PDBsum entry 1vp3

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protein ligands links
Methyltransferase PDB id
Protein chain
291 a.a. *
Waters ×171
* Residue conservation analysis
PDB id:
Name: Methyltransferase
Title: Vaccinia virus protein vp39 in complex with s-adenosylhomocy
Structure: Vp39. Chain: a. Synonym: poly(a) polymerase regulatory subunit. Engineered: yes
Source: Vaccinia virus. Organism_taxid: 10254. Strain: wr. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
1.90Å     R-factor:   0.215    
Authors: A.E.Hodel,P.D.Gershon,F.A.Quiocho
Key ref: A.E.Hodel et al. (1997). Specific protein recognition of an mRNA cap through its alkylated base. Nat Struct Biol, 4, 350-354. PubMed id: 9145102
21-Nov-96     Release date:   17-Sep-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07617  (MCE_VACCW) -  Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
333 a.a.
291 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Methyltransferase cap1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 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)
+ 5'-(N(7)-methyl 5'-triphosphoguanosine)- (purine-ribonucleotide)-(mRNA)
Bound ligand (Het Group name = SAH)
corresponds exactly
+ 5'-(N(7)- methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)- (mRNA)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     virion   1 term 
  Biological process     methylation   8 terms 
  Biochemical function     transferase activity     5 terms  


    Added reference    
Nat Struct Biol 4:350-354 (1997)
PubMed id: 9145102  
Specific protein recognition of an mRNA cap through its alkylated base.
A.E.Hodel, P.D.Gershon, X.Shi, S.M.Wang, F.A.Quiocho.
The specific binding of N7-methylguanine cap analogues to the RNA methyltransferase VP39 was observed through X-ray crystallography, providing a prototypical structure for a complex between a protein and an mRNA 5' cap.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20535623 K.RuszczyƄska-Bartnik, M.Maciejczyk, and R.Stolarski (2011).
Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap.
  J Mol Model, 17, 727-737.  
19946139 K.Van Vliet, M.R.Mohamed, L.Zhang, N.Y.Villa, S.J.Werden, J.Liu, and G.McFadden (2009).
Poxvirus proteomics and virus-host protein interactions.
  Microbiol Mol Biol Rev, 73, 730-749.  
18280238 M.V.Deshmukh, B.N.Jones, D.U.Quang-Dang, J.Flinders, S.N.Floor, C.Kim, J.Jemielity, M.Kalek, E.Darzynkiewicz, and J.D.Gross (2008).
mRNA decapping is promoted by an RNA-binding channel in Dcp2.
  Mol Cell, 29, 324-336.
PDB code: 2jvb
18186485 R.Worch, and R.Stolarski (2008).
Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
  Proteins, 71, 2026-2037.  
17606627 J.R.Zamudio, B.Mittra, S.Foldynová-Trantírková, G.M.Zeiner, J.Lukes, J.M.Bujnicki, N.R.Sturm, and D.A.Campbell (2007).
The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei.
  Mol Cell Biol, 27, 6084-6092.  
17524464 M.Kiriakidou, G.S.Tan, S.Lamprinaki, M.De Planell-Saguer, P.T.Nelson, and Z.Mourelatos (2007).
An mRNA m7G cap binding-like motif within human Ago2 represses translation.
  Cell, 129, 1141-1151.  
17416901 Y.Takagi, S.Sindkar, D.Ekonomidis, M.P.Hall, and C.K.Ho (2007).
Trypanosoma brucei encodes a bifunctional capping enzyme essential for cap 4 formation on the spliced leader RNA.
  J Biol Chem, 282, 15995-16005.  
16886072 A.Schmidt, A.Lindner, M.Nieger, M.d.e.l. .C.Ruiz-Delgado, and F.J.Ramirez (2006).
Syntheses, pi-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases.
  Org Biomol Chem, 4, 3056-3066.  
16301606 G.K.Arhin, H.Li, E.Ullu, and C.Tschudi (2006).
A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei.
  RNA, 12, 53-62.  
17028101 M.P.Hall, and C.K.Ho (2006).
Functional characterization of a 48 kDa Trypanosoma brucei cap 2 RNA methyltransferase.
  Nucleic Acids Res, 34, 5594-5602.  
15920472 A.Strasser, A.Dickmanns, R.Lührmann, and R.Ficner (2005).
Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1.
  EMBO J, 24, 2235-2243.
PDB code: 1xk5
15882623 P.F.Cho, F.Poulin, Y.A.Cho-Park, I.B.Cho-Park, J.D.Chicoine, P.Lasko, and N.Sonenberg (2005).
A new paradigm for translational control: inhibition via 5'-3' mRNA tethering by Bicoid and the eIF4E cognate 4EHP.
