PDBsum entry 4zuh

Hydrolase/peptide

PDB id: 4zuh

Contents

Protein chains

298 a.a.

Ligands

SER-ALA-VAL-LEU-GLN-SER-GLY-PHE

Waters ×267

PDB id:

4zuh

Name:

Hydrolase/peptide

Title:

Complex structure of pedv 3clpro mutant (c144a) with a peptide substrate.

Structure:

Pedv 3c-like protease. Chain: a, b. Fragment: unp residues 2998-3296. Engineered: yes. Mutation: yes. Peptide substrate savlqsgf. Chain: c. Engineered: yes

Source:

Porcine epidemic diarrhea virus. Organism_taxid: 28295. Gene: pol1. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.39Å R-factor: 0.159 R-free: 0.219

Authors:

G.Ye,Z.F.Fu,G.Q.Peng

Key ref:

G.Ye et al. (2016). Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Virology, 494, 225-235. PubMed id: 27128350 DOI: 10.1016/j.virol.2016.04.018

Date:

16-May-15 Release date: 15-Jun-16

Protein chains

R4JK63  (R4JK63_9ALPC) -  ORF1ab polyprotein from Porcine epidemic diarrhea virus

Seq: 6781 a.a.

Struc: 298 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 2: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 3: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 4: 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: 10.1016/j.virol.2016.04.018

Virology 494:225-235 (2016)

PubMed id: 27128350

Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease.

G.Ye, F.Deng, Z.Shen, R.Luo, L.Zhao, S.Xiao, Z.F.Fu, G.Peng.

ABSTRACT

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CL(pro)), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CL(pro) and a molecular complex between an inactive PEDV 3CL(pro) variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CL(pro). The dimerization of PEDV 3CL(pro) is similar to that of other Alphacoronavirus 3CL(pro)s but has several differences from that of SARS-CoV 3CL(pro) from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CL(pro)s, which may provide new insights into the recognition of substrates by 3CL(pro)s in various coronavirus genera.