PDBsum entry 1zh1

Metal binding protein

PDB id: 1zh1

Contents

Protein chains

163 a.a. *

Metals

_ZN ×2

Waters ×96

* Residue conservation analysis

PDB id:

1zh1

Name:

Metal binding protein

Title:

Structure of the zinc-binding domain of hcv ns5a

Structure:

Non-structural polyprotein. Chain: a, b. Fragment: domain i. Zinc binding domain. Engineered: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Gene: nonstructural protein 5a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.227 R-free: 0.286

Authors:

T.L.Tellinghuisen,J.Marcotrigiano,C.M.Rice

Key ref:

T.L.Tellinghuisen et al. (2005). Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase. Nature, 435, 374-379. PubMed id: 15902263 DOI: 10.1038/nature03580

Date:

22-Apr-05 Release date: 24-May-05

Protein chains

Q9WMX2  (POLG_HCVCO) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate Con1)

Seq: 3010 a.a.

Struc: 163 a.a.

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.3.4.21.98 - 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⁺
• Enzyme class 5: 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: 10.1038/nature03580

Nature 435:374-379 (2005)

PubMed id: 15902263

Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase.

T.L.Tellinghuisen, J.Marcotrigiano, C.M.Rice.

ABSTRACT

Hepatitis C virus (HCV) is a human pathogen affecting nearly 3% of the world's population. Chronic infections can lead to cirrhosis and liver cancer. The RNA replication machine of HCV is a multi-subunit membrane-associated complex. The non-structural protein NS5A is an active component of HCV replicase, as well as a pivotal regulator of replication and a modulator of cellular processes ranging from innate immunity to dysregulated cell growth. NS5A is a large phosphoprotein (56-58 kDa) with an amphipathic alpha-helix at its amino terminus that promotes membrane association. After this helix region, NS5A is organized into three domains. The N-terminal domain (domain I) coordinates a single zinc atom per protein molecule. Mutations disrupting either the membrane anchor or zinc binding of NS5A are lethal for RNA replication. However, probing the role of NS5A in replication has been hampered by a lack of structural information about this multifunctional protein. Here we report the structure of NS5A domain I at 2.5-A resolution, which contains a novel fold, a new zinc-coordination motif and a disulphide bond. We use molecular surface analysis to suggest the location of protein-, RNA- and membrane-interaction sites.

Selected figure(s)

Figure 1.
Figure 1: An overview of the NS5A domain I structure. a, Schematic of HCV genome organization and the domain structure of the NS5A protein. The portion of domain I in presented in this crystal structure is indicated by the red bar. C, capsid protein; E1 and E2, envelope glycoproteins 1 and 2 (respectively); 4A, NS4A protein. b, Ribbon diagram of the structure of domain I. The polypeptide chain is coloured from the N terminus (blue) to C terminus (red). The coordinated zinc atom is shown in yellow. The C-terminal disulphide bond is shown in blue. c, A 180° rotation showing the 'back' of domain I. d, A 90° rotation showing the 'top-down' view of domain I. e, Domain I topology organization model.

Figure 4.
Figure 4: The NS5A domain I dimer reveals potential interaction surfaces. a, Ribbon diagrams of three rotations of the domain I dimer. b, Surface-potential plots of the domain I dimer, with views corresponding to those shown in a. Analysis of images in a and b shows that the dimer creates a relatively flat, basic surface near the N terminus and a large groove between the two subdomain IB regions. c, Model of NS5A position relative to the endoplasmic reticulum membrane. The location of the conserved surface in Fig. 3b is indicated. Helices are from the recent structure of the NS5A N-terminal helix8.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2005, 435, 374-379) copyright 2005.

Figures were selected by an automated process.