Lipid Modification Database
Tag Content
LipidDB ID
LipidDB-103904-00598
Entry Name
UniProt Accession
Theoretical PI
6.56
Molecular Weight
243682.3
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
RNA-directed RNA polymerase
Protein Synonyms/Alias
VP4-VP2; P1A; Virion protein 4; P1B; Virion protein 2; P1C; Virion protein 3; P1D; Virion protein 1; P2A; 3.4.22.29; Picornain 2A; Protein 2A; P2B; P2C; 3.6.1.15; P3A; VPg; Protein 3B; P3B; 3.4.22.28; P3C; 3.4.22.28; RdRp; 2.7.7.48; 3D polymerase; 3Dpol; Protein 3D; 3D;
Gene Name
Gene Synonyms/Alias
Created Date
15-JUL-1999
 Lipid Modification Sites 
 Position   Sequence Form   Peptide   References   Modification Type 
2
Canonical
******MGAQVSTQK
[1][2]
N-Myristoylation
Organism
Coxsackievirus B3 (strain Woodruff)
NCBI Taxa ID
103904
Reference
[1] Muckelbauer JK, Kremer M, Minor I, Diana G, Dutko FJ, Groarke J, Pevear DC,Rossmann MG. The structure of coxsackievirus B3 at 3.5 A resolution. Structure.1995 Jul 15;3(7):653-67.[PMID:8591043]
[2] Lim BK, Yun SH, Ju ES, Gil CO, Kim DK, Jeon ES. Role of the myristoylationsite in expressing exogenous functional proteins in coxsackieviral vector. BiosciBiotechnol Biochem. 2012;76(6):1173-6. Epub 2012 Jun 7.[PMID:22790942]
Functional Description
Capsid protein VP1: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Capsid protein VP1 mainly forms the vertices of the capsid. Capsid protein VP1 interacts with host cell receptor to provide virion attachment to target host cells. This attachment induces virion internalization. Tyrosine kinases are probably involved in the entry process. After binding to its receptor, the capsid undergoes conformational changes. Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized. Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm. After genome has been released, the channel shrinks (By similarity).
Sequence Annotation
Topological domain: 2 1495 Cytoplasmic.
Topological domain: 1512 2185 Cytoplasmic.
Domain: 1205 1361 SF3 helicase.
Domain: 1541 1706 Peptidase C3.
Domain: 1950 2066 RdRp catalytic.
Region: 568 584 Amphipatic alpha-helix.
Region: 1430 1453 Disordered.
Active site: 872 872 For Protease 2A activity.
Active site: 890 890 For Protease 2A activity.
Active site: 961 961 For Protease 2A activity.
Active site: 1580 1580 For Protease 3C activity.
Active site: 1611 1611 For Protease 3C activity.
Active site: 1687 1687 For Protease 3C activity.
Active site: 2052 2052 For RdRp activity.
Functional site: 69 70 Cleavage; by autolysis.
Functional site: 332 333 Cleavage; by Protease 3C.
Functional site: 1001 1002 Cleavage; by Protease 3C.
Functional site: 1429 1430 Cleavage; by Protease 3C.
Functional site: 1518 1519 Cleavage; by Protease 3C.
Functional site: 1540 1541 Cleavage; by Protease 3C.
Functional site: 1723 1724 Cleavage; by Protease 3C.
Modified residue: 1521 1521 O-(5'-phospho-RNA)-tyrosine.
