Reviewed, UniProtKB/Swiss-Prot P27395 (POLG_JAEV1)

Names and origin

Protein names	Recommended name:     Genome polyprotein Cleaved into the following 10 chains:     1- Recommended name:             Protein C         Alternative name(s):             Core protein             Capsid protein     2- Recommended name:             Small envelope protein M         Alternative name(s):             Matrix protein     3- Recommended name:             Envelope protein E     4- Recommended name:             Non-structural protein 1                 Short name=NS1     5- Recommended name:             Non-structural protein 2A                 Short name=NS2A     6- Recommended name:             Flavivirin protease NS2B regulatory subunit     7- Recommended name:             Flavivirin protease NS3 catalytic subunit               EC=3.4.21.91     8- Recommended name:             Non-structural protein 4A                 Short name=NS4A     9- Recommended name:             Non-structural protein 4B                 Short name=NS4B     10- Recommended name:             RNA-directed RNA polymerase               EC=2.7.7.48         Alternative name(s):             NS5
Organism	Japanese encephalitis virus (strain SA-14) [Complete proteome]
Taxonomic identifier	11073 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Flaviviridae › Flavivirus › Japanese encephalitis virus group
Virus host	Culex tritaeniorhynchus (Mosquito) [TaxID: 7178] Ardeidae (herons) [TaxID: 8899] Homo sapiens (Human) [TaxID: 9606] Equus caballus (Horse) [TaxID: 9796] Sus scrofa (Pig) [TaxID: 9823] Bos taurus (Bovine) [TaxID: 9913] Culex gelidus [TaxID: 308713]

Protein attributes

Sequence length	3432 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	The small proteins NS2A, NS4A and NS4B are hydrophobic, suggesting a possible membrane-related function. NS5 may play a role in the viral RNA replication. The NS2B/NS3 protease complex processes the viral polyprotein.
Catalytic activity	Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala. Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	NS3 and NS2B form a heterodimer. NS3 is the catalytic subunit, whereas NS2B strongly stimulates the latter By similarity.
Subcellular location	Protein C: Virion Potential. Host membrane; Single-pass membrane protein Potential. Small envelope protein M: Virion Potential. Host membrane; Single-pass membrane protein Potential. Envelope protein E: Virion Potential. Host membrane; Multi-pass membrane protein Potential. Non-structural protein 4A: Host membrane; Single-pass membrane protein Potential. Non-structural protein 4B: Host membrane; Multi-pass membrane protein Potential.
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins By similarity.
Miscellaneous	The virion of this virus is a nucleocapsid covered by a lipoprotein envelope. The envelope contains two proteins: the protein M and glycoprotein E. The nucleocapsid is a complex of protein C and mRNA. In immature particles, there are 60 icosaedrally organized trimeric spikes on the surface. Each spike consists of three heterodimers of envelope protein M precursor (prM) and envelope protein E By similarity.
Sequence similarities	Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 peptidase S7 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Capsid protein Core protein Envelope protein Membrane Virion
Domain	Transmembrane
Ligand	ATP-binding Nucleotide-binding
Molecular function	Helicase Hydrolase Nucleotidyltransferase RNA-directed RNA polymerase Transferase
PTM	Cleavage on pair of basic residues Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA metabolic process Inferred from electronic annotation. Source: InterPro methylation 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	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW viral envelope Inferred from electronic annotation. Source: UniProtKB-KW viral nucleocapsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW double-stranded RNA binding Inferred from electronic annotation. Source: InterPro methyltransferase activity Inferred from electronic annotation. Source: InterPro serine-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
	Chain	2 – 127	126	Protein C		PRO_0000037836
	Propeptide	128 – 219	92			PRO_0000037837
	Chain	220 – 294	75	Small envelope protein M		PRO_0000037838
	Chain	295 – 794	500	Envelope protein E		PRO_0000037839
	Chain	795 – 1206	412	Non-structural protein 1		PRO_0000037840
	Chain	1207 – 1373	167	Non-structural protein 2A		PRO_0000037841
	Chain	1374 – 1504	131	Flavivirin protease NS2B regulatory subunit		PRO_0000037842
	Chain	1505 – 2123	619	Flavivirin protease NS3 catalytic subunit		PRO_0000037843
	Chain	2124 – 2412	289	Non-structural protein 4A		PRO_0000037844
	Chain	2413 – 2527	115	Non-structural protein 4B		PRO_0000037845
	Chain	2528 – 3432	905	RNA-directed RNA polymerase		PRO_0000037846
Regions
	Transmembrane	44 – 60	17	Potential
	Transmembrane	112 – 127	16	Potential
	Transmembrane	280 – 294	15	Potential
	Transmembrane	774 – 790	17	Potential
	Domain	1685 – 1841	157	Helicase ATP-binding
	Domain	1852 – 2017	166	Helicase C-terminal
	Domain	3057 – 3209	153	RdRp catalytic
	Nucleotide binding	1698 – 1705	8	ATP Potential
	Motif	1789 – 1792	4	DEAH box
Sites
	Active site	1555	1	Charge relay system By similarity
	Active site	1579	1	Charge relay system By similarity
	Active site	1639	1	Charge relay system By similarity
Amino acid modifications
	Glycosylation	142	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	448	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	924	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	1001	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	1594	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	2463	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	2491	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	2761	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	2866	1	N-linked (GlcNAc...); by host Potential
	Glycosylation	2904	1	N-linked (GlcNAc...); by host Potential
	Disulfide bond	297 ↔ 324		By similarity
	Disulfide bond	354 ↔ 410		By similarity
	Disulfide bond	368 ↔ 399		By similarity
	Disulfide bond	386 ↔ 415		By similarity
	Disulfide bond	484 ↔ 581		By similarity
	Disulfide bond	598 ↔ 629		By similarity

