PDBsum entry 4inh

Hydrolase/hydrolase inhibitor

PDB id: 4inh

Contents

Protein chains

(+ 2 more) 172 a.a.

Ligands

PHQ-ALA-LEU-1HB ×8

DMS ×4

Waters ×1541

PDB id:

4inh

Name:

Hydrolase/hydrolase inhibitor

Title:

Structural basis of substrate specificity and protease inhibition in norwalk virus

Structure:

Genome polyprotein. Chain: a, b, c, d, e, f, g, h. Fragment: norwalk virus protease (unp residues 1101-1281). Synonym: protein p48, ntpase, p41, protein p22, viral genome-linked protein, vpg, 3c-like protease, 3clpro, calicivirin, RNA-directed RNA polymerase, rdrp. Engineered: yes. Peptide inhibitor, syc59. Chain: j, m, s, t, n, o, p, q.

Source:

Norovirus hu/1968/us. Hu/nv/nv/1968/us. Organism_taxid: 524364. Strain: gi/human/united states/norwalk/1968. Gene: orf1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct.

Resolution:

1.70Å R-factor: 0.178 R-free: 0.208

Authors:

B.V.V.Prasad,Z.Muhaxhiri,L.Deng,S.Shanker,B.Sankaran,M.K.Estes, T.Palzkill,Y.Song

Key ref:

Z.Muhaxhiri et al. (2013). Structural basis of substrate specificity and protease inhibition in Norwalk virus. J Virol, 87, 4281-4292. PubMed id: 23365454 DOI: 10.1128/JVI.02869-12

Date:

04-Jan-13 Release date: 20-Feb-13

Protein chains

Q83883  (POLG_NVN68) -  Genome polyprotein from Norovirus (strain Human/NoV/United States/Norwalk/1968/GI)

Seq: 1789 a.a.

Struc: 172 a.a.*

* PDB and UniProt seqs differ at 4 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
• Enzyme class 2: E.C.3.4.22.66 - calicivirin.
• Enzyme class 3: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + 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: 10.1128/JVI.02869-12

J Virol 87:4281-4292 (2013)

PubMed id: 23365454

Structural basis of substrate specificity and protease inhibition in Norwalk virus.

Z.Muhaxhiri, L.Deng, S.Shanker, B.Sankaran, M.K.Estes, T.Palzkill, Y.Song, B.V.Prasad.

ABSTRACT

Norwalk virus (NV), the prototype human calicivirus, is the leading cause of nonbacterial acute gastroenteritis. The NV protease cleaves the polyprotein encoded by open reading frame 1 of the viral genome at five nonhomologous sites, releasing six nonstructural proteins that are essential for viral replication. The structural details of how NV protease recognizes multiple substrates are unclear. In our X-ray structure of an NV protease construct, we observed that the C-terminal tail, representing the native substrate positions P5 to P1, is inserted into the active site cleft of the neighboring protease molecule, providing atomic details of how NV protease recognizes a substrate. The crystallographic structure of NV protease with the C-terminal tail redesigned to mimic P4 to P1 of another substrate site provided further structural details on how the active site accommodates sequence variations in the substrates. Based on these structural analyses, substrate-based aldehyde inhibitors were synthesized and screened for inhibition potency. Crystallographic structures of the protease in complex with each of the three most potent inhibitors were determined. These structures showed concerted conformational changes in the S4 and S2 pockets of the protease to accommodate variations in the P4 and P2 residues of the substrate/inhibitor, which could be a mechanism for how the NV protease recognizes multiple sites in the polyprotein with differential affinities during virus replication. These structures further indicate that the mechanism of inhibition by these inhibitors involves covalent bond formation with the side chain of the conserved cysteine in the active site by nucleophilic addition, and such substrate-based aldehydes could be effective protease inhibitors.