  Cell, 121, 411-423.  
14517230 B.F.Eichman, E.J.O'Rourke, J.P.Radicella, and T.Ellenberger (2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
  EMBO J, 22, 4898-4909.
PDB codes: 1pu6 1pu7 1pu8
14573618 G.Hu, A.L.Tsai, and F.A.Quiocho (2003).
Insertion of an N7-methylguanine mRNA cap between two coplanar aromatic residues of a cap-binding protein is fast and selective for a positively charged cap.
  J Biol Chem, 278, 51515-51520.  
12646557 P.Fechter, L.Mingay, J.Sharps, A.Chambers, E.Fodor, and G.G.Brownlee (2003).
Two aromatic residues in the PB2 subunit of influenza A RNA polymerase are crucial for cap binding.
  J Biol Chem, 278, 20381-20388.  
12079779 A.Oguro, L.Johnson, and P.D.Gershon (2002).
Path of an RNA ligand around the surface of the vaccinia VP39 subunit of its cognate VP39-VP55 protein heterodimer.
  Chem Biol, 9, 679-690.  
12374755 C.Mazza, A.Segref, I.W.Mattaj, and S.Cusack (2002).
Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex.
  EMBO J, 21, 5548-5557.
PDB codes: 1h2t 1h2u 1h2v
11296240 M.L.Li, P.Rao, and R.M.Krug (2001).
The active sites of the influenza cap-dependent endonuclease are on different polymerase subunits.
  EMBO J, 20, 2078-2086.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
  10924457 B.Schwer, N.Saha, X.Mao, H.W.Chen, and S.Shuman (2000).
Structure-function analysis of yeast mRNA cap methyltransferase and high-copy suppression of conditional mutants by AdoMet synthase and the ubiquitin conjugating enzyme Cdc34p.
  Genetics, 155, 1561-1576.  
10679461 F.A.Quiocho, G.Hu, and P.D.Gershon (2000).
Structural basis of mRNA cap recognition by proteins.
  Curr Opin Struct Biol, 10, 78-86.  
10872469 A.C.Gingras, B.Raught, and N.Sonenberg (1999).
eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation.
  Annu Rev Biochem, 68, 913-963.  
10377383 G.Hu, P.D.Gershon, A.E.Hodel, and F.A.Quiocho (1999).
mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
  Proc Natl Acad Sci U S A, 96, 7149-7154.
PDB codes: 1b42 1bky 1eam 1eqa 3mag 3mct 4dcg
  10101156 S.Tharun, and R.Parker (1999).
Analysis of mutations in the yeast mRNA decapping enzyme.
  Genetics, 151, 1273-1285.  
9582349 E.Rom, H.C.Kim, A.C.Gingras, J.Marcotrigiano, D.Favre, H.Olsen, S.K.Burley, and N.Sonenberg (1998).
Cloning and characterization of 4EHP, a novel mammalian eIF4E-related cap-binding protein.
  J Biol Chem, 273, 13104-13109.  
9646873 G.Varani, and K.Nagai (1998).
RNA recognition by RNP proteins during RNA processing.
  Annu Rev Biophys Biomol Struct, 27, 407-445.  
9628920 H.Kuge, G.G.Brownlee, P.D.Gershon, and J.D.Richter (1998).
Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis.
  Nucleic Acids Res, 26, 3208-3214.  
9670026 J.Huber, U.Cronshagen, M.Kadokura, C.Marshallsay, T.Wada, M.Sekine, and R.Lührmann (1998).
Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure.
  EMBO J, 17, 4114-4126.  
9501904 N.Sonenberg, S.K.Burley, and A.C.Gingras (1998).
RNA chiropractics.
  Nat Struct Biol, 5, 172-174.  
9622508 S.W.Lockless, H.T.Cheng, A.E.Hodel, F.A.Quiocho, and P.D.Gershon (1998).
Recognition of capped RNA substrates by VP39, the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase.
  Biochemistry, 37, 8564-8574.  
9482745 T.E.LaGrandeur, and R.Parker (1998).
Isolation and characterization of Dcp1p, the yeast mRNA decapping enzyme.
  EMBO J, 17, 1487-1496.  
9261078 G.Varani (1997).
A cap for all occasions.
  Structure, 5, 855-858.  
9287339 X.Shi, T.G.Bernhardt, S.M.Wang, and P.D.Gershon (1997).
The surface region of the bifunctional vaccinia RNA modifying protein VP39 that interfaces with Poly(A) polymerase is remote from the RNA binding cleft used for its mRNA 5' cap methylation function.
  J Biol Chem, 272, 23292-23302.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.