Protein Length
2185 AA.
Protein Sequence
(Canonical)
MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP SKFTEPVKDI  60
MIKSLPALNS PTVEECGYSD RVRSITLGNS TITTQECANV VVGYGVWPDY LKDSEATAED  120
QPTQPDVATC RFYTLDSVQW QKTSPGWWWK LPDALSNLGL FGQNMQYHYL GRTGYTIHVQ  180
CNASKFHQGC LLVVCVPEAE MGCATLNNTP SSAELLGGDS AKEFADKPVA SGSNKLVQRV  240
VYNAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYTNSVP MDNMFRHNNV TLMVIPFVPL  300
DYCPGSTTYV PITITIAPMC AEYNGLRLAG HQGLPTMNTP GSCQFLTSDD FQSPSAMPQY  360
DVTPEMRIPG EVKNLMEIAE VDSVVPVQNV GEKVNSMEAY QIPVRSNEGS GTQVFGFPLQ  420
PGYSSVFSRT LLGEILNYYT HWSGSIKLTF MFCGSAMATG KFLLAYSPPG AGAPTKRVDA  480
MLGTHVVWDV GLQSSCVLCI PWISQTHYRY VASDEYTAGG FITCWYQTNI VVPADAQSSC  540
YIMCFVSACN DFSVRLLKDT PFISQQNFFQ GPVEDAITAA IGRVADTVGT GPTNSEAIPA  600
LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESTIENFLCR SACVYFTEYE NSGAKRYAEW  660
VITPRQAAQL RRKLEFFTYV RFDLELTFVI TSTQQPSTTQ NQDAQILTHQ IMYVPPGGPV  720
PDKVDSYVWQ TSTNPSVFWT EGNAPPRMSV PFLSIGNAYS NFYDGWSEFS RNGVYGINTL  780
NNMGTLYARH VNAGSTGPIK STIRIYFKPK HVKAWIPRPP RLCQYEKAKN VNFQPSGVTT  840
TRQSITTMTN TGAFGQQSGA VYVGNYRVVN RHLATSADWQ NCVWENYNRD LLVSTTTAHG  900
CDIIARCRCT TGVYFCASKN KHYPISFEGP GIVEVQESEY YPRRYQSHVL LAAGFSEPGD  960
CGGILRCEHG VIGIVTMGGE GVVGFADIRD LLWLEDDAME QGVKDYVEQL GNAFGSGFTN  1020
QICEQVNLLK ESLVGQDSIL EKSLKALVKI ISALVIVVRN HDDLITVTAT LALIGCTSSP  1080
WRWLKQKVSQ YYGIPMAERQ NNGWLKKFTE MTNACKGMEW IAIKIQKFIE WLKVKILPEV  1140
REKHEFLNRL KQLPLLESQI ATIEQSAPSQ SDQEQLFSNV QYFAHYCRKY APLYASEAKR  1200
VFSLEKKMSN YIQFKSKCRI EPVCLLLHGS PGAGKSVATN LIGRSLAEKL NSSVYSLPPD  1260
PDHFDGYKQQ AVVIMDDLCQ KPDGKDVSLF CQMVSSVDFV PPMAALEEKG ILFTSPFVLA  1320
STNAGSINAP TVSDSRALAR RFHFDMNIEV ISMYSQNGKI NMPMSVKTCD EECCPVNFKK  1380
CCPLVCGKAI QFIDRRTQVR YSLDMLVTEM FREYNHRHSV GATLEALFQG PPVYREIKIS  1440
VAPETPPPPR IADLLKSVDS EAVREYCKEK GWLVPEVNST LQIEKHVSRA FICLQAITTF  1500
VSVAGIIYII YKLFAGFQGA YTGIPNQKPK VPTLRQAKVQ GPAFEFAVAM MKRNSSTVKT  1560
EYGEFTMLGI YDRWAVLPRH AKPGPTILMN DQEVGVLDAK ELVDKDGTNL ELTLLKLNRN  1620
EKFRDIRGFL AKEEVEVNEA VLAINTSKFP NMYIPVGQVT DYGFLNLGGT PTKRMLMYNF  1680
PTRAGQCGGV LMSTGKVLGI HVGGNGHQGF SAALLKHYFN DEQGEIEFIE SSKEAGFPII  1740
NTPSKTKLEP SVFHQVFEGD KEPAVLRNGD PRLKVNFEEA IFSKYIGNVN THVDEYMMEA  1800
VDHYAGQLAT LDISTEPMKL EDAVYGTEGL EALDLTTSAG YPYVALGIKK RDILSKKTRD  1860
LTKLKECMDK YGLNLPMVTY VKDELRSAEK VAKGKSRLIE ASSLNDSVAM RQTFGNLYKT  1920
FHLNPGVVTG SAVGCDPDLF WSKIPVMLDG HLIAFDYSGY DASLSPVWFA CLKLLLEKLG  1980
YSHKETNYID YLCNSHHLYR DKHYFVRGGM PSGCSGTSIF NSMINNIIIR TLMLKVYKGI  2040
