

157

SF3 helicase

Domain

1960 – 2076

117

RdRp catalytic

Nucleotide binding

1239 – 1246

8

ATP Potential

Sites

Active site

882

1

For picornain 2A activity By similarity

Active site

900

1

For picornain 2A activity By similarity

Active site

971

1

For picornain 2A activity By similarity

Active site

1590

1

For picornain 3C activity Potential

Active site

1621

1

For picornain 3C activity Potential

Active site

1697

1

For picornain 3C activity By similarity

Site

69 – 70

2

Cleavage Potential

Site

331 – 332

2

Cleavage; by picornain 3C Potential

Site

861 – 862

2

Cleavage; by picornain 2A Potential

Site

1011 – 1012

2

Cleavage; by picornain 3C Potential

Site

1110 – 1111

2

Cleavage; by picornain 3C Potential

Site

1439 – 1440

2

Cleavage; by picornain 3C Potential

Site

1528 – 1529

2

Cleavage; by picornain 3C Potential

Site

1550 – 1551

2

Cleavage; by picornain 3C Potential

Site

1733 – 1734

2

Cleavage; by picornain 3C Potential

Amino acid modifications

Modified residue

1531

1

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

Lipidation

2

1

N-myristoyl glycine; by host By similarity

Experimental info

Sequence conflict

823 – 827

5

RLCQY → SYANT in BAA01439. Ref.2

Secondary structure

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2195

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Beta strand

25 – 29

5

Helix

36 – 38

3

Helix

50 – 52

3

Beta strand

57 – 59

3

Beta strand

63 – 65

3

Beta strand

83 – 87

5

Beta strand

90 – 96

7

Beta strand

100 – 102

3

Turn

113 – 115

3

Helix

126 – 128

3

Beta strand

138 – 140

3

Beta strand

147 – 152

6

Helix

159 – 167

9

Beta strand

168 – 180

13

Beta strand

188 – 197

10

Beta strand

203 – 205

3

Helix

212 – 215

4

Beta strand

218 – 220

3

Beta strand

225 – 227

3

Beta strand

231 – 235

5

Helix

239 – 241

3

Turn

242 – 244

3

Helix

248 – 253

6

Beta strand

254 – 260

7

Turn

261 – 263

3

Beta strand

265 – 271

7

Beta strand

276 – 278

3

Turn

282 – 284

3

Beta strand

288 – 299

12

Beta strand

308 – 324

17

Turn

339 – 342

4

Beta strand

354 – 356

3

Helix

374 – 378

5

Helix

396 – 399

4

Beta strand

401 – 407

7

Beta strand

414 – 417

4

Turn

420 – 422

3

Helix

424 – 427

4

Helix

430 – 435

6

Beta strand

438 – 442

5

Beta strand

445 – 451

7

Beta strand

458 – 466

9

Beta strand

468 – 470

3

Helix

476 – 479

4

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

Beta strand

520 – 530

11

Beta strand

537 – 547

11

Beta strand

552 – 556

5

Beta strand

565 – 567

3

Helix

603 – 605

3

Helix

613 – 616

4

Helix

629 – 631

3

Helix

633 – 637

5

Beta strand

641 – 651

11

Beta strand

653 – 655

3

Helix

656 – 658

3

Beta strand

659 – 663

5

Helix

670 – 676

7

Beta strand

679 – 696

18

Beta strand

710 – 716

7

Helix

729 – 732

4

Beta strand

734 – 736

3

Beta strand

738 – 742

5

Beta strand

749 – 752

4

Beta strand

757 – 763

7

Beta strand

767 – 770

4

Helix

779 – 782

4

Beta strand

787 – 794

8

Beta strand

801 – 819

19

Beta strand

854 – 856

3

Sequences

	Sequence		Length	Mass (Da)
	P29813-1 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 1CFC5DF288831AF0	FASTA	2,195	245,407
