PDBsum entry 2im3

Transferase

PDB id: 2im3

Contents

Protein chain

461 a.a. *

Ligands

UTP

ACY ×4

Metals

_MN ×2

_NA

Waters ×107

* Residue conservation analysis

PDB id:

2im3

Name:

Transferase

Title:

Crystal structure of poliovirus polymerase complexed with utp and mn2+

Structure:

Poliovirus polymerase. Chain: a. Fragment: RNA-directed RNA polymerase, residues 1748-2208. 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)

Resolution:

2.60Å R-factor: 0.237 R-free: 0.269

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

Date:

03-Oct-06 Release date: 12-Dec-06

Protein chain

P03300  (POLG_POL1M) -  Genome polyprotein from Poliovirus type 1 (strain Mahoney)

Seq: 2209 a.a.

Struc: 461 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

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

reference

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.

ABSTRACT

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.