PDBsum entry 1cu1

Hydrolase

PDB id: 1cu1

Contents

Protein chains

645 a.a.

Ligands

PO4 ×2

Metals

_ZN ×2

Waters ×268

PDB id:

1cu1

Name:

Hydrolase

Title:

Crystal structure of an enzyme complex from hepatitis c virus

Structure:

Protein (protease/helicase ns3). Chain: a, b. Engineered: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.200 R-free: 0.260

Authors:

N.Yao,P.C.Weber

Key ref:

N.Yao et al. (1999). Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase. Structure, 7, 1353-1363. PubMed id: 10574797 DOI: 10.1016/S0969-2126(00)80025-8

Date:

20-Aug-99 Release date: 23-Aug-00

Protein chains

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

Seq: 3010 a.a.

Struc: 645 a.a.*

* PDB and UniProt seqs differ at 18 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

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

• Enzyme class 2: 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: E.C.3.4.22.- - ?????
• Enzyme class 4: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate + H2O = ribonucleoside 5'-diphosphate + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 5: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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/S0969-2126(00)80025-8

Structure 7:1353-1363 (1999)

PubMed id: 10574797

Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase.

N.Yao, P.Reichert, S.S.Taremi, W.W.Prosise, P.C.Weber.

ABSTRACT

BACKGROUND: Hepatitis C virus (HCV) currently infects approximately 3% of the world's population. HCV RNA is translated into a polyprotein that during maturation is cleaved into functional components. One component, nonstructural protein 3 (NS3), is a 631-residue bifunctional enzyme with protease and helicase activities. The NS3 serine protease processes the HCV polyprotein by both cis and trans mechanisms. The structural aspects of cis processing, the autoproteolysis step whereby the protease releases itself from the polyprotein, have not been characterized. The structural basis for inclusion of protease and helicase activities in a single polypeptide is also unknown. RESULTS: We report here the 2.5 A resolution structure of an engineered molecule containing the complete NS3 sequence and the protease activation domain of nonstructural protein 4A (NS4A) in a single polypeptide chain (single chain or scNS3-NS4A). In the molecule, the helicase and protease domains are segregated and connected by a single strand. The helicase necleoside triphosphate and RNA interaction sites are exposed to solvent. The protease active site of scNS3-NS4A is occupied by the NS3 C terminus, which is part of the helicase domain. Thus, the intramolecular complex shows one product of NS3-mediated cleavage at the NS3-NS4A junction of the HCV polyprotein bound at the protease active site. CONCLUSIONS: The scNS3-NS4A structure provides the first atomic view of polyprotein cis processing. Both local and global structural rearrangements follow the cis cleavage reaction, and large segments of the polyprotein can be folded prior to proteolytic processing. That the product complex of the cis cleavage reaction exists in a stable molecular conformation suggests autoinhibition and substrate-induced activation mechanisms for regulation of NS3 protease activity.

Selected figure(s)

Figure 8.
Figure 8. HCV polyprotein processing in the nonstructural region. Nonstructural proteins NS3, NS4A, NS4B, NS5A and NS5B are colored purple, red, green, pink and orange, respectively. (a) Attachment of the 1984-residue polyprotein to the membrane. (b) NS4A activation and folding of the NS3 N terminus. (c) Subsequent cleavage reactions. To highlight the fact that the sequence of cleavage reactions has not been firmly established, the N terminus of the polyprotein substrate is dotted and the schematic diagrams are enclosed in a box. (d) The release of NS4B and NS5A and formation of the replication complex core.

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1353-1363) copyright 1999.

Figure was selected by an automated process.