PDBsum entry 5n2e

Transferase

PDB id: 5n2e

Contents

Protein chain

999 a.a.

Ligands

MES ×3

GOL ×2

EPE

DTT

Waters ×219

PDB id:

5n2e

Name:

Transferase

Title:

Structure of the e9 DNA polymerase from vaccinia virus

Structure:

DNA polymerase. Chain: a. Engineered: yes

Source:

Vaccinia virus (strain copenhagen). Vacv. Organism_taxid: 10249. Strain: copenhagen. Gene: pol, e9l. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five.

Resolution:

2.74Å R-factor: 0.188 R-free: 0.236

Authors:

N.Tarbouriech,W.P.Burmeister,F.Iseni

Key ref:

N.Tarbouriech et al. (2017). The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Nat Commun, 8, 1455. PubMed id: 29129932

Date:

07-Feb-17 Release date: 29-Nov-17

Protein chain

P20509  (DPOL_VACCC) -  DNA polymerase from Vaccinia virus (strain Copenhagen)

Seq: 1006 a.a.

Struc: 999 a.a.*

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

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.1.11.- - ?????

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

Added reference

Nat Commun 8:1455 (2017)

PubMed id: 29129932

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.

N.Tarbouriech, C.Ducournau, S.Hutin, P.J.Mas, P.Man, E.Forest, D.J.Hart, C.N.Peyrefitte, W.P.Burmeister, F.Iseni.

ABSTRACT

Vaccinia virus (VACV), the prototype member of the Poxviridae, replicates in the cytoplasm of an infected cell. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Here we present the crystal structure of full-length E9 at 2.7 Å resolution that permits identification of important poxvirus-specific structural insertions. One insertion in the palm domain interacts with C-terminal residues of A20 and thus serves as the processivity factor-binding site. This is in strong contrast to all other family B polymerases that bind their co-factors at the C terminus of the thumb domain. The VACV E9 structure also permits rationalization of polymerase inhibitor resistance mutations when compared with the closely related eukaryotic polymerase delta-DNA complex.