Reviewed, UniProtKB/Swiss-Prot P08291 (POLG_CXB1J)

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	Coxsackievirus B1 (strain Japan) [Complete proteome]
Taxonomic identifier	103902 [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	2182 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology.

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. 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.
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	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 – 332	331	Protein VP0 Potential		PRO_0000311045
	Chain	2 – 69	68	Protein VP4 Potential		PRO_0000039560
	Chain	70 – 332	263	Protein VP2 Potential		PRO_0000039561
	Chain	333 – 570	238	Protein VP3 Potential		PRO_0000039562
	Chain	571 – 848	278	Protein VP1 Potential		PRO_0000039563
	Chain	849 – 998	150	Picornain 2A Potential		PRO_0000039564
	Chain	999 – 1097	99	Protein 2B Potential		PRO_0000039565
	Chain	1098 – 1426	329	Protein 2C Potential		PRO_0000039566
	Chain	1427 – 1515	89	Protein 3A Potential		PRO_0000039567
	Chain	1516 – 1537	22	Protein 3B Potential		PRO_0000039568
	Chain	1538 – 1720	183	Picornain 3C Potential		PRO_0000039569
	Chain	1721 – 2182	462	RNA-directed RNA polymerase 3D-POL Potential		PRO_0000039570
Regions
	Topological domain	2 – 1492	1491	Cytoplasmic Potential
	Topological domain	1493 – 1508	16	In membrane Potential
	Topological domain	1509 – 2182	674	Cytoplasmic Potential
	Domain	1202 – 1358	157	SF3 helicase
	Domain	1947 – 2063	117	RdRp catalytic
	Nucleotide binding	1226 – 1233	8	ATP Potential
Sites
	Active site	869	1	For picornain 2A activity By similarity
	Active site	887	1	For picornain 2A activity By similarity
	Active site	958	1	For picornain 2A activity By similarity
	Active site	1577	1	For picornain 3C activity Potential
	Active site	1608	1	For picornain 3C activity Potential
	Active site	1684	1	For picornain 3C activity By similarity
	Site	69 – 70	2	Cleavage Potential
	Site	332 – 333	2	Cleavage; by picornain 3C Potential
	Site	848 – 849	2	Cleavage; by picornain 2A Potential
	Site	998 – 999	2	Cleavage; by picornain 3C Potential
	Site	1097 – 1098	2	Cleavage; by picornain 3C Potential
	Site	1426 – 1427	2	Cleavage; by picornain 3C Potential
	Site	1515 – 1516	2	Cleavage; by picornain 3C Potential
	Site	1537 – 1538	2	Cleavage; by picornain 3C Potential
	Site	1720 – 1721	2	Cleavage; by picornain 3C Potential
Amino acid modifications
	Modified residue	1518	1	O-(5'-phospho-RNA)-tyrosine By similarity
	Lipidation	2	1	N-myristoyl glycine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	P08291-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 387B9391275859B1	FASTA	2,182	243,946
	10 20 30 40 50 60 MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI 70 80 90 100 110 120 MIKSMPALNS PSAEECGYSD RVRSITLGNS TITTQECANV VVGYGVWPEY LKDNEATGED 130 140 150 160 170 180 QPTQPDVATC RFYTLESVQW MKNSAGWWWK LPDALSQMGL FGQNMQYHYL GRTGYTIHVQ 190 200 210 220 230 240 CNASKFHQGC LLVVCVPEAE MGCSNLNNTP KFAELSGGDN ARMFTDTEVG TSNDKKVQTA 250 260 270 280 290 300 VWNAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMYRHNNL TLMIIPFVPL 310 320 330 340 350 360 NYSEGSSPYV PITVTIAPMC AEYNGLRLAS SQGLPVMTTP GSTQFLTSDD FQSPSAMPQF 370 380 390 400 410 420 DVTPEMQIPG RVNNLMEIAE VDSVVPVNNT DNNVNGLKAY QIPVQSNSDN RRQVFGFPLQ 430 440 450 460 470 480 PGANNVLNRT LLGEILNYYT HWSGSIKLTF MFCGSAMATG KFLLAYSPPG AGVPKNRRDA 490 500 510 