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Protein

Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase

Gene

PAPS

Organism
Vaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.3 Publications

Catalytic activityi

S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(purine-ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-[mRNA].

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221mRNA cap
Binding sitei39 – 391S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei66 – 661S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei68 – 681S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation1 Publication
Binding sitei72 – 721S-adenosyl-L-methionine; via amide nitrogenPROSITE-ProRule annotation1 Publication
Binding sitei95 – 951S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei97 – 971S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei116 – 1161S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenPROSITE-ProRule annotation1 Publication
Binding sitei138 – 1381S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Active sitei175 – 1751For methyltransferase activity1 Publication
Binding sitei182 – 1821mRNA cap
Binding sitei233 – 2331mRNA cap

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Elongation factor, Methyltransferase, Transferase

Keywords - Biological processi

mRNA capping, mRNA processing, Protein biosynthesis, Transcription

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.57. 6591.

Names & Taxonomyi

Protein namesi
Recommended name:
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (EC:2.1.1.57)
Alternative name(s):
Poly(A) polymerase regulatory subunit
Poly(A) polymerase small subunit
Short name:
PAP-S
VP39
Gene namesi
Name:PAPS
Ordered Locus Names:VACWR095
ORF Names:J3R
OrganismiVaccinia virus (strain Western Reserve) (VACV) (Vaccinia virus (strain WR))
Taxonomic identifieri10254 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePoxviridaeChordopoxvirinaeOrthopoxvirusVaccinia virus
Virus hostiBos taurus (Bovine) [TaxID: 9913]
Proteomesi
  • UP000000344 Componenti: Genome

Subcellular locationi

  • Virion Curated

  • Note: Localizes to the virion core.Curated

GO - Cellular componenti

  • virion Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi56 – 561H → R: Complete loss of poly(A) polymerase stimulatory activity; when associated with S-58. 1 Publication
Mutagenesisi58 – 581I → S: Complete loss of poly(A) polymerase stimulatory activity; when associated with R-56. 1 Publication
Mutagenesisi96 – 961G → D: Complete loss of elongation factor activity. 1 Publication
Mutagenesisi175 – 1751K → R: Complete loss of methyltransferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 333333Cap-specific mRNA (nucleoside-2'-O-)-methyltransferasePRO_0000099112Add
BLAST

Interactioni

Subunit structurei

Methyltransferase activity: Monomer, poly(A) polymerase activity: Heterodimer composed of a catalytic component, VP55, and a processivity factor, VP39. Interacts with Rap94 and NPH-I; these interactions might help linking transcription to capping and polyadenylation.6 Publications

Protein-protein interaction databases

DIPiDIP-48310N.

Structurei

Secondary structure

1
333
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 153Combined sources
Helixi24 – 285Combined sources
Helixi37 – 5519Combined sources
Turni58 – 614Combined sources
Beta strandi63 – 686Combined sources
Helixi73 – 8412Combined sources
Beta strandi90 – 978Combined sources
Helixi101 – 1033Combined sources
Beta strandi109 – 1135Combined sources
Helixi118 – 12811Combined sources
Beta strandi133 – 1375Combined sources
Helixi150 – 16718Combined sources
Beta strandi170 – 1767Combined sources
Helixi181 – 1833Combined sources
Beta strandi188 – 1914Combined sources
Beta strandi194 – 1963Combined sources
Beta strandi208 – 2136Combined sources
Beta strandi215 – 2173Combined sources
Beta strandi221 – 2244Combined sources
Helixi226 – 24116Combined sources
Helixi243 – 2453Combined sources
Beta strandi246 – 2483Combined sources
Beta strandi253 – 2553Combined sources
Helixi258 – 26710Combined sources
Helixi279 – 29416Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AV6X-ray2.80A3-297[»]
1B42X-ray2.20A1-297[»]
1BKYX-ray2.00A1-307[»]
1EAMX-ray2.00A1-307[»]
1EQAX-ray2.20A1-297[»]
1JSZX-ray1.93A1-307[»]
1JTEX-ray2.00A1-307[»]
1JTFX-ray2.60A1-307[»]
1P39X-ray2.00A1-307[»]
1V39X-ray1.80A1-307[»]
1VP3X-ray1.90A1-333[»]
1VP9X-ray1.95A1-307[»]
1VPTX-ray1.80A1-333[»]
2GA9X-ray2.30A1-297[»]
2GAFX-ray2.40A1-297[»]
2VP3X-ray1.95A1-307[»]
3ER8X-ray3.18A/B1-297[»]
3ER9X-ray2.06A1-297[»]
3ERCX-ray3.21A/B1-297[»]
3MAGX-ray1.80A1-307[»]
3MCTX-ray2.00A1-297[»]
4DCGX-ray1.80A1-307[»]
ProteinModelPortaliP07617.
SMRiP07617. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07617.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni169 – 333165Binding to Rap94Add
BLAST
Regioni169 – 24981Binding to NPH-IAdd
BLAST
Regioni177 – 1804mRNA cap binding
Regioni205 – 2073mRNA cap binding

