PDBsum entry 1qa7

Hydrolase/hydrolase inhibitor

PDB id: 1qa7

Contents

Protein chains

213 a.a. *

Ligands

IVF ×4

DMS

GOL

Waters ×514

* Residue conservation analysis

PDB id:

1qa7

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal complex of the 3c proteinase from hepatitis a virus with its inhibitor and implications for the polyprotein processing in hav

Structure:

Hav 3c proteinase. Chain: a, b, c, d. Fragment: hav 3c proteinase. Engineered: yes. Mutation: yes. Other_details: proteinase chemically bonded to inhibitor ace-val-nfa. It was chemically synthesized as iodoacetyl-valyl-phenylalanyl amide

Source:

Hepatitis a virus. Organism_taxid: 12092. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Not given

Resolution:

1.90Å R-factor: 0.214 R-free: 0.298

Authors:

E.M.Bergmann,M.M.Cherney,J.Mckendrick,J.C.Vederas,M.N.G.James

Key ref:

E.M.Bergmann et al. (1999). Crystal structure of an inhibitor complex of the 3C proteinase from hepatitis A virus (HAV) and implications for the polyprotein processing in HAV. Virology, 265, 153-163. PubMed id: 10603326

Date:

15-Apr-99 Release date: 20-Apr-99

Protein chains

P08617  (POLG_HAVHM) -  Genome polyprotein from Human hepatitis A virus genotype IB (isolate HM175)

Seq: 2227 a.a.

Struc: 213 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: 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

Virology 265:153-163 (1999)

PubMed id: 10603326

Crystal structure of an inhibitor complex of the 3C proteinase from hepatitis A virus (HAV) and implications for the polyprotein processing in HAV.

E.M.Bergmann, M.M.Cherney, J.Mckendrick, S.Frormann, C.Luo, B.A.Malcolm, J.C.Vederas, M.N.James.

ABSTRACT

The proteolytic processing of the viral polyprotein is an essential step during the life cycle of hepatitis A virus (HAV), as it is in all positive-sense, single-stranded RNA viruses of animals. In HAV the 3C proteinase is the only proteolytic activity involved in the polyprotein processing. The specific recognition of the cleavage sites by the 3C proteinase depends on the amino acid sequence of the cleavage site. The structure of the complex of the HAV 3C proteinase and a dipeptide inhibitor has been determined by X-ray crystallography. The double-mutant of HAV 3C (C24S, F82A) was inhibited with the specific inhibitor iodoacetyl-valyl-phenylalanyl-amide. The resulting complex had an acetyl-Val-Phe-amide group covalently attached to the S(gamma) atom of the nucleophilic Cys 172 of the enzyme. Crystals of the complex of HAV 3C (C24S, F82A) acetyl-Val-Phe-amide were found to be monoclinic, space group P2(1), having 4 molecules in the asymmetric unit and diffracting to 1.9-A resolution. The final refined structure consists of 4 molecules of HAV 3C (C24S,F82A) acetyl-Val-Phe-amide, 1 molecule of DMSO, 1 molecule of glycerol, and 514 water molecules. There are considerable conformational differences among the four molecules in the asymmetric unit. The final R-factor is 20.4% for all observed reflections between 15.0- and 1.9-A resolution and the corresponding R(free) is 29.8%. The dipeptide inhibitor is bound to the S(1)(') and S(2)(') specificity subsites of the proteinase. The crystal structure reveals that the HAV 3C proteinase possesses a well-defined S(2)(') specificity pocket and suggests that the P(2)(') residue could be an important determinant for the selection of the primary cleavage site during the polyprotein processing in HAV.