PDBsum entry 3ddk

Transferase, viral protein

PDB id: 3ddk

Contents

Protein chain

462 a.a. *

Ligands

SO4 ×6

Metals

_NA ×9

Waters ×262

* Residue conservation analysis

PDB id:

3ddk

Name:

Transferase, viral protein

Title:

Coxsackievirus b3 3dpol RNA dependent RNA polymerase

Structure:

RNA polymerase b3 3dpol. Chain: a. Engineered: yes

Source:

Human coxsackievirus. Organism_taxid: 12072. Strain: b3. Gene: 3dpol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.25Å R-factor: 0.201 R-free: 0.234

Authors:

G.Campagnola,M.H.Weygandt,K.E.Scoggin,O.B.Peersen

Key ref:

G.Campagnola et al. (2008). Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases. J Virol, 82, 9458-9464. PubMed id: 18632862

Date:

05-Jun-08 Release date: 23-Sep-08

Protein chain

Q5UEA2  (Q5UEA2_9ENTO) -  Genome polyprotein from Coxsackievirus B3

Seq: 2185 a.a.

Struc: 462 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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

J Virol 82:9458-9464 (2008)

PubMed id: 18632862

Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases.

G.Campagnola, M.Weygandt, K.Scoggin, O.Peersen.

ABSTRACT

The crystal structure of the coxsackievirus B3 polymerase has been solved at 2.25-A resolution and is shown to be highly homologous to polymerases from poliovirus, rhinovirus, and foot-and-mouth disease viruses. Together, these structures highlight several conserved structural elements in picornaviral polymerases, including a proteolytic activation-dependent N-terminal structure that is essential for full activity. Interestingly, a comparison of all of the picornaviral polymerase structures shows an unusual conformation for residue 5, which is always located at a distortion in the beta-strand composed of residues 1 to 8. In our earlier structure of the poliovirus polymerase, we attributed this conformation to a crystal packing artifact, but the observation that this conformation is conserved among picornaviruses led us to examine the role of this residue in further detail. Here we use coxsackievirus polymerase to show that elongation activity correlates with the hydrophobicity of residue 5 and, surprisingly, more hydrophobic residues result in higher activity. Based on structural analysis, we propose that this residue becomes buried during the nucleotide repositioning step that occurs prior to phosphoryl transfer. We present a model in which the buried N terminus observed in all picornaviral polymerases is essential for stabilizing the structure during this conformational change.