P21231 (POLG_SBMVN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 10 chains: P1 proteinase EC=3.4.-.- Alternative name(s): N-terminal protein Helper component proteinase Short name=HC-pro EC=3.4.22.45 Protein P3 6 kDa protein 1 Short name=6K1 Cytoplasmic inclusion protein Short name=CI EC=3.6.4.- 6 kDa protein 2 Short name=6K2 Viral genome-linked protein Alternative name(s): VPg Nuclear inclusion protein A Short name=NI-a Short name=NIa EC=3.4.22.44 Alternative name(s): 49 kDa proteinase Short name=49 kDa-Pro NIa-pro Nuclear inclusion protein B Short name=NI-b Short name=NIb EC=2.7.7.48 Alternative name(s): RNA-directed RNA polymerase Capsid protein Short name=CP Alternative name(s): Coat protein
Organism	Soybean mosaic virus (strain N) (SMV) [Complete proteome]
Taxonomic identifier	12223 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Potyvirus
Virus host	Glycine max (Soybean) (Glycine hispida) [TaxID: 3847]

Protein attributes

Sequence length	3066 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 protein is involved in aphid transmission, cell-to-cell and systemis movement, encapsidation of the viral RNA and in the regulation of viral RNA amplification. Nuclear inclusion protein B is a RNA-dependent RNA polymerase that plays an essential role in the virus replication. Helper component proteinase is required for aphid transmission and also has proteolytic activity. Interacts with virions and aphid stylets. Acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. May have RNA-binding activity By similarity. Cytoplasmic inclusion protein has helicase activity. It may be involved in replication By similarity. Both 6K peptides are indispensable for virus replication By similarity. Nuclear inclusion protein A has RNA-binding and proteolytic activities.
Catalytic activity	Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein. Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved. Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subcellular location	Capsid protein: Virion Potential.
Domain	The N-terminus of helper component proteinase is involved in interaction with stylets. The central part is involved in interaction with virions and the C-terminus is involved in cell-to cell movement of the virus.
Post-translational modification	VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase By similarity. The viral RNA of potyviruses is expressed as a single polyprotein which undergoes post-translational proteolytic processing by the main proteinase NIa-pro resulting in the production of at least ten individual proteins. The P1 proteinase and the HC-pro cleave only their respective C-termini autocatalytically. 6K1 is essential for proper proteolytic separation of P3 from CI By similarity.
Sequence similarities	Belongs to the potyviruses polyprotein family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 peptidase C4 domain. Contains 1 peptidase C6 domain. Contains 1 peptidase S30 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	Capsid protein Helicase Hydrolase Nucleotidyltransferase Protease RNA-directed RNA polymerase Suppressor of RNA silencing Thiol protease Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	RNA-protein covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular component	viral capsid 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 binding 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
	Chain	1 – 308	308	P1 proteinase Potential		PRO_0000040438
	Chain	309 – 765	457	Helper component proteinase Potential		PRO_0000040439
