PDBsum entry 2ily

Go to PDB code: 
protein ligands metals links
Transferase PDB id
Jmol PyMol
Protein chain
461 a.a. *
ACY ×7
Waters ×129
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of poliovirus polymerase complexed with at
Structure: Poliovirus polymerase. Chain: a. Fragment: RNA-directed RNA polymerase, residues 461-1748. Engineered: yes. Mutation: yes
Source: Human poliovirus 1. Organism_taxid: 12081. Strain: mahoney. Gene: 3d. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PQS)
2.60Å     R-factor:   0.230     R-free:   0.250
Authors: A.A.Thompson,O.B.Peersen
Key ref:
A.A.Thompson et al. (2007). Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions. J Mol Biol, 366, 1459-1474. PubMed id: 17223130 DOI: 10.1016/j.jmb.2006.11.070
03-Oct-06     Release date:   12-Dec-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03300  (POLG_POL1M) -  Genome polyprotein
2209 a.a.
461 a.a.*
Protein chain
Pfam   ArchSchema ?
Q8QXN9  (Q8QXN9_9ENTO) -  Genome polyprotein
2209 a.a.
461 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
Bound ligand (Het Group name = ATP)
matches with 65.62% similarity
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   1 term 
  Biochemical function     RNA binding     2 terms  


DOI no: 10.1016/j.jmb.2006.11.070 J Mol Biol 366:1459-1474 (2007)
PubMed id: 17223130  
Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions.
A.A.Thompson, R.A.Albertini, O.B.Peersen.
The viral RNA-dependent RNA polymerases show a conserved structure where the fingers domain interacts with the top of the thumb domain to create a tunnel through which nucleotide triphosphates reach the active site. We have solved the crystal structures of poliovirus polymerase (3D(pol)) in complex with all four NTPs, showing that they all bind in a common pre-insertion site where the phosphate groups are not yet positioned over the active site. The NTPs interact with both the fingers and palm domains, forming bridging interactions that explain the increased thermal stability of 3D(pol) in the presence of NTPs. We have also examined the importance of the fingers-thumb domain interaction for the function and structural stability of 3D(pol). Results from thermal denaturation experiments using circular dichroism and 2-anilino-6-napthaline-sulfonate (ANS) fluorescence show that 3D(pol) has a melting temperature of only approximately 40 degrees C. NTP binding stabilizes the protein and increases the melting by 5-6 degrees C while mutations in the fingers-thumb domain interface destabilize the protein and reduce the melting point by as much as 6 degrees C. In particular, the burial of Phe30 and Phe34 from the tip of the index finger into a pocket at the top of the thumb and the presence of Trp403 on the thumb domain are key interactions required to maintain the structural integrity of the polymerase. The data suggest the fingers domain has significant conformational flexibility and exists in a highly dynamic molten globule state at physiological temperature. The role of the enclosed active site motif as a structural scaffold for constraining the fingers domain and accommodating conformational changes in 3D(pol) and other viral polymerases during the catalytic cycle is discussed.
  Selected figure(s)  
Figure 1.
Figure 1. Poliovirus 3D^pol–GTP structure and picornaviral finger-thumb interactions. (a) Front and (b) top views of the 3D^pol–GTP complex highlighting the various domains of the polymerase. The thumb domain is blue and the palm is colored grey with the conserved catalytic center colored in magenta. The fingers domain can be subdivided into individual digits where the index finger is shown in green, the middle finger in orange, the ring finger in yellow, and the pinky finger in pink. The buried N terminus is shown with a blue sphere and several of the aromatic residues important for the inter-domain interaction between the fingers and thumb domains (F30, F34 and W403) are depicted with sticks. (c) Detailed view of homologous interactions at the top of the three picornaviral polymerase thumb domains (surface representation) to illustrate the hydrophobic crevasse into which hydrophobic residues from the index fingertip are inserted. Polymerases are from poliovirus (PV^1), human rhinovirus (HRV^3), and foot-and-mouth disease virus (FMDV^4).
Figure 2.
