PDBsum entry 4k4x

Transferase/RNA

PDB id: 4k4x

Contents

Protein chains

463 a.a.

DNA/RNA

Ligands

_DG-_DG ×4

GOL ×4

Metals

_MG ×4

Waters ×729

PDB id:

4k4x

Name:

Transferase/RNA

Title:

Coxsackievirus b3 polymerase elongation complex (r2_form), RNA

Structure:

RNA-dependent RNA polymerase. Chain: a, e, i, m. Fragment: unp residues 1724-2185. Engineered: yes. RNA (5'- r( Ap Ap Gp Up Cp Up Cp Cp Ap Gp Gp Up Cp Up Cp Up Cp Gp Up Cp Gp Ap Ap A)-3'). Chain: b, f, j, n. Engineered: yes.

Source:

Human coxsackievirus b3. Organism_taxid: 12072. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

2.37Å R-factor: 0.205 R-free: 0.241

Authors:

P.Gong,O.B.Peersen

Key ref:

P.Gong et al. (2013). Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. Plos One, 8, e60272. PubMed id: 23667424 DOI: 10.1371/journal.pone.0060272

Date:

12-Apr-13 Release date: 22-May-13

Protein chains

Q5UEA2  (Q5UEA2_9ENTO) -  Genome polyprotein from Coxsackievirus B3

Seq: 2185 a.a.

Struc: 463 a.a.*

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

DNA/RNA chains

C-A-G-G-U-C-U-C-U-C-G-U-C-G-A-A 16 bases

G-U-U-C-G-A-C-G-A-G-A-G-A 13 bases

C-A-G-G-U-C-U-C-U-C-G-U-C-G-A-A 16 bases

G-U-U-C-G-A-C-G-A-G-A-G-A 13 bases

C-A-G-G-U-C-U-C-U-C-G-U-C-G-A-A 16 bases

G-U-U-C-G-A-C-G-A-G-A-G-A 13 bases

C-A-G-G-U-C-U-C-U-C-G-U-C-G-A-A 16 bases

G-U-U-C-G-A-C-G-A-G-A-G-A 13 bases

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: 10.1371/journal.pone.0060272

Plos One 8:e60272 (2013)

PubMed id: 23667424

Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.

P.Gong, M.G.Kortus, J.C.Nix, R.E.Davis, O.B.Peersen.

ABSTRACT

RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.