	Chain	766 – 1112	347	Protein P3 By similarity		PRO_0000040440
	Chain	1113 – 1164	52	6 kDa protein 1 By similarity		PRO_0000040441
	Chain	1165 – 1798	634	Cytoplasmic inclusion protein By similarity		PRO_0000040442
	Chain	1799 – 1851	53	6 kDa protein 2 By similarity		PRO_0000040443
	Chain	1852 – 2041	190	Viral genome-linked protein By similarity		PRO_0000040444
	Chain	2042 – 2284	243	Nuclear inclusion protein A By similarity		PRO_0000040445
	Chain	2285 – 2801	517	Nuclear inclusion protein B By similarity		PRO_0000040446
	Chain	2802 – 3066	265	Capsid protein By similarity		PRO_0000040447
Regions
	Domain	1236 – 1388	153	Helicase ATP-binding
	Domain	1407 – 1566	160	Helicase C-terminal
	Domain	2042 – 2260	219	Peptidase C4
	Domain	2526 – 2650	125	RdRp catalytic
	Nucleotide binding	1249 – 1256	8	ATP Potential
	Motif	361 – 364	4	Involved in interaction with stylet and aphid transmission By similarity
	Motif	617 – 619	3	Involved in virions binding and aphid transmission By similarity
	Motif	1338 – 1341	4	DECH box
	Motif	1891 – 1900	10	Nuclear localization signal Potential
Sites
	Active site	262	1	For P1 proteinase activity By similarity
	Active site	651	1	For helper component proteinase activity By similarity
	Active site	724	1	For helper component proteinase activity By similarity
	Active site	2087	1	For nuclear inclusion protein A activity By similarity
	Active site	2122	1	For nuclear inclusion protein A activity By similarity
	Active site	2192	1	For nuclear inclusion protein A activity By similarity
	Site	308 – 309	2	Cleavage; by P1 proteinase Potential
	Site	765 – 766	2	Cleavage; by HC-pro Potential
	Site	1112 – 1113	2	Cleavage; by NIa-pro By similarity
	Site	1164 – 1165	2	Cleavage; by NIa-pro By similarity
	Site	1798 – 1799	2	Cleavage; by NIa-pro By similarity
	Site	1851 – 1852	2	Cleavage; by NIa-pro By similarity
	Site	2041 – 2042	2	Cleavage; by NIa-pro By similarity
	Site	2284 – 2285	2	Cleavage; by NIa-pro By similarity
	Site	2801 – 2802	2	Cleavage; by NIa-pro By similarity
Amino acid modifications
	Modified residue	1915	1	O-(5'-phospho-RNA)-tyrosine By similarity
Experimental info
	Sequence conflict	2764	1	A → L AA sequence Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P21231 [UniParc]. Last modified June 6, 2002. Version 2. Checksum: 394149153DD5328F	FASTA	3,066	349,846
	10 20 30 40 50 60 MATIMIGSMA ISVPNTHVSC ASNSVMPVQA VQMAKQVPSA RGVLYTLKRE GSTQVHKHEE 70 80 90 100 110 120 ALRKFQEAFD QDVGIQRRLL VNKHSSIQST KKNGLTLRRL TLEQARAKEA AIARRKQEEE 130 140 150 160 170 180 DFLNGKYEQQ FYAGVSATKS MKFEGGSVGF RTKYWRPTPK KTKERRATSQ CRKPTYVLEE 190 200 210 220 230 240 VLSIASKSGK LVEFITGKGK RVKVCYVRKH GAILPKFSLP HEEGKYIHQE LQYASTYEFL 250 260 270 280 290 300 PYICMFAKYK SINADDITYG DSGLLFDERS SLTTNHTKLP YFVVRGRRNG KLVNALEVVE 310 320 330 340 350 360 NMEDIQHYSQ NPEAQFFRGW KKVFDKMPPH VENHECTTDF TNEQCGELAA AISQSIFPVK 370 380 390 400 410 420 KLSCKQCRQH IKHLSWEEYK QFLLAHMGCH GPEWETFQEI DGMRYVKRVI ETSTAENASL 430 440 450 460 470 480 QTSLEIVRLT QNYKSTHMLQ IQDINKALMK GPSVTQSELE QASKQLLAMT QWWKNHMTLT 490 500 510 520 530 540 DEDALKVFRN KRSSKALLNP SLLCDNQLDK NGNFVWGERG RHSKRFFANY FEEVVPSEGY 550 560 570 580 590 600 SKYVIRKNPN GQRELAIGSL IVPLDFERAR MALQGKSVTR EPITMSCISR QDGNFVYPCC 610 620 630 640 650 660 CVTHDDGKAF YSELRSPTKR HLVIGTSGDP KYIDLPATDA DRMYIAKEGF CYLNIFLAML 670 680 690 700 710 720 VNVNEDEAKD FTKMVRDVIV PRLGKWPTML DVATAAYMLT VFHPETRNAE LPRILVDHAC 730 740 750 760 770 780 QTMHVIDSFG SLTVGYHVLK AGTVNQLIQF ASNDLQSEMK FYRVGGEVQQ RMKCETALIT 790 800 810 820 830 840 SIFKPKRMIQ ILENDPYILL MGLVSPSILI HMYRMKHFEK GVELWISKEH