	10 20 30 40 50 60 MGAQVSTQKT GAHETGLNAS GSSIIHYTNI NYYKDAASNS ANRQEFSQDP GKFTEPVKDI 70 80 90 100 110 120 MVKSLPALNS PSAEECGYSD RVRSITLGNS TITTQESANV VVGYGRWPEY LKDNEATAED 130 140 150 160 170 180 QPTQPDVATC RFYTLESVTW ERDSPGWWWK FPDALKDMGL FGQNMYYHYL GRAGYTLHVQ 190 200 210 220 230 240 CNASKFHQGC LLVVCVPEAE MGCSQVDGTV NEHGLSEGET AKKFSSTSTN GTNTVQTIVT 250 260 270 280 290 300 NAGMGVGVGN LTIYPHQWIN LRTNNCATIV MPYINNVPMD NMFRHHNFTL MIIPFVPLDY 310 320 330 340 350 360 SSDSSTYVPI TVTVAPMCAE YNGLRLSTSL QGLPVMNTPG SNQFLTSDDF QSPSAMPQFD 370 380 390 400 410 420 VTPELNIPGE VQNLMEIAEV DSVVPVNNVE GKLDTMEVYR IPVQSGNHQS DQVFGFQVQP 430 440 450 460 470 480 GLDSVFKHTL LGEILNYFAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKNRKDAM 490 500 510 520 530 540 LGTHIIWDVG LQSSCVLCVP WISQTHYRLV QQDEYTSAGN VTCWYQTGIV VPAGTPTSCS 550 560 570 580 590 600 IMCFVSACND FSVRLLKDTP FIEQTALLQG DVVEAVENAV ARVADTIGSG PSNSQAVPAL 610 620 630 640 650 660 TAVETGHTSQ VTPSDTMQTR HVKNYHSRSE SSIENFLSRS ACVYMGGYHT TNTDQTKLFA 670 680 690 700 710 720 SWTISARRMV QMRRKLEIFT YVRFDVEVTF VITSKQDQGS RLGQDMPPLT HQIMYIPPGG 730 740 750 760 770 780 PIPKSVTDYA WQTSTNPSIF WTEGNAPPRM SIPFISIGNA YSNFYDGWSH FSQNGVYGYN 790 800 810 820 830 840 TLNHMGQIYV RHVNGSSPLP MTSTVRMYFK PKHVKAWVPR PPRLCQYKNA STVNFTPTNV 850 860 870 880 890 900 TDKRTSINYI PETVKPDLSN YGAFGYQSGA VYVVNYRVVN RHLATHTDWQ NCVWEDYNRD 910 920 930 940 950 960 LLISTTTAHG CDVIARCRCS TGVYYCQSKG KHYPVNFEGP GLVEVQESEY YPKRYQSHVL 970 980 990 1000 1010 1020 LAAGFSEPGD CGGILRCEHG VIGIVTMGGE GVVGFADVRD LLWLEDDAME QGVKDYVEQL 1030 1040 1050 1060 1070 1080 GNAFGSGFTN QICEQVNLLK ESLVGQDSIL EKSLKALVKI ISALVIVVRN HDDLITVTAT 1090 1100 1110 1120 1130 1140 LALIGCTSSP WRWLKQKVSQ YYGIPMAERQ NNGWLKKFTE MTNSCKGMEW ISIKIQKFIE 1150 1160 1170 1180 1190 1200 WLKVKILPEV REKHEFLNRL KQLPLLESQI ATIEQSAPSQ SDQEQLFSNV QYFAHYCRKY 1210 1220 1230 1240 1250 1260 APLYASEAKR VFSLEKKMSN YIQFKSKCRI EPVCLLLHGS PGAGKSVATN LIGRSLAEKL 1270 1280 1290 1300 1310 1320 NSSVYTLPPD PDHFDGYKQQ AVVIVDDLCQ NPDGKDVSLF CQMVSSVDFV PPMAALEEKG 1330 1340 1350 1360 1370 1380 ILFTSLFVLA STNAGSINAP TVSDSRALAR RFHFDMNIEV ISMYSQNGKI NMPMSEKTCD 1390 1400 1410 1420 1430 1440 EECCPVNFKR CCPLVCGKAI QFIDRRTQVR YSLDMLVTEM FREYNHRHSV GATLEALFQG 1450 1460 1470 1480 1490 1500 PPIYREIKIS VAPETPPPPA IADLLKSVDS EAVREYCKEK GWLVPEVNST LQIEKHVSRA 1510 1520 1530 1540 1550 1560 FICLQALTTF VSVAGIIYII YKLFAGFQGA YTGMPNQKPK VPTLRQAKVQ GPAFEFAVAM 1570 1580 1590 1600 1610 1620 MKRNSSTVKT EYREFTMLGI YDRWAVLPRH AKPGPTILMN NQEVGVLDAK ELVDKDGTNL 1630 1640 1650 1660 1670 1680 ELTLLKLNRN EKFRDIRGFL AKEEVEANQA VLAINTSKFP NMYIPVGQVT DYGFLNLGGT 1690 1700 1710 1720 1730 1740 PTKRMLMSNF PTRAGQCGGV LMSTGKVLGI HVGGNGHQGF SAALLKHYFN DEQGEIEFIE 1750 1760 1770 1780 1790 1800 SSKDAGFPII NTPSKTKLEP SVFHQVFEGD KEPAVLRNGD PRLKANFEEA IFSKYIGNVN 1810 1820 1830 1840 1850 1860 THVDEYMLEA VDHYAGQLAT LDISTEPMRL EDAVYGTEGL EALDLTTSAG YPYVALGIKK 1870 1880 1890 1900 1910 1920 RDILSRRTRD LTKLKECMDK YGLNLPMVTY VKDELRSADK VAKGKSRLIE ASSLNDSVAM 1930 1940 1950 1960 1970 1980 RQTFGNLYRT FHLNPGIVTG SAVGCDPDLF WSKIPVMLDG HLIAFDYSGY DASLSPVWFA 1990 2000 2010 2020 2030 2040 CLKLLLEKLG YTHKETNYID YLCNSHHLYR DKHYFERGGM PSGYSGTSMF NSMINNIIIR 2050 2060 2070 2080 2090 2100 TLMLKVYKGI DLDQFRMIAY GDDVIASYPW PIDASLLAET GKGYGLIMTP ADKGECFNEV 2110 2120 2130 2140 2150 2160 TWTNVTFLKR YFRADEQYPF LVHPVMPMKD IHESIRWTKD PKNTQDHVRS LCLLAWHNGE 2170 2180 2190 HEYEEFIRKI RSVPVGRCLT LPAFSTLRRK WLDSF