Figure 2. Structures of 3D^pol complexed with ribonucleotides in the presence of Mg^2+. The NTPs make bridging interactions between the fingers and palm domains. The bases are stacked on Arg174 from the ring finger, the ribose interacts with Arg174 and Asp238 from the palm, and the triphosphate moiety interacts with Arg163 and Lys167 from the ring finger and the backbone amide of residue 236 from the palm. (a) A 2.35 Å resolution 2F[o]–F[c] electron density map contoured at 1.5σ around UTP. (b) A 2.25 Å resolution 2F[o]–F[c] electron density map contoured at 1.5σ around CTP. (c) A 2.6 Å resolution 2F[o]–F[c] electron density map contoured at 1.5σ around ATP and (d) A 2.6 Å resolution F[o]–F[c] electron density map (blue) contoured at 1.8σ around ATP. (e) A 2.35 Å resolution 2F[o]–F[c] electron density map contoured at 1.5σ around GTP. (f) Comparison of the apo 3D^pol structure (red) with all the 3D^pol–NTP structures (grey) showing the minor shift in the ring finger position as result of interactions with bound NTPs.
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 366, 1459-1474) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20051491 J.F.Spagnolo, E.Rossignol, E.Bullitt, and K.Kirkegaard (2010).
Enzymatic and nonenzymatic functions of viral RNA-dependent RNA polymerases within oligomeric arrays.
  RNA, 16, 382-393.  
20534860 K.Konduru, and G.G.Kaplan (2010).
Determinants in 3Dpol modulate the rate of growth of hepatitis A virus.
  J Virol, 84, 8342-8347.  
20111609 M.Yokoyama, H.Mori, and H.Sato (2010).
Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection.
  PLoS One, 5, e8867.  
21148772 P.Gong, and O.B.Peersen (2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 22505-22510.
PDB codes: 3ol6 3ol7 3ol8 3ol9 3ola 3olb
20534858 S.E.Hobdey, B.J.Kempf, B.P.Steil, D.J.Barton, and O.B.Peersen (2010).
Poliovirus polymerase residue 5 plays a critical role in elongation complex stability.
  J Virol, 84, 8072-8084.  
19812169 A.Zamoto-Niikura, K.Terasaki, T.Ikegami, C.J.Peters, and S.Makino (2009).
Rift valley fever virus L protein forms a biologically active oligomer.
  J Virol, 83, 12779-12789.  
18773930 B.P.Steil, and D.J.Barton (2009).
Cis-active RNA elements (CREs) and picornavirus RNA replication.
  Virus Res, 139, 240-252.  
18829745 A.Arias, J.J.Arnold, M.Sierra, E.D.Smidansky, E.Domingo, and C.E.Cameron (2008).
Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin.
  J Virol, 82, 12346-12355.  
18632861 A.Gruez, B.Selisko, M.Roberts, G.Bricogne, C.Bussetta, I.Jabafi, B.Coutard, A.M.De Palma, J.Neyts, and B.Canard (2008).
The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases.
  J Virol, 82, 9577-9590.
PDB codes: 3cdu 3cdw
18574240 A.Nikonov, E.Juronen, and M.Ustav (2008).
Functional characterization of fingers subdomain-specific monoclonal antibodies inhibiting the hepatitis C virus RNA-dependent RNA polymerase.
  J Biol Chem, 283, 24089-24102.  
18184655 D.F.Zamyatkin, F.Parra, J.M.Alonso, D.A.Harki, B.R.Peterson, P.Grochulski, and K.K.Ng (2008).
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.
  J Biol Chem, 283, 7705-7712.
PDB codes: 3bsn 3bso
18632862 G.Campagnola, M.Weygandt, K.Scoggin, and O.Peersen (2008).
Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases.
  J Virol, 82, 9458-9464.
PDB code: 3ddk
17526498 E.Kashkina, M.Anikin, F.Brueckner, E.Lehmann, S.N.Kochetkov, W.T.McAllister, P.Cramer, and D.Temiakov (2007).
Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site.
  J Biol Chem, 282, 21578-21582.  
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.