Sequences

	Sequence		Length	Mass (Da)
	P27395-1 [UniParc]. Last modified August 1, 1992. Version 1. Checksum: 11B9423735B1B5FE	FASTA	3,432	380,211
	10 20 30 40 50 60 MTKKPGGPGK NRAINMLKRG LPRVFPLVGV KRVVMSLLDG RGPVRFVLAL ITFFKFTALA 70 80 90 100 110 120 PTKALLGRWK AVEKSVAMKH LTSFKRELGT LIDAVNKRGR KQNKRGGNEG SIMWLASLAV 130 140 150 160 170 180 VIACAGAMKL SNFQGKLLMT INNTDIADVI VIPTSKGENR CWVRAIDVGY MCEDTITYEC 190 200 210 220 230 240 PKLTMGNDPE DVDCWCDNQE VYVQYGRCTR TRHSKRSRRS VSVQTHGESS LVNKKEAWLD 250 260 270 280 290 300 STKATRYLMK TENWIIRNPG YAFLAAVLGW MLGSNNGQRV VFTILLLLVA PAYSFNCLGM 310 320 330 340 350 360 GNRDFIEGAS GATWVDLVLE GDSCLTIMAN DKPTLDVRMI NIEASQLAEV RSYCYHASVT 370 380 390 400 410 420 DISTVARCPT TGEAHNEKRA DSSYVCKQGF TDRGWGNGCG LFGKGSIDTC AKFSCTSKAI 430 440 450 460 470 480 GRTIQPENIK YEVGIFVHGT TTSENHGNYS AQVGASQAAK FTVTPNAPSI TLKLGDYGEV 490 500 510 520 530 540 TLDCEPRSGL NTEAFYVMTV GSKSFLVHRE WFHDLALPWT SPSSTAWRNR ELLMEFEGAH 550 560 570 580 590 600 ATKQSVVALG SQEGGLHQAL AGAIVVEYSS SVKLTSGHLK CRLKMDKLAL KGTTYGMCTE 610 620 630 640 650 660 KFSFAKNPVD TGHGTVVIEL SYSGSDGPCK IPIVSVASLN DMTPVGRLVT VNPFVATSSA 670 680 690 700 710 720 NSKVLVEMEP PFGDSYIVVG RGDKQINHHW HKAGSTLGKA FSTTLKGAQR LAALGDTAWD 730 740 750 760 770 780 FGSIGGVFNS IGRAVHQVFG GAFRTLFGGM SWITQGLMGA LLLWMGVNAR DRSIALAFLA 790 800 810 820 830 840 TGGVLVFLAT NVHADTGCAI DITRKEMRCG SGIFVHNDVE AWVDRYKYLP ETPRSLAKIV 850 860 870 880 890 900 HKAHKEGVCG VRSVTRLEHQ MWEAVRDELN VLLKENAVDL SVVVNKPVGR YRSAPKRLSM 910 920 930 940 950 960 TQEKFEMGWK AWGKSILFAP ELANSTFVVD GPETKECPDE HRAWNSMQIE DFGFGITSTR 970 980 990 1000 1010 1020 VWLKIREEST DECDGAIIGT AVKGHVAVHS DLSYWIESRY NDTWKLERAV FGEVKSCTWP 1030 1040 1050 1060 1070 1080 ETHTLWGDDV EESELIIPHT IAGPKSKHNR REGYKTQNQG PWDENGIVLD FDYCPGTKVT 1090 1100 1110 1120 1130 1140 ITEDCSKRGP SVRTTTDSGK LITDWCCRSC SLPPLRFRTE