PDBsum entry: 1onb

Hydrolase

PDB id: 1onb

Contents

Protein chain

138 a.a. *

* Residue conservation analysis

PDB id:

1onb

Name:

Hydrolase

Title:

Solution structure of an engineered arginine-rich subdomain 2 of the hepatitis c virus ns3 RNA helicase

Structure:

Helicase ns3. Chain: a. Fragment: arginine-rich subdomain 2. Engineered: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Gene: ns3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

25 models

Authors:

D.Liu,Y.S.Wang,J.J.Gesell,D.F.Wyss

Key ref:

D.Liu et al. (2001). Solution structure and backbone dynamics of an engineered arginine-rich subdomain 2 of the hepatitis C virus NS3 RNA helicase. J Mol Biol, 314, 543-561. PubMed id: 11846566 DOI: 10.1006/jmbi.2001.5146

Date:

27-Feb-03 Release date: 11-Mar-03

Protein chain

P27958  (POLG_HCVH) -  Genome polyprotein

Seq: 3011 a.a.

Struc: 138 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
• 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.3.6.1.15 - Nucleoside-triphosphatase.
• Reaction: NTP + H₂O = NDP + phosphate
• Enzyme class 4: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

reference

DOI no: 10.1006/jmbi.2001.5146

J Mol Biol 314:543-561 (2001)

PubMed id: 11846566

Solution structure and backbone dynamics of an engineered arginine-rich subdomain 2 of the hepatitis C virus NS3 RNA helicase.

D.Liu, Y.S.Wang, J.J.Gesell, D.F.Wyss.

ABSTRACT

The NS3 protein of the hepatitis C virus (HCV) is a 631 amino acid residue bifunctional enzyme with a serine protease localized to the N-terminal 181 residues and an RNA helicase located in the C-terminal 450 residues. The HCV NS3 RNA helicase consists of three well-defined subdomains which all contribute to its helicase activity. The second subdomain of the HCV helicase is flexibly linked to the remainder of the NS3 protein and could undergo rigid-body movements during the unwinding of double-stranded RNA. It also contains several motifs that are implicated in RNA binding and in coupling NTP hydrolysis to nucleic acid unwinding and translocation. As part of our efforts to use NMR techniques to assist in deciphering the enzyme's structure-function relationships and developing specific small molecule inhibitors, we have determined the solution structure of an engineered subdomain 2 of the NS3 RNA helicase of HCV, d(2Delta)-HCVh, and studied the backbone dynamics of this protein by (15)N-relaxation experiments using a model-free approach. The NMR studies on this 142-residue construct reveal that overall subdomain 2 of the HCV helicase is globular and well structured in solution even in the absence of the remaining parts of the NS3 protein. Its solution structure is very similar to the corresponding parts in the X-ray structures of the HCV NS3 helicase domain and intact bifunctional HCV NS3 protein. Slow hydrogen-deuterium exchange rates map to a well-structured, stable hydrophobic core region away from the subdomain interfaces. In contrast, the regions facing the subdomain interfaces in the HCV NS3 helicase domain are less well structured in d(2Delta)-HCVh, show fast hydrogen-deuterium exchange rates, and the analysis of the dynamic properties of d(2Delta)-HCVh reveals that these regions of the protein show distinct dynamical features. In particular, residues in motif V, which may be involved in transducing allosteric effects of nucleotide binding and hydrolysis on RNA binding, exhibit slow conformational exchange on the milli- to microsecond time-scale. The intrinsic conformational flexibility of this loop region may facilitate conformational changes required for helicase function.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the ensemble of 25 NMR solution structures of d[2D]-HCVh generated by superimposition of the backbone atoms (N, C^a, C' and O) of residues 334-430 and 452-478 (omitting the flexible N and C termini, residues 327-333 and 479-481, respectively, as well as the engineered loop I1-I4). The six b-strands of the parallel b-sheet are shown in red, the two b-strands of the short b-hairpin are colored cyan, and the three a-helices are shown in green. The orientation is similar to that in Figure 3(a).

Figure 3.
Figure 3. Solution structure of d[2D]-HCVh. (a, b) Ribbon representation of two views (which differ by a 90° rotation about a vertical axis and a 180° rotation about a horizontal axis) of a representative d[2D]-HCVh structure. The secondary structure elements are labeled according to Figure 1. In addition, the loop regions of the conserved motifs IV, V, and VI [23], and the engineered b-hairpin (yellow) are indicated. (c) Residues with hydrophobic side-chains are unevenly distributed between the two sides of the central b-sheet. Side-chains of residues which form the hydrophobic core region are colored red. Side-chains of residues on the opposite side of the central b-sheet are colored green for polar and negatively charged residues, yellow for positively charged residues, and magenta for hydrophobic residues. The orientation is similar to that in (a). (d) Backbone of the crystal structure of the HCV NS3 helicase domain (chain A of PDB 1HEI) [20] with the secondary structure elements shown for subdomain 2 illustrating the position of the conserved motifs IV, V, and VI with respect to the other two subdomains. The hydrophobic core region is located on the face of the central b-sheet which is oriented away from the subdomain interfaces towards helicases a1 and a2. (a) and (b) were prepared using MOLMOL [69].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 543-561) copyright 2001.

Figures were selected by an automated process.