PDBsum entry 5mv0

Viral protein

PDB id: 5mv0

Contents

Protein chains

200 a.a.

Ligands

PO4 ×4

Waters ×620

PDB id:

5mv0

Name:

Viral protein

Title:

Structure of an n-terminal domain of a reptarenavirus l protein

Structure:

L protein. Chain: a, b, c, d. Fragment: n-terminus, unp residues 1-205. Engineered: yes

Source:

Cas virus. Organism_taxid: 1223561. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.93Å R-factor: 0.175 R-free: 0.215

Authors:

M.Rosenthal,N.Gogrefe,J.Reguera,D.Vogel,B.Rauschenberger,S.Cusack, S.Gunther,S.Reindl

Key ref:

M.Rosenthal et al. (2017). Structural insights into reptarenavirus cap-snatching machinery. PLoS Pathog, 13, e1006400. PubMed id: 28505175

Date:

14-Jan-17 Release date: 17-May-17

Protein chains

J7HBG8  (J7HBG8_9VIRU) -  RNA-directed RNA polymerase L from CAS virus

Seq: 2046 a.a.

Struc: 200 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

PLoS Pathog 13:e1006400 (2017)

PubMed id: 28505175

Structural insights into reptarenavirus cap-snatching machinery.

M.Rosenthal, N.Gogrefe, D.Vogel, J.Reguera, B.Rauschenberger, S.Cusack, S.Günther, S.Reindl.

ABSTRACT

Cap-snatching was first discovered in influenza virus. Structures of the involved domains of the influenza virus polymerase, namely the endonuclease in the PA subunit and the cap-binding domain in the PB2 subunit, have been solved. Cap-snatching endonucleases have also been demonstrated at the very N-terminus of the L proteins of mammarena-, orthobunya-, and hantaviruses. However, a cap-binding domain has not been identified in an arena- or bunyavirus L protein so far. We solved the structure of the 326 C-terminal residues of the L protein of California Academy of Sciences virus (CASV), a reptarenavirus, by X-ray crystallography. The individual domains of this 37-kDa fragment (L-Cterm) as well as the domain arrangement are structurally similar to the cap-binding and adjacent domains of influenza virus polymerase PB2 subunit, despite the absence of sequence homology, suggesting a common evolutionary origin. This enabled identification of a region in CASV L-Cterm with similarity to a cap-binding site; however, the typical sandwich of two aromatic residues was missing. Consistent with this, cap-binding to CASV L-Cterm could not be detected biochemically. In addition, we solved the crystal structure of the corresponding endonuclease in the N-terminus of CASV L protein. It shows a typical endonuclease fold with an active site configuration that is essentially identical to that of known mammarenavirus endonuclease structures. In conclusion, we provide evidence for a presumably functional cap-snatching endonuclease in the N-terminus and a degenerate cap-binding domain in the C-terminus of a reptarenavirus L protein. Implications of these findings for the cap-snatching mechanism in arenaviruses are discussed.