NGCWYGMEIR PVMHDETTLV 1150 1160 1170 1180 1190 1200 RSQVDAFKGE MVDPFQLGLL VMFLATQEVL RKRWTARLTI PAVLGVLLVL MLGGITYTDL 1210 1220 1230 1240 1250 1260 ARYVVLVAAA FAEANSGGDV LHLALIAVFK IQPAFLVMNM LSTRWTNQEN VILVLGAAFF 1270 1280 1290 1300 1310 1320 QLASVDLQIG VHGILNAAAI AWMIVRAITF PTTSSVTMPV LALLTPGMRA LYLDTYRIIL 1330 1340 1350 1360 1370 1380 LVIGICSLLH ERKKTMAKKK GAVLLGLALT STGWFSPTTI AAGLMVCNPN KKRGWPATEF 1390 1400 1410 1420 1430 1440 LSAVGLMFAI VGGLAELDIE SMSIPFMLAG LMAVSYVVSG KATDMWLERA ADISWEMDAA 1450 1460 1470 1480 1490 1500 ITGSSRRLDV KLDDDGDFHL IDDPGVPWKV WVLRMSCIGL AALTPWAIVP AAFGYWLTLK 1510 1520 1530 1540 1550 1560 TTKRGGVFWD TPSPKPCSKG DTTTGVYRIM ARGILGTYQA GVGVMYENVF HTLWHTTRGA 1570 1580 1590 1600 1610 1620 AIMSGEGKLT PYWGSVREDR IAYGGPWRFD RKWNGTDDVQ VIVVEPGKAA VNIQTKPGVF 1630 1640 1650 1660 1670 1680 RTPFGEVGAV SLDYPRGTSG SPILDSNGDI IGLYGNGVEL GDGSYVSAIV QGDRQEEPVP 1690 1700 1710 1720 1730 1740 EAYTPNMLRK RQMTVLDLHP GSGKTRKILP QIIKDAIQQR LRTAVLAPTR VVAAEMAEAL 1750 1760 1770 1780 1790 1800 RGLPVRYQTS AVQREHQGNE IVDVMCHATL THRLMSPNRV PNYNLFVMDE AHFTDPASIA 1810 1820 1830 1840 1850 1860 ARGYIATKVE LGEAAAIFMT ATPPGTTDPF PDSNAPIHDL QDEIPDRAWS SGYEWITEYA 1870 1880 1890 1900 1910 1920 GKTVWFVASV KMGNEIAMCL QRAGKKVIQL NRKSYDTEYP KCKNGDWDFV ITTDISEMGA 1930 1940 1950 1960 1970 1980 NFGASRVIDC RKSVKPTILE EGEGRVILGN PSPITSASAA QRRGRVGRNP NQVGDEYHYG 1990 2000 2010 2020 2030 2040 GATSEDDSNL AHWTEAKIML DNIHMPNGLV AQLYGPEREK AFTMDGEYRL RGEEKKNFLE 2050 2060 2070 2080 2090 2100 LLRTADLPVW LAYKVASNGI QYTDRKWCFD GPRTNAILED NTEVEIVTRM GERKILKPRW 2110 2120 2130 2140 2150 2160 LDARVYADHQ ALKWFKDFAA GKRSAVSFIE VLGRMPEHFM GKTREALDTM YLVATAEKGG 2170 2180 2190 2200 2210 2220 KAHRMALEEL PDALETITLI VAITVMTGGF FLLMMQRKGI GKMGLGALVL TLATFFLWAA 2230 2240 2250 2260 2270 2280 EVPGTKIAGT LLIALLLMVV LIPEPEKQRS QTDNQLAVFL ICVLTVVGVV AANEYGMLEK 