PDBsum entry 4a1t

Hydrolase/peptide

PDB id: 4a1t

Contents

Protein chains

193 a.a.

17 a.a.

18 a.a.

Ligands

BCT

GOL ×3

DTT

Metals

_ZN ×2

__K ×4

_CL ×9

Waters ×217

PDB id:

4a1t

Name:

Hydrolase/peptide

Title:

Co-complex of the of ns3-4a protease with the inhibitory peptide cp5- 46-a (in-house data)

Structure:

Nonstructural protein 4a, serine protease ns3. Chain: a, b. Fragment: residues 1678-1690,1028-1206. Synonym: ns3-4a protease, ns4a, hepacivirin, ns3p, p70. Engineered: yes. Other_details: fusion protein of 4a (1678-1690) with ns3 (1028-1206). Cp5-46-a peptide. Chain: c, d. Engineered: yes.

Source:

Hepatitis c virus. Organism_taxid: 11103. Strain: 1b. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta2. Other_details: hcv replicon i389/ns3-3'utr (aj242654). Synthetic: yes. Synthetic construct.

Resolution:

2.05Å R-factor: 0.198 R-free: 0.245

Authors:

S.Schmelz,J.Kuegler,J.Collins,D.W.Heinz

Key ref:

J.Kügler et al. (2012). High affinity peptide inhibitors of the hepatitis C virus NS3-4A protease refractory to common resistant mutants. J Biol Chem, 287, 39224-39232. PubMed id: 22965230

Date:

19-Sep-11 Release date: 19-Sep-12

Protein chains

P26662  (POLG_HCVJA) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate Japanese)

Seq: 3010 a.a.

Struc: 193 a.a.*

Protein chain

No UniProt id for this chain

Struc: 17 a.a.

Protein chain

No UniProt id for this chain

Struc: 18 a.a.

* PDB and UniProt seqs differ at 20 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 4: Chains A, B: E.C.3.4.22.- - ?????
• Enzyme class 5: Chains A, B: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 6: Chains A, B: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + 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 Biol Chem 287:39224-39232 (2012)

PubMed id: 22965230

High affinity peptide inhibitors of the hepatitis C virus NS3-4A protease refractory to common resistant mutants.

J.Kügler, S.Schmelz, J.Gentzsch, S.Haid, E.Pollmann, J.van den Heuvel, R.Franke, T.Pietschmann, D.W.Heinz, J.Collins.

ABSTRACT

Hepatitis C virus (HCV) NS3-4A protease is essential for viral replication. All current small molecular weight drugs against NS3-4A are substrate peptidomimetics that have a similar binding and resistance profile. We developed inhibitory peptides (IPs) capping the active site and binding via a novel "tyrosine" finger at an alternative NS3-4A site that is of particular interest for further HCV drug development. The peptides are not cleaved due to a combination of geometrical constraints and impairment of the oxyanion hole function. Selection and optimization through combinatorial phagemid display, protein crystallography, and further modifications resulted in a 32-amino acid peptide with a K(i) of 0.53 nm. Inhibition of viral replication in cell culture was demonstrated by fusion to a cell-penetrating peptide. Negligible susceptibility to known (A156V and R155K) resistance mutations of the NS3-4A protease was observed. This work shows for the first time that antiviral peptides can target an intracellular site and reveals a novel druggable site on the HCV protease.