Q9QF31 (POLG_CX16T) 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	Coxsackievirus A16 (strain Tainan/5079/98) [Complete proteome]
Taxonomic identifier	231417 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Picornaviridae › Enterovirus › Enterovirus A › Human coxsackievirus A16
Virus host	Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	2193 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. 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	Activation of host autophagy 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 Ion transport Transport Viral RNA replication Viral attachment to host cell Viral immunoevasion 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	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 proteolysis 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 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 – 323	322	Protein VP0 Potential		PRO_0000311042
	Chain	2 – 69	68	Protein VP4 Potential		PRO_0000039525
	Chain	70 – 323	254	Protein VP2 Potential		PRO_0000039526
	Chain	324 – 565	242	Protein VP3 Potential		PRO_0000039527
	Chain	566 – 862	297	Protein VP1 Potential		PRO_0000039528
	Chain	863 – 1012	150	Picornain 2A Potential		PRO_0000039529
	Chain	1013 – 1111	99	Protein 2B Potential		PRO_0000039530
	Chain	1112 – 1440	329	Protein 2C Potential		PRO_0000039531
	Chain	1441 – 1526	86	Protein 3A Potential		PRO_0000039532
	Chain	1527 – 1548	22	Protein 3B Potential		PRO_0000039533
	Chain	1549 – 1731	183	Picornain 3C Potential		PRO_0000039534
	Chain	1732 – 2193	462	RNA-directed RNA polymerase 3D-POL Potential		PRO_0000039535
Regions
	Topological domain	2 – 1503	1502	Cytoplasmic Potential
	Intramembrane	1504 – 1519	16	Potential
	Topological domain	1520 – 2193	674	Cytoplasmic Potential
	Domain	1216 – 1374	159	SF3 helicase
	Domain	1958 – 2074	117	RdRp catalytic
	Nucleotide binding	1240 – 1247	8	ATP Potential
Sites
	Active site	883	1	For picornain 2A activity By similarity
	Active site	901	1	For picornain 2A activity By similarity
	Active site	972	1	For picornain 2A activity By similarity
	Active site	1588	1	For picornain 3C activity Potential
	Active site	1619	1	For picornain 3C activity Potential
	Active site	1695	1	For picornain 3C activity By similarity
	Site	25	1	Involved in the interaction with human RTN3 By similarity
	Site	69 – 70	2	Cleavage Potential
	Site	323 – 324	2	Cleavage; by picornain 3C Potential
	Site	862 – 863	2	Cleavage; by picornain 2A Potential
	Site	1012 – 1013	2	Cleavage; by picornain 3C Potential
	Site	1111 – 1112	2	Cleavage; by picornain 3C Potential
	Site	1440 – 1441	2	Cleavage; by picornain 3C Potential
	Site	1526 – 1527	2	Cleavage; by picornain 3C Potential
	Site	1548 – 1549	2	Cleavage; by picornain 3C Potential
	Site	1731 – 1732	2	Cleavage; by picornain 3C Potential
Amino acid modifications
	Modified residue	1529	1	O-(5'-phospho-RNA)-tyrosine By similarity
	Lipidation	2	1	N-myristoyl glycine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9QF31 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 927839DB58F61E7F	FASTA	2,193	243,184
	10 20 30 40 50 60 MGSQVSTQRS GSHENSNSAS EGSTINYTTI NYYKDAYAAS AGRQDMSQDP KKFTDPVMDV 70 80 90 100 110 120 IHEMAPPLKS PSAEACGYSD RVAQLTIGNS TITTQEAANI VIAYGEWPEY CPDTDATAVD 130 140 150 160 170 180 KPTRPDVSVN RFFTLDTKSW AKDSKGWYWK FPDVLTEVGV FGQNAQFHYL YRSGFCVHVQ 190 200 210 220 230 240 CNASKFHQGA LLVAVLPEYV LGTIAGGTGN ENSHPPYATT QPGQVGAVLT HPYVLDAGIP 250 260 270 280 290 300 LSQLTVCPHQ WINLRTNNCA TIIVPYMNTV PFDSALNHCN FGLLVVPVVP LDFNAGATSE 310 320 330 340 350 360 IPITVTIAPM CAEFAGLRQA VKQGIPTELK PGTNQFLTTD DGVSAPILPG FHPTPPIHIP 370 380 390 400 410 420 GEVHNLLEIC RVETILEVNN LKTNETTPMQ RLCFPVSVQS KTGELCAAFR ADPGRDGPWQ 430 440 450 460 470 480 STILGQLCRY YTQWSGSLEV TFMFAGSFMA TGKMLIAYTP PGGNVPADRI TAMLGTHVIW 490 500 510 520 530 540 DFGLQSSVTL