2290 2300 2310 2320 2330 2340 TKADLKSMFG GKTQASGLTG LPSMALDLRP ATAWALYGGS TVVLTPLLKH LITSEYVTTS 2350 2360 2370 2380 2390 2400 LASINSQAGS LFVLPRGVPF TDLDLTVGLV FLGCWGQITL TTFLTAMVLA TLHYGYMLPG 2410 2420 2430 2440 2450 2460 WQAEALRAAQ RRTAAGIMKN AVVDGMVATD VPELERTTPL MQKKVGQVLL IGVSVAAFLV 2470 2480 2490 2500 2510 2520 NPNVTTVREA GVLVTAATLT LWDNGASAVW NSTTATGLCH VMRGSYLAGG SIAWTLIKNA 2530 2540 2550 2560 2570 2580 DKPSLKRGRP GGRTLGEQWK EKLNAMSREE FFKYRREAII EVDRTEARRA RRENNIVGGH 2590 2600 2610 2620 2630 2640 PVSRGSAKLR WLVEKGFVSP IGKVIDLGCG RGGWSYYAAT LKKVQEVRGY TKGGAGHEEP 2650 2660 2670 2680 2690 2700 MLMQSYGWNL VSLKSGVDVF YKPSEPSDTL FCDIGESSPS PEVEEQRTLR VLEMTSDWLH 2710 2720 2730 2740 2750 2760 RGPREFCIKV LCPYMPKVIE KMEVLQRRFG GGLVRLPLSR NSNHEMYWVS GAAGNVVHAV 2770 2780 2790 2800 2810 2820 NMTSQVLLGR MDRTVWRGPK YEEDVNLGSG TRAVGKGEVH SNQEKIKKRI QKLKEEFATT 2830 2840 2850 2860 2870 2880 WHKDPEHPYR TWTYHGSYEV KATGSASSLV NGVVELMSKP WDAIANVTTM AMTDTTPFGQ 2890 2900 2910 2920 2930 2940 QRVFKEKVDT KAPEPPAGAK EVLNETTNWL WAHLSREKRP RLCTKEEFIK KVNSNAALGA 2950 2960 2970 2980 2990 3000 VFAEQNQWST AREAVDDPRF WEMVDEEREN HLRGECHTCI YNMMGKREKK PGEFGKAKGS 3010 3020 3030 3040 3050 3060 RAIWFMWLGA RYLEFEALGF LNEDHWLSRE NSGGGVEGSG VQKLGYILRD IAGKQGGKMY 3070 3080 3090 3100 3110 3120 ADDTAGWDTR ITRTDLENEA KVLELLDGEH RMLARAIIEL TYRHKVVKVM RPAAEGKTVM 3130 3140 3150 3160 3170 3180 DVISREDQRG SGQVVTYALN TFTNIAVQLV RLMEAEGVIG PQHLEQLPRK TKIAVRTWLF 3190 3200 3210 3220 3230 3240 ENGEERVTRM AISGDDCVVK PLDDRFATAL HFLNAMSKVR KDIQEWKPSH GWHDWQQVPF 3250 3260 3270 3280 3290 3300 CSNHFQEIVM KDGRSIVVPC RGQDELIGRA RISPGAGWNV KDTACLAKAY AQMWLLLYFH 3310 3320 3330 3340 3350 3360 RRDLRLMANA ICSAVPVDWV PTGRTSWSIH SKGEWMTTED MLQVWNRVWI EENEWMMDKT 3370 3380 3390 3400 3410 3420 PITSWTDVPY VGKREDIWCG SLIGTRSRAT WAENIYAAIN QVRAVIGKEN YVDYMTSLRR 3430 YEDVLIQEDR VI

