Reviewed, UniProtKB/Swiss-Prot P90245 (POL1_BAMMN)

Names and origin

Protein names	Recommended name:     Genome polyprotein 1 Cleaved into the following 8 chains:     1- Recommended name:             Protein P3     2- Recommended name:             6 kDa protein 1                 Short name=6K1     3- Recommended name:             Cytoplasmic inclusion protein                 Short name=CI     4- Recommended name:             6 kDa protein 2                 Short name=6K2     5- Recommended name:             Viral genome-linked protein         Alternative name(s):             VPg     6- Recommended name:             Nuclear inclusion protein A                 Short name=NI-a                 Short name=NIa               EC=3.4.22.44         Alternative name(s):             NIa-pro     7- Recommended name:             Nuclear inclusion protein B                 Short name=NI-b                 Short name=NIb               EC=2.7.7.48         Alternative name(s):             RNA-directed RNA polymerase     8- Recommended name:             Coat protein                 Short name=CP
Organism	Barley mild mosaic virus (strain Na1) (BaMMV) [Complete proteome]
Taxonomic identifier	103900 [NCBI]
Taxonomic lineage	Viruses › ssRNA positive-strand viruses, no DNA stage › Potyviridae › Bymovirus
Virus host	Hordeum vulgare (Barley) [TaxID: 4513]

Protein attributes

Sequence length	2258 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	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 proteolytic activity By similarity.
Catalytic activity	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	Coat protein: Virion Potential.
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 RNA1 of bymoviruses 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 eight individual proteins Potential.
Sequence similarities	Belongs to the bymoviruses polyprotein 1 family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 peptidase C4 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	RNA replication
Cellular component	Capsid protein Virion
Ligand	ATP-binding Nucleotide-binding
Molecular function	Helicase Hydrolase Nucleotidyltransferase RNA-directed RNA polymerase Transferase
PTM	Covalent protein-RNA linkage Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	RNA-protein covalent cross-linking 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	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: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type peptidase activity Inferred from electronic annotation. Source: InterPro helicase activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 292	292	Protein P3 Potential		PRO_0000040530
	Chain	293 – 359	67	6 kDa protein 1 Potential		PRO_0000040531
	Chain	360 – 1017	658	Cytoplasmic inclusion protein Potential		PRO_0000040532
	Chain	1018 – 1081	64	6 kDa protein 2 Potential		PRO_0000040533
	Chain	1082 – 1260	179	Viral genome-linked protein Potential		PRO_0000040534
	Chain	1261 – 1473	213	Nuclear inclusion protein A Potential		PRO_0000040535
	Chain	1474 – 2007	534	Nuclear inclusion protein B Potential		PRO_0000040536
	Chain	2008 – 2258	251	Coat protein Potential		PRO_0000040537
Regions
	Domain	439 – 597	159	Helicase ATP-binding
	Domain	612 – 778	167	Helicase C-terminal
	Domain	1745 – 1869	125	RdRp catalytic
	Nucleotide binding	487 – 494	8	ATP Potential
Sites
	Active site	1302	1	For nuclear inclusion protein A activity By similarity
	Active site	1338	1	For nuclear inclusion protein A activity By similarity
	Active site	1405	1	For nuclear inclusion protein A activity By similarity
	Site	292 – 293	2	Cleavage Potential
	Site	359 – 360	2	Cleavage Potential
	Site	1017 – 1018	2	Cleavage Potential
	Site	1081 – 1082	2	Cleavage Potential
	Site	1260 – 1261	2	Cleavage Potential
	Site	1473 – 1474	2	Cleavage Potential
	Site	2007 – 2008	2	Cleavage Potential
Amino acid modifications
	Modified residue	1141	1	O-(5'-phospho-RNA)-tyrosine By similarity

