PDBsum entry 1bky

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mRNA processing PDB id
Protein chain
291 a.a. *
Waters ×354
* Residue conservation analysis
PDB id:
Name: mRNA processing
Title: Vaccinia methyltransferase vp39 complexed with m1cyt and s- adenosylhomocysteine
Structure: Vp39. Chain: a. Synonym: poly(a) polymerase regulatory subunit. Engineered: yes. Mutation: yes
Source: Vaccinia virus. Organism_taxid: 10245. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
2.00Å     R-factor:   0.227     R-free:   0.261
Authors: G.Hu,A.E.Hodel,P.D.Gershon,F.A.Quiocho
Key ref:
G.Hu et al. (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. PubMed id: 10377383 DOI: 10.1073/pnas.96.13.7149
13-Jul-98     Release date:   22-Jul-99    
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    
DOI no: 10.1073/pnas.96.13.7149 Proc Natl Acad Sci U S A 96:7149-7154 (1999)
PubMed id: 10377383  
mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
G.Hu, P.D.Gershon, A.E.Hodel, F.A.Quiocho.
We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii) substantial areas of overlap in the two-stacked rings, (iii) a 3.4-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.
  Selected figure(s)  
Figure 1.
Fig. 1. Interaction of VP39 with m^3Ade. (a) The 1.83-Å difference electron density of VP39 crystal soaked in 10 mM m^3Ade contoured at the 2.5 level (see Table 1 and Materials and Methods). Dashed lines represent hydrogen bonds (cyan) and salt links (magenta). (b) Equivalent to a but soaked in 10 mM adenine and with a 1.92-Å difference Fourier (Table 1). (c) Stacking of the adeninium ring of m^3Ade with the aromatic side chains of Tyr 22 and Phe 180, projected parallel to the base ring. The atomic surface is shown in mesh representation. The (N)3-methyl group lies 6 Å from the peptide carbonyl oxygen of Tyr 204. (d) Same as c but projected perpendicular to the base ring with surface mesh and peptide backbone omitted for clarity.
Figure 2.
Fig. 2. Interaction of VP39 with m^3Cyt. Dashed lines are colored as in Fig. 1. (a) The 1.86-Å difference electron density (2.5 level) for VP39 crystal soaked in 10 mM m^3Cyt (see Table 1 and Materials and Methods). (b) Identical to a but soaked in 10 mM Cyt (Table 1). (c) Stacking of cytosinium ring patterned after Fig. 1c. The (N)1-methyl group lies within 3.3 Å of the carbonyl oxygen of Tyr 204. (d) Same as c but fashioned after Fig. 1d.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20943891 G.H.Chang, E.Oliver, I.Stanton, M.Wilson, B.J.Luo, L.Lin, A.Davidson, and S.Siddell (2011).
Genetic analysis of murine hepatitis virus non-structural protein 16.
  J Gen Virol, 92, 122-127.  
21394906 I.Bald, Y.G.Wang, M.Dong, C.B.Rosen, J.B.Ravnsbaek, G.L.Zhuang, K.V.Gothelf, J.G.Wang, and F.Besenbacher (2011).
Control of self-assembled 2D nanostructures by methylation of guanine.
  Small, 7, 939-949.  
19926722 D.Benarroch, M.Jankowska-Anyszka, J.Stepinski, E.Darzynkiewicz, and S.Shuman (2010).
Cap analog substrates reveal three clades of cap guanine-N2 methyltransferases with distinct methyl acceptor specificities.
  RNA, 16, 211-220.  
20164193 M.A.Mir, S.Sheema, A.Haseeb, and A.Haque (2010).
Hantavirus nucleocapsid protein has distinct m7G cap- and RNA-binding sites.
  J Biol Chem, 285, 11357-11368.  
19933321 Q.Cao, K.Padmanabhan, and J.D.Richter (2010).
Pumilio 2 controls translation by competing with eIF4E for 7-methyl guanosine cap recognition.
  RNA, 16, 221-227.  
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.  
18417574 E.Decroly, I.Imbert, B.Coutard, M.Bouvet, B.Selisko, K.Alvarez, A.E.Gorbalenya, E.J.Snijder, and B.Canard (2008).
Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity.