References

[1]	"Nucleotide sequence of the virulent SA-14 strain of Japanese encephalitis virus and its attenuated vaccine derivative, SA-14-14-2." Nitayaphan S., Grant J.A., Chang G.J.J., Trent D.W. Virology 177:541-552(1990) [PubMed: 2371768] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases

EMBLGenBankDDBJ

M55506 Genomic RNA. Translation: AAA46248.1.
M55506 Genomic RNA. Translation: AAA46249.1. Different initiation.

PIR

GNWVJS. A35519.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2Z83	X-ray	1.80	A	1685-2123	[»]

SMR

P27395. Positions 295-693, 1514-1680, 2533-2794.

ModBase

Search...

Family and domain databases

InterPro

IPR014001. DEAD-like_N.
IPR011492. DEAD_Flavivir.
IPR001650. DNA/RNA_helicase_C.
IPR002464. DNA/RNA_helicase_DEAH_CS.
IPR000069. Env_glycoprot_M_flavivir.
IPR013756. Flav_glyE_cen_2.
IPR011999. Flav_glyE_cen_dm.
IPR013754. Flav_glyE_dim.
IPR001122. Flavi_capsidC.
IPR001157. Flavi_NS1.
IPR000752. Flavi_NS2A.
IPR000487. Flavi_NS2B.
IPR000404. Flavi_NS4A.
IPR001528. Flavi_NS4B.
IPR002535. Flavi_propep.
IPR000336. Flv_glyE_Ig-like.
IPR014412. Gen_Poly_FLV.
IPR014021. Helicase_SF1/SF2_ATP-bd.
IPR001850. Peptidase_S7.
IPR000208. RNA_pol_flaviviral.
IPR007094. RNA_pol_PSvir.
IPR002877. rRNA_MeTrfase_RrmJ/FtsJ.
[Graphical view]

Gene3D

G3DSA:3.30.67.10. Flav_glyE_cen_2. 1 hit.
G3DSA:2.60.98.10. Flav_glyE_dim. 1 hit.
G3DSA:2.60.40.350. Flv_glyE_Ig-like. 1 hit.

Pfam

PF01003. Flavi_capsid. 1 hit.
PF07652. Flavi_DEAD. 1 hit.
PF02832. Flavi_glycop_C. 1 hit.
PF00869. Flavi_glycoprot. 1 hit.
PF01004. Flavi_M. 1 hit.
PF00948. Flavi_NS1. 1 hit.
PF01005. Flavi_NS2A. 1 hit.
PF01002. Flavi_NS2B. 1 hit.
PF01350. Flavi_NS4A. 1 hit.
PF01349. Flavi_NS4B. 1 hit.
PF00972. Flavi_NS5. 1 hit.
PF01570. Flavi_propep. 1 hit.
PF01728. FtsJ. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00949. Peptidase_S7. 1 hit.
[Graphical view]

PIRSF

PIRSF003817. Gen_Poly_FLV. 1 hit.

ProDom

PD001496. Flavi_NS1. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS00690. DEAH_ATP_HELICASE. False negative.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

POLG_JAEV1

Accession

Primary (citable) accession number: P27395
Secondary accession number(s): Q82920 , Q82921, Q82922, Q82923, Q82924, Q82925, Q82926, Q82927, Q82928

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1992
Last sequence update:	August 1, 1992
Last modified:	June 16, 2009
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)