SVAKIFIILE 850 860 870 880 890 900 QLTKRVAAND VLLEQLEMIS ETSERFMSIL EDCPQAPHSY KTAKDLLTMY IERKASNNQL 910 920 930 940 950 960 VENGFVDMND KLYMAYEKIY SDRLKQEWRA LSWLEKFSIT WQLKRFAPHT EKCLTKKVVE 970 980 990 1000 1010 1020 ESSASSGNFA SVCFMNAQSH LRNVRNTLFQ KCDQVWTASV RAFVKLIIST LHRCYSDIVY 1030 1040 1050 1060 1070 1080 LVNICIIFSL LVQMTSVLQG IVNTVRRDKA LLSGWKRKED EEAVIHLYEM CEKMEGGHPS 1090 1100 1110 1120 1130 1140 IEKFLDHVKG VRPDLLPVAV SMTGQSEDVS AQAKTATQLQ LEKIVAFMAL LTMCIDNERS 1150 1160 1170 1180 1190 1200 DAVFKVLSKL KAFFSTMGED VKVQSLDEIQ SIDEDKKLTI DFDLETNKES SSVSFDVKFE 1210 1220 1230 1240 1250 1260 AWWNRQLEQN RVIPHYRSTG EFLEFTRETA AKIANLVATS SHTEFLIRGA VGSGKSTGLP 1270 1280 1290 1300 1310 1320 HHLSKKGKVL LLEPTRPLAE NVSKQLSFEP FYHNVTLRMR GMSKFGSSNI VVMTSGFAFH 1330 1340 1350 1360 1370 1380 YYVNNPQQLS DFDFIIIDEC HVQDSPTIAF NCALKEFEFS GKLIKVSATP PGRECEFTTQ 1390 1400 1410 1420 1430 1440 HPVKLKVEDH LSFQNFVQAQ GTGSNADMIQ HGNNLLVYVA SYNEVDQLSR LLTEKHYKVT 1450 1460 1470 1480 1490 1500 KVDGRTMQMG NVEIATTGTE GKPHFIVATN IIENGVTLDI DCVIDFGLKV VATLDTDNRC 1510 1520 1530 1540 1550 1560 VRYNKQSVSY GERIQRLGRV GRCKPGFALR IGHTGKGVEE VPEFIATEAA FLSFAYGLPV 1570 1580 1590 1600 1610 1620 TTQSVSTNIL SRCTVKQARV ALNFELTPFF TTNFIKYDGS MHPEIHRLLK SYKLRESEML 1630 1640 1650 1660 1670 1680 LTKIAIPYQF VGQWVTVKEY ERQGIHLNCP EKVKIPFYVH GIPDKLYEML WDTVCKYKND 1690 1700 1710 1720 1730 1740 AGFGSVKSVN ATKISYTLST DPTAIPRTLA ILDHLLSEEM TKKSHFDTIG SAVTGYSFSL 1750 1760 1770 1780 1790 1800 AGIADGFRKR YLKDYTQHNI AVLQQAKAQL LEFDCNKVDI NNLHNVEGIG ILNAVQLQSK 1810 1820 1830 1840 1850 1860 HEVSKFLQLK GKWDGKKFMN DAVVAIFTLV GGGWMLWDYF TRVIREPVST QGKKRQIQKL 1870 1880 1890 1900 1910 1920 KFRDAFDRKI GREVYADDYT MEHTFGEAYT KKGKQKGSTR TKGMGRKSRN FIHLYGVEPE 1930 1940 1950 1960 1970 1980 NYSMIRFVDP LTGHTMDEHP RVDIRMVQQE FEEIRKDMIG EGELDRQRVY HNPGLQAYFI 1990 2000 2010 2020 2030 2040 GKNTEEALKV DLTPHRPTLL CQNSNAIAGF PEREDELRQT GLPQVVSKSD VPRAKERVEM 2050 2060 2070 2080 2090 2100 ESKSVYKGLR DYSGISTLIC QLTNSSDGHK ETMFGVGYGS FIITNGHLFR RNNGMLTVKT 2110 2120 2130 2140 2150 2160 WHGEFVIHNT TQLKIHFIQG KDVILIRMPK DFPPFGKRNL FRQPKREERV CMVGTNFQEK 2170 2180 2190 2200 2210 2220 SLRATVSESS MILPEGKGSF WIHWITTQDG FCGLPLVSVN DGHIVGIHGL TSNDSEKNFF 2230 2240 2250 2260 2270 2280 VPLTDGFEKE YLENADNLSW DKHWFWEPSK IAWGSLNLVE EQPKEEFKIS KLVSDLFGNT 2290 2300 2310 2320 2330 2340 VTVQGRKERW VLDAMEGNLA ACGQADSALV TKHVVKGKCP YFAQYLSVNQ EAKSFFEPLM 2350 2360 2370 2380 2390 2400 GAYQPSRLNK DAFKRDFFKY NKPVVLNEVD FQSFERAVAG VKLMMMEFDF KECVYVTDPD 2410 2420 2430 2440 2450 2460 EIYDSLNMKA AVGAQYKGKK QDYFSGMDSF DKERLLYLSC ERLFYGEKGV WNGSLKAELR 2470 2480 2490 2500 2510 2520 PIEKVQANKT RTFTAAPIDT LLGAKVCVDD FNNQFYSLNL TCPWTVGMTK FYRGWDKLMR 2530 2540 2550 2560 2570 2580 SLPDGWVYCH ADGSQFDSSL TPLLLNAVLD VRSFFMEDWW VGREMLENLY AEIVYTPILA 2590 2600 2610 2620 2630 2640 PDGTIFKKFR GNNSGQPSTV VDNTLMVVIA MYYSCCKQGW SEEDIQERLV FFANGDDIIL 2650 2660 2670 2680 2690 2700 AVSDKDTWLY DTLSTSFAEL GLNYNFEERT KKREELWFMS HKAVLVDGIY IPKLEPERIV 2710 2720 2730 2740 2750 2760 SILEWDRSKE LMHRTEAICA SMIEAWGYTE LLQEIRKFYL WLLNKDEFKE LASSGKAPYI 2770 2780 2790 2800 2810 2820 AETALRKLYT DVNAQTSELQ RYLEVLDFNH ADDCCESVSL QSGKEKEGDM DADKDPKKST 2830 2840 2850 2860 2870 2880 SSSKGAGTSS KDVNVGSKGK VVPRLQKITR KMNLPMVEGK IILSLDHLLE YKPNQVDLFN 2890 2900 2910 2920 2930 2940 TRATRTQFEA WYNAVKDEYE LDDEQMGVVM NGFMVWCIDN GTSPDANGVW VMMDGEEQIE 2950 2960 2970 2980 2990 3000 YPLKPIVENA KPTLRQIMHH FSDAAEAYIE MRNSESPYMP RYGLLRNLRD RELARYAFDF 3010 3020 3030 3040 3050 3060 YEVTSKTPNR AREAIAQMKA AALSGVNNKL FGLDGNISTN SENTERHTAR DVNQNMHTLL GMGPPQ