  J Virol, 82, 8071-8084.  
18305027 H.Dong, S.Ren, B.Zhang, Y.Zhou, F.Puig-Basagoiti, H.Li, and P.Y.Shi (2008).
West Nile virus methyltransferase catalyzes two methylations of the viral RNA cap through a substrate-repositioning mechanism.
  J Virol, 82, 4295-4307.  
17369309 J.Zuberek, D.Kubacka, A.Jablonowska, J.Jemielity, J.Stepinski, N.Sonenberg, and E.Darzynkiewicz (2007).
Weak binding affinity of human 4EHP for mRNA cap analogs.
  RNA, 13, 691-697.  
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.  
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.  
15468317 A.Golovin, D.Dimitropoulos, T.Oldfield, A.Rachedi, and K.Henrick (2005).
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.
  Proteins, 58, 190-199.  
16338414 H.Fan, A.Ooi, Y.W.Tan, S.Wang, S.Fang, D.X.Liu, and J.Lescar (2005).
The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties.
  Structure, 13, 1859-1868.
PDB codes: 2btl 2bxx
16043498 R.Worch, A.Niedzwiecka, J.Stepinski, C.Mazza, M.Jankowska-Anyszka, E.Darzynkiewicz, S.Cusack, and R.Stolarski (2005).
Specificity of recognition of mRNA 5' cap by human nuclear cap-binding complex.
  RNA, 11, 1355-1363.  
16118820 X.Guan, L.Q.Gu, S.Cheley, O.Braha, and H.Bayley (2005).
Stochastic sensing of TNT with a genetically engineered pore.
  Chembiochem, 6, 1875-1881.  
15153109 B.Joshi, A.Cameron, and R.Jagus (2004).
Characterization of mammalian eIF4E-family members.
  Eur J Biochem, 271, 2189-2203.  
15576352 P...Falnes (2004).
Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins.
  Nucleic Acids Res, 32, 6260-6267.  
14747996 R.Meurisse, R.Brasseur, and A.Thomas (2004).
Aromatic side-chain interactions in proteins: near- and far-sequence Tyr-X pairs.
  Proteins, 54, 478-490.  
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
12944262 K.Ruszczynska, K.Kamienska-Trela, J.Wojcik, J.Stepinski, E.Darzynkiewicz, and R.Stolarski (2003).
Charge distribution in 7-methylguanine regarding cation-pi interaction with protein factor eIF4E.
  Biophys J, 85, 1450-1456.  
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
12076527 F.Ferron, S.Longhi, B.Henrissat, and B.Canard (2002).
Viral RNA-polymerases -- a predicted 2'-O-ribose methyltransferase domain shared by all Mononegavirales.
  Trends Biochem Sci, 27, 222-224.  
12358434 K.A.Hudak, J.D.Bauman, and N.E.Tumer (2002).
Pokeweed antiviral protein binds to the cap structure of eukaryotic mRNA and depurinates the mRNA downstream of the cap.
  RNA, 8, 1148-1159.  
12032088 M.P.Egloff, D.Benarroch, B.Selisko, J.L.Romette, and B.Canard (2002).
An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization.
  EMBO J, 21, 2757-2768.
PDB codes: 1l9k 2p1d
11880600 W.H.Noon, Y.Kong, and J.Ma (2002).
Molecular dynamics analysis of a buckyball-antibody complex.
  Proc Natl Acad Sci U S A, 99, 6466-6470.  
11472630 J.M.Bujnicki, M.Feder, M.Radlinska, and L.Rychlewski (2001).
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
  BMC Bioinformatics, 2, 2.
PDB code: 1ic3
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11106395 A.Y.Lau, M.D.Wyatt, B.J.Glassner, L.D.Samson, and T.Ellenberger (2000).
Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
  Proc Natl Acad Sci U S A, 97, 13573-13578.
PDB codes: 1ewn 1f4r 1f6o
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.  
10983982 H.Bügl, E.B.Fauman, B.L.Staker, F.Zheng, S.R.Kushner, M.A.Saper, J.C.Bardwell, and U.Jakob (2000).
RNA methylation under heat shock control.
  Mol Cell, 6, 349-360.
PDB codes: 1eiz 1ej0
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 codes are shown on the right.