PDBsum entry 2jqf

Viral protein

PDB id: 2jqf

Contents

Protein chains

166 a.a. *

* Residue conservation analysis

PDB id:

2jqf

Name:

Viral protein

Title:

Full length leader protease of foot and mouth disease virus c51a mutant

Structure:

Genome polyprotein. Chain: r, s. Fragment: residues 29-201. Engineered: yes. Mutation: yes

Source:

Foot-and-mouth disease virus (strain o1). Organism_taxid: 73482. Strain: o1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: (de)plyss.

NMR struc:

10 models

Authors:

R.Cencic,C.Mayer,M.A.Juliano,L.Juliano,R.Konrat,G.Kontaxis,T.Skern

Key ref:

R.Cencic et al. (2007). Investigating the substrate specificity and oligomerisation of the leader protease of foot and mouth disease virus using NMR. J Mol Biol, 373, 1071-1087. PubMed id: 17897674 DOI: 10.1016/j.jmb.2007.08.061

Date:

01-Jun-07 Release date: 17-Jul-07

Protein chains

P03305  (POLG_FMDVO) -  Genome polyprotein from Foot-and-mouth disease virus (isolate Bovine/Germany/O1Kaufbeuren/1966 serotype O)

Seq: 2332 a.a.

Struc: 166 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: 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 3: E.C.3.4.22.46 - L-peptidase.
• Reaction: Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
• Enzyme class 4: 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.2007.08.061

J Mol Biol 373:1071-1087 (2007)

PubMed id: 17897674

Investigating the substrate specificity and oligomerisation of the leader protease of foot and mouth disease virus using NMR.

R.Cencic, C.Mayer, M.A.Juliano, L.Juliano, R.Konrat, G.Kontaxis, T.Skern.

ABSTRACT

The leader protease (Lbpro) of foot-and-mouth disease virus frees itself during translation from the viral polyprotein by cleavage between its own C terminus and the N terminus of the subsequent protein, VP4. Lbpro also specifically cleaves the host proteins eukaryotic initiation factor (eIF) 4GI and 4GII, thus disabling host cell protein synthesis. We used NMR to study full-length Lbpro as well as a shortened species lacking six C-terminal amino acid residues (sLbpro) to examine the mechanism of self-processing, the quaternary structure and the substrate specificity. Both Lbpro forms have the same structure in solution as in the crystal. In the solution structure of sLbpro, the 12 residue C-terminal extension was flexible and disordered. In contrast, the 18 residue C-terminal extension of full-length Lbpro was bound by the substrate-binding site of a neighbouring molecule, resulting in the formation of a stable dimer in solution. The Lbpro dimer could not be dissociated by increasing the ionic strength or by dilution. Furthermore, titration with model peptides mimicking the substrates destabilised the dimer interface without dissociating the dimer. The peptides were, however, bound by sLbpro in the canonical substrate binding site. Peptide binding gave rise to chemical shifts of residues around the sLbpro substrate binding site. Shifts of Asn146 and Glu147 indicated that these residues might form the enzyme's S1' site and interact with the P1' arginine residue of the eIF4GI cleavage site. Furthermore, differences in substrate specificity between sLbpro and Lbpro observed with an in vitro translated protein indicate some involvement of the C terminus in substrate recognition.

Selected figure(s)

Figure 1.
Figure 1. Flexibility of the C-terminal extension (CTE) of sLb^proC51A. (a) Ensemble of ten sLb^pro NMR structures (shown in stereo). Regions of regular secondary structure were used for the coordinate overlay of the final NMR solution structures. α-Helices are shown in green and β-strands in magenta. The variability of the structures of the extended CTE region demonstrates its structural flexibility and presumable lack of defined structure. (b) ^15N T[2] transverse relaxation times in ms of sLb^proC51A (blue) and Lb^proC51A (red). Relaxation times were measured as described in Materials and Methods. The unstructured CTE is reflected in its T[2] relaxation times being substantially longer than the globular domain. The roughly twofold difference in relaxation rates between the two species implies that Lb^proC51A is a dimer, whereas sLb^proC51A is a monomer.

Figure 3.
Figure 3. Solution structure of Lb^pro C51A (a) Comparison of the dimeric X-ray crystal structure of full-length FMDV Lb^pro C51A (PDB ID code 1QOL, shown in blue/cyan) with the NMR solution structure (shown in red/magenta), which is derived from simple symmetry arguments. Strict enforcement of 2-fold symmetry between the two halves is required to explain that symmetry of the measured residual dipolar couplings results in a change of the relative orientation of the two monomers by about 25–30°. For clarity, the two halves of each monomer are shown in different colours, and the N and C termini are labelled. The structures of one half of the dimer (the left monomers) were overlaid to illustrate the dramatic change of the position of the other half of the dimer. Residue C133 is shown as ball-and-stick for orientation. (b) Similar results are obtained using rigid body simulated annealing refinement with a limited number of RDCs as orientational restraints and a weak restraint for the radius of gyration. The bundle of structures obtained by that procedure is in excellent agreement with the model derived from simple symmetry reasons shown in (a). The crystal structure dimer of Lb^pro (PDB ID code 1QOL) is again shown for reference in blue/cyan. For clarity, the two halves of each monomer of the structure bundle are shown in different colours (red/magenta) and the N and C termini are labelled. Again, the structures of only one half of the dimer (the left monomers) were overlaid.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 1071-1087) copyright 2007.

Figures were selected by an automated process.