PDBsum entry 1ns3

Complex (hydrolase/peptide)

PDB id: 1ns3

Contents

Protein chains

178 a.a.

13 a.a.

Metals

_ZN ×2

Waters ×2

PDB id:

1ns3

Name:

Complex (hydrolase/peptide)

Title:

Structure of hcv protease (bk strain)

Structure:

Ns3 protease. Chain: a, b. Engineered: yes. Ns4a peptide. Chain: c, d. Engineered: yes. Mutation: yes

Source:

Hepatitis c virus. Organism_taxid: 11105. Strain: isolate bk. Variant: isolate bk. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

24mer (from PQS)

Resolution:

2.80Å R-factor: 0.204

Authors:

Y.Yan,S.Munshi,Z.Chen

Key ref:

Y.Yan et al. (1998). Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form. Protein Sci, 7, 837-847. PubMed id: 9568891 DOI: 10.1002/pro.5560070402

Date:

05-Apr-97 Release date: 08-Apr-98

Protein chains

P26663  (POLG_HCVBK) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate BK)

Seq: 3010 a.a.

Struc: 178 a.a.*

Protein chains

P26663  (POLG_HCVBK) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate BK)

Seq: 3010 a.a.

Struc: 13 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chains A, B, C, D: 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 3: Chains A, B, C, D: E.C.3.4.22.- - ?????
• Enzyme class 4: Chains A, B, C, D: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 5: Chains A, B, C, D: 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

DOI no: 10.1002/pro.5560070402

Protein Sci 7:837-847 (1998)

PubMed id: 9568891

Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form.

Y.Yan, Y.Li, S.Munshi, V.Sardana, J.L.Cole, M.Sardana, C.Steinkuehler, L.Tomei, R.De Francesco, L.C.Kuo, Z.Chen.

ABSTRACT

The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6(3)22 to a resolution of 2.2 A. This protease is bound with a 14-mer peptide representing the central region of the NS4A protein. There are two molecules of the NS3(1-180)-NS4A(21'-34') complex per asymmetric unit. Each displays a familiar chymotrypsin-like fold that includes two beta-barrel domains and four short alpha-helices. The catalytic triad (Ser-139, His-57, and Asp-81) is located in the crevice between the beta-barrel domains. The NS4A peptide forms an almost completely enclosed peptide surface association with the protease. In contrast to the reported H strain complex of NS3 protease-NS4A peptide in a trigonal crystal form (Kim JL et al., 1996, Cell 87:343-355), the N-terminus of the NS3 protease is well-ordered in both molecules in the asymmetric unit of our hexagonal crystal form. The folding of the N-terminal region of the NS3 protease is due to the formation of a three-helix bundle as a result of crystal packing. When compared with the unbound structure (Love RA et al., 1996, Cell 87:331-342), the binding of the NS4A peptide leads to the ordering of the N-terminal 28 residues of the NS3 protease into a beta-strand and an alpha-helix and also causes local rearrangements important for a catalytically favorable conformation at the active site. Our analysis provides experimental support for the proposal that binding of an NS4A-mimicking peptide, which increases catalytic rates, is necessary but not sufficient for formation of a well-ordered, compact and, hence, highly active protease molecule.