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. Poxvirus/kinetoplastid 2'-O-MTase family.PROSITE-ProRule annotation

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR000176. mRNA_MeTrfase-like.
IPR025804. Pox/kineto_cap_MeTfrase.
IPR030375. Poxvir_cap_MeTfrase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01358. PARP_regulatory. 1 hit.
[Graphical view]
PIRSFiPIRSF003726. PolA_polym_reg_poxV. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51612. SAM_MT_2O_PK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P07617-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVVSLDKPF MYFEEIDNEL DYEPESANEV AKKLPYQGQL KLLLGELFFL
60 70 80 90 100
SKLQRHGILD GATVVYIGSA PGTHIRYLRD HFYNLGVIIK WMLIDGRHHD
110 120 130 140 150
PILNGLRDVT LVTRFVDEEY LRSIKKQLHP SKIILISDVR SKRGGNEPST
160 170 180 190 200
ADLLSNYALQ NVMISILNPV ASSLKWRCPF PDQWIKDFYI PHGNKMLQPF
210 220 230 240 250
APSYSAEMRL LSIYTGENMR LTRVTKSDAV NYEKKMYYLN KIVRNKVVVN
260 270 280 290 300
FDYPNQEYDY FHMYFMLRTV YCNKTFPTTK AKVLFLQQSI FRFLNIPTTS
310 320 330
TEKVSHEPIQ RKISSKNSMS KNRNSKRSVR SNK
Length:333
Mass (Da):38,888
Last modified:April 1, 1988 - v1
Checksum:i55A299DA4AAE1AD4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01978 Genomic DNA. Translation: CAA26017.1.
AY243312 Genomic DNA. Translation: AAO89374.1.
PIRiH23092. QQVZF9.
RefSeqiYP_232977.1. NC_006998.1.

Genome annotation databases

GeneIDi3707551.
KEGGivg:3707551.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01978 Genomic DNA. Translation: CAA26017.1.
AY243312 Genomic DNA. Translation: AAO89374.1.
PIRiH23092. QQVZF9.
RefSeqiYP_232977.1. NC_006998.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AV6X-ray2.80A3-297[»]
1B42X-ray2.20A1-297[»]
1BKYX-ray2.00A1-307[»]
1EAMX-ray2.00A1-307[»]
1EQAX-ray2.20A1-297[»]
1JSZX-ray1.93A1-307[»]
1JTEX-ray2.00A1-307[»]
1JTFX-ray2.60A1-307[»]
1P39X-ray2.00A1-307[»]
1V39X-ray1.80A1-307[»]
1VP3X-ray1.90A1-333[»]
1VP9X-ray1.95A1-307[»]
1VPTX-ray1.80A1-333[»]
2GA9X-ray2.30A1-297[»]
2GAFX-ray2.40A1-297[»]
2VP3X-ray1.95A1-307[»]
3ER8X-ray3.18A/B1-297[»]
3ER9X-ray2.06A1-297[»]
3ERCX-ray3.21A/B1-297[»]
3MAGX-ray1.80A1-307[»]
3MCTX-ray2.00A1-297[»]
4DCGX-ray1.80A1-307[»]
ProteinModelPortaliP07617.
SMRiP07617. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48310N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi3707551.
KEGGivg:3707551.

Enzyme and pathway databases

BRENDAi2.1.1.57. 6591.

Miscellaneous databases

EvolutionaryTraceiP07617.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR000176. mRNA_MeTrfase-like.
IPR025804. Pox/kineto_cap_MeTfrase.
IPR030375. Poxvir_cap_MeTfrase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01358. PARP_regulatory. 1 hit.
[Graphical view]
PIRSFiPIRSF003726. PolA_polym_reg_poxV. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51612. SAM_MT_2O_PK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMCE_VACCW
AccessioniPrimary (citable) accession number: P07617
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: December 9, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.