P03599 (POL2_CPMVS) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: RNA2 polyprotein Alternative name(s): Genome polyprotein M P2 Cleaved into the following 4 chains: Movement protein Short name=MP Large coat protein Short name=LCP Alternative name(s): Coat protein VP37 Small coat protein, N-terminus part Short name=SCP Alternative name(s): Coat protein VP23 Small coat protein, C-terminus part
Organism	Cowpea mosaic virus (strain SB) (CPMV) [Reference proteome]
Taxonomic identifier	928299 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Picornavirales › Secoviridae › Comovirinae › Comovirus › Cowpea mosaic virus
Virus host	Cajanus cajan (Pigeon pea) (Cajanus indicus) [TaxID: 3821] Crotalaria juncea (Sunn hemp) [TaxID: 3829] Vigna unguiculata (Cowpea) [TaxID: 3917]

Protein attributes

Sequence length	1046 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	Movement protein: transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Acts by forming a tubular structure at the host plasmodesmata, enlarging it enough to allow free passage of virion capsids. Binds to GTP and to single-stranded RNA and single-stranded DNA in a non-sequence-specific manner. Ref.2 Ref.4 Ref.5 The cleavable C-terminus of small coat protein seems to be involved in the packaging of the virion RNAs. Also seems to act as suppressor of post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Ref.2 Ref.4 Ref.5
Subcellular location	Movement protein: Host cell junction › host plasmodesma. Note: Assembles in tubules that are embedded within modified plasmodesmata. Large coat protein: Virion Potential.
Post-translational modification	Specific enzymatic cleavages by RNA1 encoded picornain 3C-like protease in vivo yield mature proteins By similarity. The C-terminal 24 amino acids of small coat protein are cleaved. Ref.2
Miscellaneous	The virus capsid is composed of 60 icosahedral units, each of which is composed of one copy each of the two coat proteins.
Sequence similarities	Belongs to the comoviridae genome polyprotein M family.
Caution	It is uncertain whether Met-1 or Met-118 is the initiator.
Mass spectrometry	Molecular mass is 21121.8 Da from positions 834 - 1022. Determined by ESI. Ref.2

Ontologies

Keywords
Biological process	Transport
Cellular component	Host cell junction Virion
Ligand	DNA-binding GTP-binding Nucleotide-binding RNA-binding
Molecular function	Capsid protein Suppressor of RNA silencing Viral movement protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	spread of virus in host, cell to cell Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	host cell plasmodesma Inferred from electronic annotation. Source: UniProtKB-SubCell viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW GTP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding 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 – 459

459

Movement protein By similarity

PRO_0000037024

Chain

460 – 833

374

Large coat protein By similarity

PRO_0000037025

Chain

834 – 1022

189

Small coat protein, N-terminus part

PRO_0000037026

Chain

1023 – 1046

24

Small coat protein, C-terminus part

PRO_0000037027

Sites

Site

459 – 460

2

Cleavage By similarity

Site

833 – 834

2

Cleavage By similarity

Site

1022 – 1023

2

Cleavage

Experimental info

Mutagenesis

259

1

V → A: Complete loss of GTP binding; when associated with A-260. Ref.5

Mutagenesis

260

1

D → A: Complete loss of GTP binding; when associated with A-259. Ref.5

Secondary structure

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1046

Helix Strand Turn

Details...

