PDBsum entry 2gaf

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protein Protein-protein interface(s) links
Transferase PDB id
Protein chains
286 a.a. *
447 a.a. *
Waters ×140
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of the vaccinia polyadenylate polymerase heterodimer (apo form)
Structure: Cap-specific mRNA (nucleoside-2'-o-)- methyltransferase. Chain: a. Synonym: polya, polymerase regulatory subunit, polya, polymerase small subunit, pap-s, vp39. Engineered: yes. Mutation: yes. Poly(a) polymerase catalytic subunit. Chain: d.
Source: Vaccinia virus. Organism_taxid: 10245. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.243     R-free:   0.288
Authors: C.M.Moure,B.R.Bowman,P.D.Gershon,F.A.Quiocho
Key ref:
C.M.Moure et al. (2006). Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity. Mol Cell, 22, 339-349. PubMed id: 16678106 DOI: 10.1016/j.molcel.2006.03.015
08-Mar-06     Release date:   16-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07617  (MCE_VACCW) -  Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
333 a.a.
286 a.a.*
Protein chain
Pfam   ArchSchema ?
Q1PIV4  (Q1PIV4_9POXV) -  Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
333 a.a.
286 a.a.*
Protein chain
Pfam   ArchSchema ?
P23371  (PAP1_VACCW) -  Poly(A) polymerase catalytic subunit
479 a.a.
447 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chain A: 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)
= S-adenosyl-L-homocysteine
+ 5'-(N(7)- methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)- (mRNA)
   Enzyme class 2: Chain D: E.C.  - Polynucleotide adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + RNA(n) = diphosphate + RNA(n+1)
+ RNA(n)
= diphosphate
+ RNA(n+1)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   4 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1016/j.molcel.2006.03.015 Mol Cell 22:339-349 (2006)
PubMed id: 16678106  
Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.
C.M.Moure, B.R.Bowman, P.D.Gershon, F.A.Quiocho.
Polyadenylation of mRNAs in poxviruses, crucial for virion maturation, is carried out by a poly(A) polymerase heterodimer composed of a catalytic component, VP55, and a processivity factor, VP39. The ATP-gamma-S bound and unbound crystal structures of the vaccinia polymerase reveal an unusual architecture for VP55 that comprises of N-terminal, central or catalytic, and C-terminal domains with different topologies and that differs from many polymerases, including the eukaryotic poly(A) polymerases. Residues in the active site of VP55, located between the catalytic and C-terminal domains, make specific interactions with the adenine of the ATP analog, establishing the molecular basis of ATP recognition. VP55's concave surface docks the globular VP39. A model for RNA primer binding that involves all three VP55 domains and VP39 is proposed. The model supports biochemical evidence that VP39 functions as a processivity factor by partially enclosing the RNA primer at the heterodimer interface.
  Selected figure(s)  
Figure 1.
Figure 1. Structure of the Poly(A) Polymerase Heterodimer
(A) Ribbon diagram. This view represents the “front face” of the heterodimer. The three domains of VP55 are the N domain (green), the catalytic or central domain (yellow), and the C domain (salmon). VP39 is colored in cyan. Disordered polypeptide segments in VP55 (residues 118–129 and 150–160) and VP39 (residues 27–32 and 142–144) are represented by dashed lines. Helices in the entire VP55 are identified by letters, and β strands in the catalytic domain are identified by numbers. Helices in VP39 are identified by numbers preceded by α. The three active site aspartates and the two bound molecules of ATP-γ-S (one in the active site and the other [ATP second site] on the protein surface) in VP55 are shown as ball-and-stick models. “CAP” marks the location of the m^7G cap binding site in VP39, which is adjacent to the methyltransferase active site.
(B) Topology diagram of the catalytic domain of VP55.
(C) Topology diagram of the canonical palm motif of DNA polymerase β.
Note that in both (B) and (C) strands 1–5 are equivalent.
Figure 2.
Figure 2. The Active Site of VP55
(A) Stereo view of the ATP analog bound in the active site. Residues in yellow are from the catalytic domain, and those in salmon are from the C domain (see Figure 1A). The F[o] − F[c] electron density map (cyan) is a simulated annealing omit map, contoured at 2.5 σ. It was calculated at 2.3 Å from a model in which residues within a 5 Å sphere around the ATP-γ-S molecule were deleted. Salt links and hydrogen bonds (distances from 2.5 to 3.5 Å) between VP55 residues and the ATP analog are shown as black dotted lines. The two metal ions (magenta) are labeled “A” and “B.” The metals coordination spheres are shown as magenta dotted lines. Cyan spheres represent water molecules.
(B) Close-up view of the coordination spheres of metals A and B.
(C) ATP-γ-S secondary binding site interactions. The electron density map (in blue) corresponds to an F[o] − F[c] simulated annealing omit map contoured at 3 σ. This map was calculated by omitting residues lying in a sphere of 5 Å around the nucleotide.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 339-349) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20509894 J.Farlow, M.A.Ichou, J.Huggins, and S.Ibrahim (2010).
Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus.
  Virol J, 7, 110.  
19814999 L.S.Chen, L.Du-Cuny, V.Vethantham, D.H.Hawke, J.L.Manley, S.Zhang, and V.Gandhi (2010).
Chain termination and inhibition of mammalian poly(A) polymerase by modified ATP analogues.
  Biochem Pharmacol, 79, 669-677.  
19446524 C.Li, H.Li, S.Zhou, E.Sun, J.Yoshizawa, T.L.Poulos, and P.D.Gershon (2009).
Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
  Structure, 17, 680-689.
PDB codes: 3er8 3er9 3erc
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.  
18177750 G.Martin, S.Doublié, and W.Keller (2008).
Determinants of substrate specificity in RNA-dependent nucleotidyl transferases.
  Biochim Biophys Acta, 1779, 206-216.  
18367228 M.N.Becker, T.M.Todd, and R.W.Moyer (2008).
An Amsacta moorei entomopoxvirus ortholog of the poly(A) polymerase small subunit exhibits methyltransferase activity and is non-essential for virus growth.
  Virology, 375, 624-636.  
18191648 R.Aphasizhev, and I.Aphasizheva (2008).
Terminal RNA uridylyltransferases of trypanosomes.
  Biochim Biophys Acta, 1779, 270-280.  
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17189640 J.Stagno, I.Aphasizheva, A.Rosengarth, H.Luecke, and R.Aphasizhev (2007).
UTP-bound and Apo structures of a minimal RNA uridylyltransferase.
  J Mol Biol, 366, 882-899.
PDB codes: 2ikf 2nom
17785418 J.Stagno, I.Aphasizheva, R.Aphasizhev, and H.Luecke (2007).
Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.
  Proc Natl Acad Sci U S A, 104, 14634-14639.
PDB codes: 2q0c 2q0d 2q0e 2q0f 2q0g
17085042 J.R.Mesters, J.Tan, and R.Hilgenfeld (2006).
Viral enzymes.
  Curr Opin Struct Biol, 16, 776-786.  
17005674 S.Tomar, R.W.Hardy, J.L.Smith, and R.J.Kuhn (2006).
Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity.
  J Virol, 80, 9962-9969.  
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.