PDBsum entry 2b0f

Hydrolase/hydrolase inhibitor

PDB id: 2b0f

Contents

Protein chain

182 a.a. *

Ligands

ACE-LEU-GLU-ALA-LEU-PHE-YTF

* Residue conservation analysis

PDB id:

2b0f

Name:

Hydrolase/hydrolase inhibitor

Title:

Nmr structure of the human rhinovirus 3c protease (serotype 14) with covalently bound ace-lealfq-ethylpropionate inhibitor

Structure:

Protease 3c. Chain: a. Fragment: human rhinovirus serotype 14 3c protease. Synonym: picornain 3c,p3c. Engineered: yes. Ace-lealfq-ethylpropionate. Chain: b. Engineered: yes

Source:

Rhinovirus b14. Organism_taxid: 12131. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Other_details: peptidyl inhibitor synthesized via solid and solution phase pedtide synthesis

NMR struc:

20 models

Authors:

T.C.Bjorndahl,L.C.Andrew,D.S.Wishart

Key ref:

T.C.Bjorndahl et al. (2007). NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison. Biochemistry, 46, 12945-12958. PubMed id: 17944485

Date:

13-Sep-05 Release date: 05-Sep-06

Protein chain

P03303  (POLG_HRV14) -  Genome polyprotein from Human rhinovirus 14

Seq: 2179 a.a.

Struc: 182 a.a.

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

Biochemistry 46:12945-12958 (2007)

PubMed id: 17944485

NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison.

T.C.Bjorndahl, L.C.Andrew, V.Semenchenko, D.S.Wishart.

ABSTRACT

The human rhinovirus (HRV) is a positive sense RNA virus responsible for about 30% of "common colds". It relies on a 182 residue cysteine protease (3C) to proteolytically process its single gene product. Inhibition of this enzyme in vitro and in vivo has consistently demonstrated cessation of viral replication. This suggests that 3C protease inhibitors could serve as good drug candidates. However, significant proteolytic substrate diversity exists within the 110+ known rhinovirus serotypes. To investigate this variability we used NMR to solve the structure of the rhinovirus serotype 14 3C protease (subgenus B) covalently bound to a peptide (acetyl-LEALFQ-ethylpropionate) inhibitor. The inhibitor-bound structure was determined to an overall rmsd of 0.82 A (backbone atoms) and 1.49 A (all heavy atoms). Comparison with the X-ray structure of the serotype 2 HRV 3C protease from subgenus A (51% sequence identity) bound to the inhibitor ruprintrivir allowed the identification of conserved intermolecular interactions involved in proximal substrate binding as well as subgenus differences that might account for the variability observed in SAR studies. To better characterize the 3C protease and investigate the structural and dynamic differences between the apo and bound states we also solved the solution structure of the apo form. The apo structure has an overall rmsd of 1.07 +/- 0.17 A over backbone atoms, which is greater by 0.25 A than what is seen for the inhibited enzyme (2B0F.pdb). This increase is localized to the enzyme's C-terminal beta-barrel domain, which is responsible for recognizing and binding proteolytic substrates. Amide hydrogen exchange dynamics revealed dramatic differences between the two enzyme states. Furthermore, a number of residues exhibited exchange-broadened amide NMR signals in the apo state compared to the inhibited state. The majority of these residues are associated with proteolytic substrate interaction.