Helix

464 – 466

3

Helix

468 – 470

3

Turn

479 – 482

4

Beta strand

483 – 491

9

Beta strand

500 – 505

6

Helix

506 – 510

5

Helix

518 – 523

6

Beta strand

525 – 527

3

Beta strand

529 – 536

8

Beta strand

546 – 555

10

Helix

563 – 566

4

Beta strand

569 – 574

6

Turn

576 – 578

3

Beta strand

580 – 586

7

Helix

597 – 602

6

Beta strand

606 – 613

8

Beta strand

623 – 634

12

Beta strand

645 – 661

17

Beta strand

663 – 666

4

Beta strand

669 – 674

6

Beta strand

680 – 682

3

Beta strand

685 – 687

3

Helix

690 – 695

6

Beta strand

698 – 711

14

Beta strand

721 – 727

7

Helix

737 – 739

3

Beta strand

742 – 745

4

Beta strand

753 – 758

6

Helix

760 – 762

3

Beta strand

767 – 769

3

Helix

777 – 779

3

Beta strand

782 – 791

10

Beta strand

801 – 818

18

Beta strand

845 – 851

7

Beta strand

861 – 866

6

Turn

867 – 870

4

Beta strand

871 – 874

4

Beta strand

881 – 884

4

Helix

888 – 895

8

Beta strand

896 – 911

16

Helix

916 – 918

3

Beta strand

923 – 929

7

Beta strand

938 – 943

6

Beta strand

949 – 957

9

Turn

960 – 962

3

Turn

970 – 973

4

Beta strand

978 – 984

7

Turn

986 – 988

3

Beta strand

989 – 998

10

Beta strand

1003 – 1009

7

Sequences

	Sequence		Length	Mass (Da)
	P03599 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 350EBECBF6558A1E	FASTA	1,046	116,218
	10 20 30 40 50 60 MFSFTEAKSK ISLWTRSAAP LNNVYLSYSC RCGLGKRKLA GGCCSAPYIT CYDSADFRRV 70 80 90 100 110 120 QYLYFCLTRY CCLYFFLLLL ADWFYKKSSI FFETEFSRGF RTWRKIVKLL YILPKFEMES 130 140 150 160 170 180 IMSRGIPSGI LEEKAIQFKR AKEGNKPLKD EIPKPEDMYV SHTSKWNVLR KMSQKTVDLS 190 200 210 220 230 240 KAAAGMGFIN KHMLTGNILA QPTTVLDIPV TKDKTLAMAS DFIRKENLKT SAIHIGAIEI 250 260 270 280 290 300 IIQSFASPES DLMGGFLLVD SLHTDTANAI RSIFVAPMRG GRPVRVVTFP NTLAPVSCDL 310 320 330 340 350 360 NNRFKLICSL PNCDIVQGSQ VAEVSVNVAG CATSIEKSHT PSQLYTEEFE KEGAVVVEYL 370 380 390 400 410 420 GRQTYCAQPS NLPTEEKLRS LKFDFHVEQP SVLKLSNSCN AHFVKGESLK YSISGKEAEN 430 440 450 460 470 480 HAVHATVVSR EGASAAPKQY DPILGRVLDP RNGNVAFPQM EQNLFALSLD DTSSVRGSLL 490 500 510 520 530 540 DTKFAQTRVL LSKAMAGGDV LLDEYLYDVV NGQDFRATVA FLRTHVITGK IKVTATTNIS 550 560 570 580 590 600 DNSGCCLMLA INSGVRGKYS TDVYTICSQD SMTWNPGCKK NFSFTFNPNP CGDSWSAEMI 610 620 630 640 650 660 SRSRVRMTVI CVSGWTLSPT TDVIAKLDWS IVNEKCEPTI YHLADCQNWL PLNRWMGKLT 670 680 690 700 710 720 FPQGVTSEVR RMPLSIGGGA GATQAFLANM PNSWISMWRY FRGELHFEVT KMSSPYIKAT 730 740 750 760 770 780 VTFLIAFGNL SDAFGFYESF PHRIVQFAEV EEKCTLVFSQ QEFVTAWSTQ VNPRTTLEAD 790 800 810 820 830 840 GCPYLYAIIH DSTTGTISGD FNLGVKLVGI KDFCGIGSNP GIDGSRLLGA IAQGPVCAEA 850 860 870 880 890 900 SDVYSPCMIA STPPAPFSDV TAVTFDLING KITPVGDDNW NTHIYNPPIM NVLRTAAWKS 910 920 930 940 950 960 GTIHVQLNVR GAGVKRADWD GQVFVYLRQS MNPESYDART FVISQPGSAM LNFSFDIIGP 970 980 990 1000 1010 1020 NSGFEFAESP WANQTTWYLE CVATNPRQIQ QFEVNMRFDP NFRVAGNILM PPFPLSTETP 1030 1040 PLLKFRFRDI ERSKRSVMVG HTATAA

References

[1]	"Primary structure and gene organization of the middle-component RNA of cowpea mosaic virus." van Wezenbeek P., Verver J., Harmsen J., Vos P., van Kammen A. EMBO J. 2:941-946(1983) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"The cleavable carboxyl-terminus of the small coat protein of cowpea mosaic virus is involved in RNA encapsidation." Taylor K.M., Spall V.E., Butler P.J.G., Lomonossoff G.P. Virology 255:129-137(1999) [PubMed] [Europe PMC] [Abstract] Cited for: MASS SPECTROMETRY, FUNCTION, CLEAVAGE OF SMALL COAT PROTEIN.
[3]	"Glycosylation of the capsid proteins of cowpea mosaic virus: a reinvestigation shows the absence of sugar residues." Altmann F., Lomonossoff G.P. J. Gen. Virol. 81:1111-1114(2000) [PubMed] [Europe PMC] [Abstract] Cited for: ABSENCE OF GLYCOSYLATION AT COAT PROTEINS.
[4]	"Surface-exposed C-terminal amino acids of the small coat protein of Cowpea mosaic virus are required for suppression of silencing." Canizares M.C., Taylor K.M., Lomonossoff G.P. J. Gen. Virol. 85:3431-3435(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF SMALL COAT PROTEIN C-TERMINUS AS SUPPRESSOR OF RNA SILENCING.
[5]	"The movement protein of cowpea mosaic virus binds GTP and single-stranded nucleic acid in vitro." Carvalho C.M., Pouwels J., van Lent J.W., Bisseling T., Goldbach R.W., Wellink J. J. Virol. 78:1591-1594(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF MOVEMENT PROTEIN, MUTAGENESIS OF VAL-259 AND ASP-260.
[6]	"The refined crystal structure of cowpea mosaic virus at 2.8 A resolution." Lin T., Chen Z., Usha R., Stauffacher C.V., Dai J.B., Schmidt T., Johnson J.E. Virology 265:20-34(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 460-1022. Strain: Bi1 mutant.
+	Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X00729 Genomic RNA. Translation: CAA25314.1.

RefSeq

NP_613285.1. NC_003550.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NY7	X-ray	3.00	1	834-1022	[»]
			2	460-828	[»]
2BFU	X-ray	4.00	L	460-828	[»]
			S	834-1022	[»]

ProteinModelPortal

P03599.

SMR

P03599. Positions 460-828, 834-1022.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR003181. Como_LCP.
IPR003182. Como_SCP.
[Graphical view]

Pfam

PF02247. Como_LCP. 1 hit.
PF02248. Como_SCP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P03599.

PMAP-CutDB

P03599.

Entry information

Entry name

POL2_CPMVS

Accession

Primary (citable) accession number: P03599
Secondary accession number(s): Q84103

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	April 3, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program