References

[1]	"The genome of echovirus 11." Dahllund L., Nissinen L., Pulli T., Hyttinen V.P., Stanway G., Hyypiae T. Virus Res. 35:215-222(1995) [PubMed: 7762294] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Echoviruses include genetically distinct serotypes." Auvinen P., Hyypiae T. J. Gen. Virol. 71:2133-2139(1990) [PubMed: 2170575] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 822-2195.
[3]	"Decay-accelerating factor (CD55), a glycosylphosphatidylinositol-anchored complement regulatory protein, is a receptor for several echoviruses." Bergelson J.M., Chan M., Solomon K.R., St John N.F., Lin H., Finberg R.W. Proc. Natl. Acad. Sci. U.S.A. 91:6245-6248(1994) [PubMed: 7517044] [Abstract] Cited for: INTERACTION WITH HOST CD55.
[4]	"Determination of the structure of a decay accelerating factor-binding clinical isolate of echovirus 11 allows mapping of mutants with altered receptor requirements for infection." Stuart A.D., McKee T.A., Williams P.A., Harley C., Shen S., Stuart D.I., Brown T.D., Lea S.M. J. Virol. 76:7694-7704(2002) [PubMed: 12097583] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 1-859. Strain: Isolate clinical EV11-207.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBLGenBankDDBJ

X80059 Genomic RNA. Translation: CAA56365.1.
D10582 Genomic RNA. Translation: BAA01439.1.

PIR

GNNYEC. A36642.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H8T	X-ray	2.90	A	570-860	[»]
			B	70-331	[»]
			C	332-569	[»]
			D	2-69	[»]
2C8I	electron microscopy	14.00	A	570-857	[»]
			B	79-328	[»]
			C	332-569	[»]
			D	2-69	[»]

SMR

P29813. Positions 861-1010, 862-1011, 1551-2195.

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.
IPR000199. Pept_C3_picorn.
IPR000081. Peptidase_C3.
IPR003138. Pico_P1A.
IPR002527. Pico_P2B.
IPR001676. Picornavirus_capsid.
IPR001205. RNA_pol_P3D.
IPR007094. RNA_pol_PSvir.
[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

PD001125. Pept_C3_picorn. 1 hit.
PD001306. Peptidase_C3_2. 1 hit.
PD001274. 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_EC11G

Accession

Primary (citable) accession number: P29813
Secondary accession number(s): Q66785

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 91 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)