DLDQFRMIAY GDDVIASYPW PIDASLLAEA GKDYGLIMTP ADKGECFNEV TWTNVTFLKR  2100
YFRADEQYPF LVHPVMPMKD IHESIRWTKD PKNTQDHVRS LCLLAWHNGE HEYEEFIRKI  2160
RSVPVGRCLT LPAFSTIRRK WLDSF                                        2185
FASTA
(Canonical)
>LipidDB-103904-00598|Q66282
MGAQVSTQKTGAHETGLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDI
MIKSLPALNSPTVEECGYSDRVRSITLGNSTITTQECANVVVGYGVWPDYLKDSEATAED
QPTQPDVATCRFYTLDSVQWQKTSPGWWWKLPDALSNLGLFGQNMQYHYLGRTGYTIHVQ
CNASKFHQGCLLVVCVPEAEMGCATLNNTPSSAELLGGDSAKEFADKPVASGSNKLVQRV
VYNAGMGVGVGNLTIFPHQWINLRTNNSATIVMPYTNSVPMDNMFRHNNVTLMVIPFVPL
DYCPGSTTYVPITITIAPMCAEYNGLRLAGHQGLPTMNTPGSCQFLTSDDFQSPSAMPQY
DVTPEMRIPGEVKNLMEIAEVDSVVPVQNVGEKVNSMEAYQIPVRSNEGSGTQVFGFPLQ
PGYSSVFSRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGAPTKRVDA
MLGTHVVWDVGLQSSCVLCIPWISQTHYRYVASDEYTAGGFITCWYQTNIVVPADAQSSC
YIMCFVSACNDFSVRLLKDTPFISQQNFFQGPVEDAITAAIGRVADTVGTGPTNSEAIPA
LTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTIENFLCRSACVYFTEYENSGAKRYAEW
VITPRQAAQLRRKLEFFTYVRFDLELTFVITSTQQPSTTQNQDAQILTHQIMYVPPGGPV
PDKVDSYVWQTSTNPSVFWTEGNAPPRMSVPFLSIGNAYSNFYDGWSEFSRNGVYGINTL
NNMGTLYARHVNAGSTGPIKSTIRIYFKPKHVKAWIPRPPRLCQYEKAKNVNFQPSGVTT
TRQSITTMTNTGAFGQQSGAVYVGNYRVVNRHLATSADWQNCVWENYNRDLLVSTTTAHG
CDIIARCRCTTGVYFCASKNKHYPISFEGPGIVEVQESEYYPRRYQSHVLLAAGFSEPGD
CGGILRCEHGVIGIVTMGGEGVVGFADIRDLLWLEDDAMEQGVKDYVEQLGNAFGSGFTN
QICEQVNLLKESLVGQDSILEKSLKALVKIISALVIVVRNHDDLITVTATLALIGCTSSP
WRWLKQKVSQYYGIPMAERQNNGWLKKFTEMTNACKGMEWIAIKIQKFIEWLKVKILPEV
REKHEFLNRLKQLPLLESQIATIEQSAPSQSDQEQLFSNVQYFAHYCRKYAPLYASEAKR
VFSLEKKMSNYIQFKSKCRIEPVCLLLHGSPGAGKSVATNLIGRSLAEKLNSSVYSLPPD
PDHFDGYKQQAVVIMDDLCQKPDGKDVSLFCQMVSSVDFVPPMAALEEKGILFTSPFVLA
STNAGSINAPTVSDSRALARRFHFDMNIEVISMYSQNGKINMPMSVKTCDEECCPVNFKK
CCPLVCGKAIQFIDRRTQVRYSLDMLVTEMFREYNHRHSVGATLEALFQGPPVYREIKIS
VAPETPPPPRIADLLKSVDSEAVREYCKEKGWLVPEVNSTLQIEKHVSRAFICLQAITTF
VSVAGIIYIIYKLFAGFQGAYTGIPNQKPKVPTLRQAKVQGPAFEFAVAMMKRNSSTVKT
EYGEFTMLGIYDRWAVLPRHAKPGPTILMNDQEVGVLDAKELVDKDGTNLELTLLKLNRN
EKFRDIRGFLAKEEVEVNEAVLAINTSKFPNMYIPVGQVTDYGFLNLGGTPTKRMLMYNF
PTRAGQCGGVLMSTGKVLGIHVGGNGHQGFSAALLKHYFNDEQGEIEFIESSKEAGFPII
NTPSKTKLEPSVFHQVFEGDKEPAVLRNGDPRLKVNFEEAIFSKYIGNVNTHVDEYMMEA
VDHYAGQLATLDISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRD
LTKLKECMDKYGLNLPMVTYVKDELRSAEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKT
FHLNPGVVTGSAVGCDPDLFWSKIPVMLDGHLIAFDYSGYDASLSPVWFACLKLLLEKLG
YSHKETNYIDYLCNSHHLYRDKHYFVRGGMPSGCSGTSIFNSMINNIIIRTLMLKVYKGI
DLDQFRMIAYGDDVIASYPWPIDASLLAEAGKDYGLIMTPADKGECFNEVTWTNVTFLKR
YFRADEQYPFLVHPVMPMKDIHESIRWTKDPKNTQDHVRSLCLLAWHNGEHEYEEFIRKI
