PDBsum entry 2qid

Viral protein/inhibitor

PDB id: 2qid

Contents

Protein chains

177 a.a. *

72 a.a. *

Waters ×176

* Residue conservation analysis

Obsolete entry

PDB id:

2qid

Name:

Viral protein/inhibitor

Title:

Dengue virus ns3-protease complexed with mung-bean bowman-birk inhibitor

Structure:

Non-structural protein 1 (ns1). Chain: a, b. Fragment: ns3 protease domain. Engineered: yes. Bowman-birk type trypsin inhibitor. Chain: c. Fragment: mbbbi

Source:

Dengue virus. Organism_taxid: 12637. Strain: jamaica. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: serotype 2. Vigna radiata var. Radiata. Mung bean. Organism_taxid: 3916.

Resolution:

2.10Å R-factor: 0.199 R-free: 0.243

Authors:

K.H.M.Murthy,K.Judge,L.Delucas,R.Padmanabhan

Key ref:

H.M.Murthy et al. (2000). Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design. J Mol Biol, 301, 759-767. PubMed id: 10966782 DOI: 10.1006/jmbi.2000.3924

Date:

03-Jul-07 Release date: 21-Aug-07

Protein chains

P14340  (POLG_DEN2N) -  Genome polyprotein from Dengue virus type 2 (strain Thailand/NGS-C/1944)

Seq: 3391 a.a.

Struc: 177 a.a.*

Protein chain

P01062  (IBB_VIGRR) -  Bowman-Birk type trypsin inhibitor from Vigna radiata var. radiata

Seq: 72 a.a.

Struc: 72 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DOI no: 10.1006/jmbi.2000.3924

J Mol Biol 301:759-767 (2000)

PubMed id: 10966782

Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design.

H.M.Murthy, K.Judge, L.DeLucas, R.Padmanabhan.

ABSTRACT

Dengue viruses are members of the Flaviviridae and cause dengue fever and the more severe dengue hemorrhagic fever. Although nearly 40 % of the world's population is at risk of dengue infection, there is currently no effective vaccine or chemotherapy for the disease. Processing of the dengue polyprotein into structural and non-structural proteins in a host, which is essential for assembly of infective virions, is carried out by the combined action of host proteases and the trypsin-like, two-component viral NS2B/NS3 serine protease. Although NS2B strongly stimulates the catalytic NS3 protease domain, the latter is fully active against small substrates and possesses detectable activity against larger substrates, making both forms of the enzyme possible targets for drug design. In the crystal structure of a complex of the protease with a Bowman-Birk inhibitor reported here, an Arg residue at the P1 position of the inhibitor is bound in a manner distinctly different from that in other serine proteases of comparable specificity. However, because the regulatory component, NS2B, is not present in the complex, the physiological implications of this observations are currently unclear. The redundant nature of interaction of P1 Arg and Lys residues with Asp129, Tyr150 and Ser163 of the enzyme provides an explanation for the observed behavior of several site-specific mutants of Asp129 in the protease. The strong level of conservation of residues in the protease that interact with the P1 Arg, along with conservation of Arg at P1 of most cleavage sites in other flaviviruses, suggests that observations from this structure are likely to be applicable to many flaviviruses. The structure provides a starting point for design of site-specific mutations to probe the mechanism of catalysis by the catalytic domain, its activation by the regulatory domain and for design of specific inhibitors of enzymatic activity.

Selected figure(s)

Figure 1.
Figure 1. (a) Electron density around disordered Arg47 (stereo view). A 2F[o] -F[c] map computed with phases calculated without Arg47 is shown with the final model superimposed. Data to 2.1 Å were used to calculate the map, which is contoured at 1 s. (b) Differences between unliganded and inhibited protease (stereo view). A section of the C-terminal b barrel is show as an a carbon trace. Unliganded protease (magenta) molecule 1 (cyan) and molecule 2 (yellow) in this complex, all transformed to the unliganded protease reference frame, are shown. Conformation of Asp129 in the unliganded form is shown in magenta and that in molecule 2 of the complex in yellow. Both conformations of Arg47 are also shown for reference. Hydrogen bonds between side-chains of Arg47B and Asp129 are shown as broken lines. The Figure was made with: (a) O (Jones et al., 1991); (b) RIBBONS (Carson, 1987).

Figure 2.
Figure 2. Interactions of P1 sites with respective S1 pockets. C^a trace of the protease is gray and that of the inhibitor is orange. (a) Interaction of Lys20 with the S1 pocket on molecule 1 of the enzyme (stereo view). Residues that make van der Waals contacts (cyan) and those that make electrostatic interactions (yellow) with Lys20 (carbon, magenta; nitrogen, blue; oxygen, red) of the inhibitor are shown. (b) Interactions of Arg47 with the S1 pocket on molecule 2 (stereo view). Protease residues that make van der Waals contacts with Arg47 are cyan. Residues Tyr150 and Ser163, which make electrostatic contacts with conformation A are yellow, and Asp129 which makes two hydrogen bonds with Arg47B is red. The two conformations of the Arg residue are labeled A and B, and shown in the same color scheme used for (a). (c) Spacefilling representation of the S1 pocket (stereo view). Calculated molecular surface for all the residues (listed in Table 2) in the S1 pocket of molecule 2 of the protease is represented by cyan dots. Both conformations of Arg47 are shown using the color scheme of (a). Position of Lys20, with its carbon atoms color-coded magenta, relative to that of Arg47 is also shown. The position was derived by superposition of C^a atoms of residues 18-23, the loop carrying Lys20, of MbBBI over residues 45-50, the loop carrying Arg47. The two loops superpose with an rms deviation of 0.27 Å. Tyr150 and Ser163 are yellow and Asp129 is red. Electrostatic interactions and hydrogen bonds are shown by broken lines. Note that the hydrogen bond between Lys20 and Tyr150 is not included for clarity. The Figure was made with: (a) and (b) RIBBONS (Carson, 1987); (c) GRASP (Nicholls et al., 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 759-767) copyright 2000.