References

[1]	"Two genes of soybean mosaic virus are involved in the interaction with the Rsv1 resistance allele of soybean." Eggenberger A.L., Beachy R.N., Hill J.H. Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"The nucleotide sequence of a soybean mosaic virus coat protein-coding region and its expression in Escherichia coli, Agrobacterium tumefaciens and tobacco callus." Eggenberger A.L., Stark D.M., Beachy R.N. J. Gen. Virol. 70:1853-1860(1989) [PubMed: 2661723] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2764-3066, PROTEIN SEQUENCE OF 2845-2859.
[3]	"Potyvirus proteins: a wealth of functions." Urcuqui-Inchima S., Haenni A.L., Bernardi F. Virus Res. 74:157-175(2001) [PubMed: 11226583] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBL GenBank DDBJ	D00507 Genomic RNA. Translation: BAA00398.2.
PIR	PS0081.
RefSeq	NP_072165.1. NC_002634.1.
3D structure databases
ProteinModelPortal	P21231.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	918483.
Family and domain databases
InterPro	IPR014001. DEAD-like_helicase. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR001650. Helicase_C. IPR009003. Pept_cys/ser_Trypsin-like. IPR002540. Pept_S30_P1_potyvir. IPR001730. Peptidase_C4. IPR001456. Peptidase_C6. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. [Graphical view]
Pfam	PF00270. DEAD. 1 hit. PF00271. Helicase_C. 1 hit. PF00863. Peptidase_C4. 1 hit. PF00851. Peptidase_C6. 1 hit. PF01577. Peptidase_S30. 1 hit. PF00767. Poty_coat. 1 hit. PF08440. Poty_PP. 1 hit. PF00680. RdRP_1. 1 hit. [Graphical view]
PRINTS	PR00966. NIAPOTYPTASE.
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
SUPFAM	SSF50494. Pept_Ser_Cys. 1 hit.
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51436. POTYVIRUS_NIA_PRO. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

POLG_SBMVN

Accession

Primary (citable) accession number: P21231

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	June 6, 2002
Last modified:	November 16, 2011
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program