Sequences

	Sequence		Length	Mass (Da)
	P90245-1 [UniParc]. Last modified May 1, 1997. Version 1. Checksum: 38A06A36F19D4D4A	FASTA	2,258	256,357
	10 20 30 40 50 60 MEEFIPEVFY QNQVQSLKKI LKSWKRDTSI YAYLAREQEV LAFLVLSPAH IAKLNKLLTE 70 80 90 100 110 120 ESARCALLAQ NCETIEALAV VRQALQGVTL HFGDNGMEKG WLHMMKALDA CLDESFSENA 130 140 150 160 170 180 AALKKSIQAV GHKLIAAKNR IESCERSVNH LTTFQFAREY GLSTTYFEKL SNFGGHIRSF 190 200 210 220 230 240 VWSSDSGEIF PKPKRSSRTK RISTFTSYYW GEFWCNCIWL LCSLWSPARW CFNSVVFIWS 250 260 270 280 290 300 LCGVLNLSMV VLQFTLKRHF GRYYFRYVMS GVLAICAVCC VHLKNRKGPI LQASQKDKRF 310 320 330 340 350 360 IGILAFCITV IYMFDVDLAD SLSNNLHKIS RLVNLFLDDN RGFATPALDN LTDFTTILQS 370 380 390 400 410 420 GTSSDDLKIV QDTLAVVLQV DDEDATQDDA IYDSDGLQTF KQWVSHNQLA GMQLARPLQY 430 440 450 460 470 480 PCSTTYGLTA DNVAELATSM AQEAKQWSQV VGHTGSGKST RLPTAYANCL KGLAGRKKNV 490 500 510 520 530 540 LVCEPTRAAT VNVTSGISQN FGRLVYGRHE GWSNLGDKTI QVMTYGSALA AWKVDNKFLS 550 560 570 580 590 600 QFDAVFLDES HLITTHALVF ESICQEVTNV RKFYVSATPR DGKKCPEAVR RYEIKTVKSE 610 620 630 640 650 660 CSSVDTFVRS QDKENSLYVL QHETVLVFLA GKAECDRAAS NWNKLYSTNM YAYSLTGDNF 670 680 690 700 710 720 TVAYENIVTR MLTDRIIVFC TNILETGVTL NVDCVVDFGF TMRPELDLVD KSLTLMRRRV 730 740 750 760 770 780 TENERAQRIG RAGRLRTGHA ICIGNPETRH DLVPPETLYE AALLSFVHGV QFYINEHFEN 790 800 810 820 830 840 AWIEGVTKSQ ASVMTQFKLS PFLMRDIVRD DGAIPLSLHK ILKNYTHRNT DLIGTKLSVM 850 860 870 880 890 900 SHVYNSWPLY RTVHQSIFRG DSNVPQALKH ARVPFNVSTA HDFPWENFAQ ACLEFQPRVL 910 920 930 940 950 960 QVFSDSSSTS RIINLQIGKM HIVNSMEEVK ININSYQRSA ENLRSVKDSF ESSIFRTKLL 970 980 990 1000 1010 1020 RGNPTGKITK RIETLLDNVR VLQQVHAKLE IIAYSGGEKL NMDKKSVDEL NEIVELQSKN 1030 1040 1050 1060 1070 1080 SLTAEELARI LHLTKPTSTF FNLFAERGRQ MLVTLLVMVA ASLMYLVFWV SPRKQDDITI 1090 1100 1110 1120 1130 1140 EGKGRAYNRD KRMGYDSYEE DEVRHKINKK FKERSTRFSN DSKPETSSKY RNLKQEFVNF 1150 1160 1170 1180 1190 1200 YDLKTDANVL QAVFTAMDGA VLLQTEAPMA DIDRVNRLLN DHFEDSESQA AHEGLNTMVK 1210 1220 1230 1240 1250 1260 CHLTMKDGRQ FELDMEQHDP ETIAKLGGEV GFRMNRYDLR QVGATRYINP KAQTSAATLE 1270 1280 1290 1300 1310 1320 GMTMKPMSAF TIDSAKMVGF IKTAKDTLNC ILYGDWIIAP AHIQQGEGDI TFIFQHTQFT 1330 1340 1350 1360 1370 1380 TTTERLASYG IRQFKGLDLV VIRRPQQIRA VKKDMRASIL DTPTEVQMLY LSTKGGKYQV 1390 1400 1410 1420 1430 1440 STSAVCFPHY NNRWGHVIST AEGMCGCIVF NPTTNHIVGI HVSYNDTRRR NEFQAFTSDV 1450 1460 1470 