VVPWISNTHY RAHARAGYFD YYTTGIITIW YQTNYVVPIG APTTAYIVAL 550 560 570 580 590 600 AAAQDNFTMK LCKDTEDIEQ TANIQGDPIA DMIDQTVNNQ VNRSLTALQV LPTAADTEAS 610 620 630 640 650 660 SHRLGTGVVP ALQAAETGAS SNASDKNLIE TRCVLNHHST QETAIGNFFS RAGLVSIITM 670 680 690 700 710 720 PTTGTQNTDG YVNWDIDLMG YAQLRRKCEL FTYMRFDAEF TFVVAKPNGE LVPQLLQYMY 730 740 750 760 770 780 VPPGAPKPTS RDSFAWQTAT NPSVFVKMTD PPAQVSVPFM SPASAYQWFY DGYPTFGEHL 790 800 810 820 830 840 QANDLDYGQC PNNMMGTFSI RTVGTEKSPH SITLRVYMRI KHVRAWIPRP LRNQPYLFKT 850 860 870 880 890 900 NPNYKGNDIK CTSTSRDKIT TLGKFGQQSG AIYVGNYRVV NRHLATHNDW ANLVWEDSSR 910 920 930 940 950 960 DLLVSSTTAQ GCDTIARCNC QTGVYYCSSK RKHYPVSFTK PSLIFVEASE YYPARYQSHL 970 980 990 1000 1010 1020 MLAVGHSEPG DCGGILRCQH GVVGIVSTGG NGLVGFADVR DLLWLDEEAM EQGVSDYIKG 1030 1040 1050 1060 1070 1080 LGDAFGVGFT DAVSREVEAL KNHLIGSEGA VEKILKNLVK LISALVIVVR SDYDMVTLTA 1090 1100 1110 1120 1130 1140 TLALIGCHGS PWAWIKAKTA SILGIPIVQK QSASWLKKFN DMANAAKGLE WISSKISKFI 1150 1160 1170 1180 1190 1200 DWLKEKIIPA AKEKVEFLNN LKQLPLLENQ ISNLEQSAAS QEDLEAMFGN VSYLAHFCRK 1210 1220 1230 1240 1250 1260 FQPLYATEAK RVYALEKRMN NYMQFKSKHR IEPVCLIIRG SPGTGKSLAT GIIARAIADK 1270 1280 1290 1300 1310 1320 YHSSVYSLPP DPDHFDGYKQ QVVTVMDDLC QNPDGKDMSL FCQMVSTVDF IPPMASLEEK 1330 1340 1350 1360 1370 1380 GVSFTSKFVI ASTNASNIVV PTVSDSDAIR RRFYMDCDIE VTDSYKTDLG RLDAGRAAKL 1390 1400 1410 1420 1430 1440 CTENNTANFK RCSPLVCGKA IQLRDRKSKV RYSIDTVVSE LIREYNNRSA IGNTIEALFQ 1450 1460 1470 1480 1490 1500 GPLKFKPIRI SLEEKPAPDA ISDLLASVDS EEVRQYCREQ GWIIPETPTN VERHLNRAVL 1510 1520 1530 1540 1550 1560 VMQSIATVVA VVSLVYVIYK LFAGFQGAYS GAPKQALKKP VLRTATVQGP SLDFALSLLR 1570 1580 1590 1600 1610 1620 RNIRQVQTDQ GHFTMLGVRD RLAILPRHSQ PGKTIWVEHK LINVLDAVEL VDEQGVNLEL 1630 1640 1650 1660 1670 1680 TLVTLDTNEK FRDVTKFIPE TITGASDATL VINTEHMPSM FVPVGDVVQY GFLNLSGKPT 1690 1700 1710 1720 1730 1740 HRTMMYNFPT KAGQCGGVVT SVGKIIGIHI GGNGRQGFCA GLKRGYFASE QGEIQWMKPN 1750 1760 1770 1780 1790 1800 KETGRLNING PTRTKLEPSV FHDVFEGNKE PAVLTSKDPR LEVDFEQALF SKYVGNTLHE 1810 1820 1830 1840 1850 1860 PDEYVTQAAL HYANQLKQLD ININKMSMEE ACYGTEYLEA IDLHTSAGYP YSALGVKKRD 1870 1880 1890 1900 1910 1920 ILDPITRDTT KMKFYMDKYG LDLPYSTYVK DELRSLDKIK KGKSRLIEAS SLNDSVYLRM 1930 1940 1950 1960 1970 1980 TFGHLYETFH ANPGTVTGSA VGCNPDVFWS KLPILLPGSL FAFDYSGYDA SLSPVWFRAL 1990 2000 2010 2020 2030 2040 EVVLREIGYS EEAVSLIEGI NHTHHVYRNK TYCVLGGMPS GCSGTSIFNS MINNIIIRTL 2050 2060 2070 2080 2090 2100 LIKTFKGIDL DELNMVAYGD DVLASYPFPI DCSELAKTGK EYGLTMTPAD KSPCFNEVTW 2110 2120 2130 2140 2150 2160 ENATFLKRGF LPDHQFPFLI HPTMPMREIH ESIRWTKDAR NTQDHVRSLC LLAWHNGKEE 2170 2180 2190 YEKFVSTIRS VPIGKALAIP NFENLRRNWL ELF

References

[1]	"Complete genome analysis of enterovirus 71 isolated from an outbreak in Taiwan and rapid identification of enterovirus 71 and coxsackievirus A16 by RT-PCR." Yan J.-J., Su I.-J., Chen P.-F., Liu C.-C., Yu C.-K., Wang J.-R. J. Med. Virol. 65:331-339(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Reticulon 3 binds the 2C protein of enterovirus 71 and is required for viral replication." Tang W.-F., Yang S.-Y., Wu B.-W., Jheng J.-R., Chen Y.-L., Shih C.-H., Lin K.-H., Lai H.-C., Tang P., Horng J.-T. J. Biol. Chem. 282:5888-5898(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HUMAN RTN3.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF177911 Genomic RNA. Translation: AAD55085.1.
3D structure databases
ProteinModelPortal	Q9QF31.
SMR	Q9QF31. Positions 2-68, 74-565, 863-1012, 1549-2193.
ModBase	Search...
Protein family/group databases
MEROPS	C03.020.
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...

Entry information

Entry name

POLG_CX16T

Accession

Primary (citable) accession number: Q9QF31

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 105 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program