520 530 540 MLGTHVIWDV GLQSSCVLCV PWISQTHYRY VVEDEYTAAG YVTCWYQTNI IVPADVQSTC 550 560 570 580 590 600 DILCFVSACN DFSVRMLKDT PFIRQDNFYQ GPVEESVERA MVRVADTVSS KPTNSESIPA 610 620 630 640 650 660 LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYN NNSEKGYAEW 670 680 690 700 710 720 VINTRQVAQL LRRKLEFTYL RFDLELTFVI TSAQEPSTAT SVDAPVQTQQ IMYVPPGGPV 730 740 750 760 770 780 PTKVTDYAWQ TSTNPSVFWT EGNAPPRMSI PFISIGNAYS CFYDGWTQFS RNGVYGINTL 790 800 810 820 830 840 NNMGTLYMRH VNEAGQGPIK STVRIYFKPK HVKAWVPRPP RLCQYEKQKN VNFNPTGVTT 850 860 870 880 890 900 TRSNITTTGA FGQQSGAVYV GNYRVVNRHL ATREDWQRCV WEDYNRDLLV STTTAHGCDI 910 920 930 940 950 960 IARCQCTTGV YFCASRNKHY PVSFEGPGLV EVQESEYYPK RYQSHVLLAA GFSEPGDCGG 970 980 990 1000 1010 1020 ILRCEHGVVG IVTMGGEGVV GFADVRDLLW LEDDAMEQGV KDYVEQLGNA FGSGFTNQVC 1030 1040 1050 1060 1070 1080 EQVNLLKESL VGQDSILEKS LKALVKIVSA LVIVVRNHDD LITVTATLAL IGCTSSPWRW 1090 1100 1110 1120 1130 1140 LKQKVSQYYG IPMAERQNSG WLKKFTEMTN ACKGMEWIAI KIQKFIEWLK VKILPEVKEK 1150 1160 1170 1180 1190 1200 HEFLNRLKQL PLLESQIATI EQSAPSQSDQ EQLFSNVQYF AHYCRKYAPL YAAEAKRVFS 1210 1220 1230 1240 1250 1260 LEKKMSNYIQ FKSKCRIEPV CLLLHGSPGA GKSVATNLIG RSLAEKLNSS VYSLPPDPDH 1270 1280 1290 1300 1310 1320 FDGYKQQAVV IMDDLCQNPD GKDVSLFCQM VSSVDFVPPM AALEEKGILF TSPFVLASTN 1330 1340 1350 1360 1370 1380 AGSINAPTVS DSRALARRFH FDMNIEVISM YSQNGKINMP MSVKTCDEEC CPVNFKKCCP 1390 1400 1410 1420 1430 1440 LVCGKAIQFI DRRTQVRYSL DMLVTEMFRE YNHRHSVGAT LEALFQGPPI YREIKISIAP 1450 1460 1470 1480 1490 1500 ETPPPPAIAD LLKSVDSEAV REYCKEKGWL VPEINSTLQI EKHVSRAFIC LQALTTFVSV 1510 1520 1530 1540 1550 1560 AGIIYIIYKL FAGFQGAYTG MPNQKPKVPT LRQAKVQGPV FEFAVAMMKR NSSTVKTEYG 1570 1580 1590 1600 1610 1620 EFTMLGIYDR WAVLPRHAKP GPTILMNDQE IGVLDAKELV DKDGTNLELT LLKLNRNEKF 1630 1640 1650 1660 1670 1680 RDIRGFLAKE EVEVNEAVLA INTSKFPNMY IPVGQVTEYG FLNLGGTPTK RMLMYNFPTR 1690 1700 1710 1720 1730 1740 AGQCGGVLMS TGKVLGIHVG GNGHQGFSAA LLKHYFNDEQ GEIEFIESSK EAGFPVINTP 1750 1760 1770 1780 1790 1800 SKTKLEPSVF HQVFEGNKEP AVLRNGDPRL RANFEEAIFS KYIGNVNTHV DEYMLEAVDH 1810 1820 1830 1840 1850 1860 YAGQLATLDI STEPMRLEDA VYGTEGLEAL DLTTSAGYPY VALGIKKRDI LSKKTRDLTK 1870 1880 1890 1900 1910 1920 LKECMDKYGL NLPMVTYVKD ELRSAEKVAK GKSRLIEASS LNDSVAMRQT FGNLYKTFHL 1930 1940 1950 1960 1970 1980 NPGIVTGSAV GCDPDLFWSK IPVMLDGHLV AFDYSGYDAS LSPVWFACLK LLLEKLGYSH 1990 2000 2010 2020 2030 2040 KETNYIDYLC NSHHLYRDKH YFVRGGMPSG CSGTSIFNSM INNIIIRTLM LKVYKGIDLD 2050 2060 2070 2080 2090 2100 QFRMIAYGDD VIASYPWPID ASLLAEAGRD CGLIMTPADK GDCFNEVTWA NVTFLKRYFR 2110 2120 2130 2140 2150 2160 ADEQYPFLVH PVMPMKDIHE SIRWTKDPKN TQDHVRSLCL LAWHNGEHEY EEFIRKIRSV 2170 2180 PVGACLTLPA FSTLRRKWLD SF

References

[1]	"Complete nucleotide sequence of the genome of coxsackievirus B1." Iizuka N., Kuge S., Nomoto A. Virology 156:64-73(1987) [PubMed: 3027969] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	M16560 Genomic RNA. Translation: AAC00531.1.
PIR	GNNYB1. A26353.
RefSeq	NP_040958.1.
3D structure databases
HSSP	HSSP built from PDB template 1D4M based on UniProtKB P21404.
ModBase	Search...
Protein family/group databases
MEROPS	C03.011.
Genome annotation databases
GeneID	1461114.
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_CXB1J

Accession

Primary (citable) accession number: P08291

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 96 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)