PDBsum entry 2mxd

Viral protein

PDB id: 2mxd

Contents

Protein chain

62 a.a.

PDB id:

2mxd

Name:

Viral protein

Title:

Solution structure of vpg of porcine sapovirus

Structure:

Viral protein genome-linked. Chain: a. Fragment: unp residues 948-1006. Synonym: vpg. Engineered: yes

Source:

Porcine enteric sapovirus. Organism_taxid: 106333. Gene: orf1. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

J.Kim,H.Hwang,H.Min,H.Yun,K.Cho,J.G.Pelton,D.E.Wemmer,C.Lee

Key ref:

H.J.Hwang et al. (2015). Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch. Biochem Biophys Res Commun, 459, 610-616. PubMed id: 25753201 DOI: 10.1016/j.bbrc.2015.02.156

Date:

24-Dec-14 Release date: 15-Apr-15

Protein chain

Q9QEJ5  (POLG_PESV) -  Genome polyprotein from Porcine enteric sapovirus (isolate Swine/United States/Cowden/1980)

Seq: 2254 a.a.

Struc: 62 a.a.*

* PDB and UniProt seqs differ at 3 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.3.4.22.66 - calicivirin.
• 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

DOI no: 10.1016/j.bbrc.2015.02.156

Biochem Biophys Res Commun 459:610-616 (2015)

PubMed id: 25753201

Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch.

H.J.Hwang, H.J.Min, H.Yun, J.G.Pelton, D.E.Wemmer, K.O.Cho, J.S.Kim, C.W.Lee.

ABSTRACT

Viral protein genome-linked (VPg) proteins play a critical role in the life cycle of vertebrate and plant positive-sense RNA viruses by acting as a protein primer for genome replication and as a protein cap for translation initiation. Here we report the solution structure of the porcine sapovirus VPg core (VPg(C)) determined by multi-dimensional NMR spectroscopy. The structure of VPg(C) is composed of three α-helices stabilized by several conserved hydrophobic residues that form a helical bundle core similar to that of feline calicivirus VPg. The putative nucleotide acceptor Tyr956 within the first helix of the core is completely exposed to solvent accessible surface to facilitate nucleotidylation by viral RNA polymerase. Comparison of VPg structures suggests that the surface for nucleotidylation site is highly conserved among the Caliciviridae family, whereas the backbone core structures are different. These structural features suggest that caliciviruses share common mechanisms of VPg-dependent viral replication and translation.