1480 1490 1500 LTTINAPGHE IPFSPWVFDW KFCGYTTKPR NMQSAPSTLE RLNINATGFG FKLNAQGIKP 1510 1520 1530 1540 1550 1560 AMLRSTETFS REFPNTQFKL IGEVKKGLID KHTITGENPY FLEFLNTFKP YQWVQAFMDE 1570 1580 1590 1600 1610 1620 YAPSILAYDA YFKDLKKYDR PPHASVFCED TLTKAKHKMI KILEEAGMGR TLVRTTEQVL 1630 1640 1650 1660 1670 1680 LDMAWTTSGG PLYHGKKIDI VQHLSDDELV QFSEACQQAL ITGTLDGVWN GSLKAELRSS 1690 1700 1710 1720 1730 1740 QKILERKTRV FTAAPITSLI AMKYYVDDFN KQFYKTHLKA PHTVGINKFN RGWQNLYEKL 1750 1760 1770 1780 1790 1800 NKPGWTHGSG DGSRFDSSID GFLFDVIKDI RKHFMDAEHH KQLDTIYEEI VNTKICLANG 1810 1820 1830 1840 1850 1860 LVIQKNCGNN SGQPSTVVDN TLALMTSFLY AYARLTGDDT FELMDENFVF VCNGDDNKFA 1870 1880 1890 1900 1910 1920 MSPSFMVKFG CDFSPFLSEL GLTYEFDEAT EDICENPYMS LTMVRTSFGI GFSLSIERIV 1930 1940 1950 1960 1970 1980 AILQWSRAGG VLHAYLSGIA ALFESFNTPK LFNLVHTYLL WLVTEHEEEL FSMMELKDMF 1990 2000 2010 2020 2030 2040 MPLPTKEQIA LLHYVGTEPI MEETYLQSGK DDPDPIVPPV SDTDLTNMAA APPDNRRSRA 2050 2060 2070 2080 2090 2100 VVPRGTSDWN LPEPKMRMLG FKSKINIETL ADVPEGYMNT FASVATETQR RKWEEATRGD 2110 2120 2130 2140 2150 2160 FGITDNEKWE KLLIAACIYF ADNGTSPNFD EELTMEVNGG LNSIKEYPVR PFVVRAKKIS 2170 2180 2190 2200 2210 2220 TLRRIFRCYS IETKLMFVKL RRVPQWAIKH GCLDEIVFDF MIPDQFTSRT ALETLKQTKL 2230 2240 2250 AAIGVGTSNS LLTSEQTNMR TTETRRRNDY DGHEALLR

References

[1]	"The complete nucleotide sequence and genome organization of barley mild mosaic virus (Na1 strain)." Kashiwazaki S. Arch. Virol. 141:2077-2089(1996) [PubMed: 8973524] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	D83408 Genomic RNA. Translation: BAA18953.1.
3D structure databases
HSSP	HSSP built from PDB template 1HEI based on UniProtKB P27958.
ModBase	Search...
Family and domain databases
InterPro	IPR014001. DEAD-like_N. IPR001650. DNA/RNA_helicase_C. IPR014021. Helicase_SF1/SF2_ATP-bd. IPR001730. Peptidase_C4. IPR001592. Poty_coat. IPR013648. PP_Potyviridae. IPR001205. RNA-dir_pol_picornavirus. IPR007094. RNA-dir_pol_PSvirus. [Graphical view]
Pfam	PF00271. Helicase_C. 1 hit. PF00863. Peptidase_C4. 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]
PROSITE	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

POL1_BAMMN

Accession

Primary (citable) accession number: P90245

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	May 1, 1997
Last modified:	October 13, 2009
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)