PDBsum entry 2w5e

Hydrolase

PDB id: 2w5e

Contents

Protein chains

(+ 0 more) 162 a.a. *

Metals

_CL ×28

_CD ×18

Waters ×336

* Residue conservation analysis

PDB id:

2w5e

Name:

Hydrolase

Title:

Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 angstrom resolution

Structure:

Putative serine protease. Chain: a, b, c, d, e, f. Fragment: residues 432-587. Engineered: yes

Source:

Human astrovirus 1. Organism_taxid: 12456. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.234 R-free: 0.258

Authors:

S.Speroni,J.Rohayem,S.Nenci,D.Bonivento,I.Robel,J.Barthel,B.Coutard, B.Canard,A.Mattevi

Key ref:

S.Speroni et al. (2009). Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 A resolution. J Mol Biol, 387, 1137-1152. PubMed id: 19249313 DOI: 10.1016/j.jmb.2009.02.044

Date:

10-Dec-08 Release date: 10-Mar-09

Protein chains

P0C6K4  (NS1A_HASV1) -  Non-structural polyprotein 1A from Human astrovirus-1

Seq: 935 a.a.

Struc: 162 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1016/j.jmb.2009.02.044

J Mol Biol 387:1137-1152 (2009)

PubMed id: 19249313

Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 A resolution.

S.Speroni, J.Rohayem, S.Nenci, D.Bonivento, I.Robel, J.Barthel, V.B.Luzhkov, B.Coutard, B.Canard, A.Mattevi.

ABSTRACT

Astroviruses are single-stranded RNA viruses with a replication strategy based on the proteolytic processing of a polyprotein precursor and subsequent release of the viral enzymes of replication. So far, the catalytic properties of the astrovirus protease as well as its structure have remained uncharacterized. In this study, the three-dimensional crystal structure of the predicted protease of human pathogenic astrovirus has been solved to 2.0 A resolution. The protein displays the typical properties of trypsin-like enzymes but also several characteristic features: (i) a catalytic Asp-His-Ser triad in which the aspartate side chain is oriented away from the histidine, being replaced by a water molecule; (ii) a non-common conformation and composition of the S1 pocket; and (iii) the lack of the typical surface beta-ribbons together with a "featureless" shape of the substrate-binding site. Hydrolytic activity assays indicate that the S1 pocket recognises Glu and Asp side chains specifically, which, therefore, are predicted to occupy the P1 position on the substrate cleavage site. The positive electrostatic potential featured by the S1 region underlies this specificity. The comparative structural analysis highlights the peculiarity of the astrovirus protease, and differentiates it from the human and viral serine proteases.

Selected figure(s)

Figure 4.
Fig. 4. Crystal structure of HAstV protease. (a) The monomer. The N- and C-terminal domains are coloured cyan and light blue, respectively. The active site residues are depicted as red sticks and lie at the interface between the two domains. (b) HAstV protease crystallises as a hexamer, which is composed of three dimers labelled A-B, C-D, and E-F. Cadmium ions are shown as orange balls. (c) The dimer. The two subunits interact along the β-strand bII, forming six intermolecular hydrogen bonds that generate an intermolecular β-sheet across the two subunits. Moreover, a number of intermolecular interactions are mediated by cadmium ions (green spheres) and His[6]-tag residues (shown as ball-and-sticks). The depicted dimer corresponds to subunit A and B in b, and it is viewed along its 2-fold axis.

Figure 6.
Fig. 6. Catalytic triad conformations in: (a) HAstV; (b) human pathogenic rhinovirus (PDB entry code 1cqq); and (c) hepatitis A virus (PDB entry code 1qa7) proteases. In the HAstV structure, Asp489 of the catalytic triad points away from His461 (Fig. 3) in a geometry similar to that observed in the ligand-free structure of hepatitis A virus enzyme. The conformation of Asp489 leaves room for a water molecule to hydrogen bond His461 and Gln567 (broken lines). The canonical catalytic triad architecture is present in the protease of rhinovirus.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 387, 1137-1152) copyright 2009.

Figures were selected by an automated process.