RSVPVGRCLTLPAFSTIRRKWLDSF
Gene Ontology
GO:0044161; C:host cell cytoplasmic vesicle; IEA:UniProtKB-KW
GO:0044385; C:integral to membrane of host cell; IEA:UniProtKB-KW
GO:0016020; C:membrane; IEA:UniProtKB-KW
GO:0039618; C:T=pseudo3 icosahedral viral capsid; IEA:UniProtKB-KW
GO:0005524; F:ATP binding; IEA:UniProtKB-KW
GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro
GO:0005216; F:ion channel activity; IEA:UniProtKB-KW
GO:0003723; F:RNA binding; IEA:UniProtKB-KW
GO:0003724; F:RNA helicase activity; IEA:InterPro
GO:0003968; F:RNA-directed RNA polymerase activity; IEA:UniProtKB-KW
GO:0005198; F:structural molecule activity; IEA:InterPro
GO:0006260; P:DNA replication; IEA:UniProtKB-KW
GO:0075509; P:endocytosis involved in viral entry into host cell; IEA:UniProtKB-KW
GO:0039520; P:induction by virus of host autophagy; IDA:UniProtKB
GO:0039707; P:pore formation by virus in membrane of host cell; IEA:UniProtKB-KW
GO:0044694; P:pore-mediated entry of viral genome into host cell; IEA:UniProtKB-KW
GO:0051259; P:protein oligomerization; IEA:UniProtKB-KW
GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW
GO:0039657; P:suppression by virus of host gene expression; IEA:UniProtKB-KW
GO:0039522; P:suppression by virus of host mRNA export from nucleus; IEA:UniProtKB-KW
GO:0039544; P:suppression by virus of host RIG-I activity by RIG-I proteolysis; ISS:UniProtKB
GO:0039611; P:suppression by virus of host translation initiation factor activity; ISS:UniProtKB
GO:0006351; P:transcription, DNA-templated; IEA:InterPro
GO:0039694; P:viral RNA genome replication; IEA:InterPro
GO:0019062; P:virion attachment to host cell; IEA:UniProtKB-KW
Interpro
InterPro; IPR003593; AAA+_ATPase
InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir
InterPro; IPR014759; Helicase_SF3_ssRNA_vir
InterPro; IPR027417; P-loop_NTPase
InterPro; IPR014838; P3A
InterPro; IPR000081; Peptidase_C3
InterPro; IPR000199; Peptidase_C3A/C3B_picornavir
InterPro; IPR003138; Pico_P1A
InterPro; IPR002527; Pico_P2B
InterPro; IPR001676; Picornavirus_capsid
InterPro; IPR001205; RNA-dir_pol_C
InterPro; IPR007094; RNA-dir_pol_PSvirus
InterPro; IPR009003; Trypsin-like_Pept_dom
InterPro; IPR029053; Viral_coat
Pfam
Pfam; PF08727; P3A;
Pfam; PF00548; Peptidase_C3;
Pfam; PF02226; Pico_P1A;
Pfam; PF00947; Pico_P2A;
Pfam; PF01552; Pico_P2B;
Pfam; PF00680; RdRP_1;
Pfam; PF00073; Rhv;
Pfam; PF00910; RNA_helicase;
SMART
SMART; SM00382; AAA;
PROSITE
PROSITE; PS50507; RDRP_SSRNA_POS;
PROSITE; PS51218; SF3_HELICASE_2;
PRINTS