PDBsum entry 6h1v

DNA binding protein

PDB id: 6h1v

Contents

Protein chain

1114 a.a.

DNA/RNA

Ligands

SF4

DTP

Metals

_MG

Waters ×6

PDB id:

6h1v

Name:

DNA binding protein

Title:

The crystal structure of pol2core in complex with DNA and an incoming nucleotide, carrying an fe-s cluster

Structure:

DNA polymerase epsilon catalytic subunit a. Chain: a. Synonym: DNA polymerase ii subunit a. Engineered: yes. Mutation: yes. DNA (5'-d(p Tp Ap Ap Cp Cp Gp Cp Gp Tp Tp (Doc))-3'). Chain: p. Engineered: yes. Mutation: yes.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Gene: pol2, dun2, ynl262w, n0825. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Synthetic: yes. Synthetic construct.

Resolution:

2.70Å R-factor: 0.240 R-free: 0.266

Authors:

V.Parkash,E.Johansson

Key ref:

J.Ter Beek et al. (2019). Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ϵ. Nucleic Acids Res, 47, 5712-5722. PubMed id: 30968138 DOI: 10.1093/nar/gkz248

Date:

12-Jul-18 Release date: 24-Apr-19

Protein chain

P21951  (DPOE_YEAST) -  DNA polymerase epsilon catalytic subunit A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2222 a.a.

Struc: 1114 a.a.*

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

DNA/RNA chains

T-A-A-C-C-G-C-G-T-T-DOC 11 bases

T-C-T-T-G-A-A-C-G-C-G-G-T-T-A 15 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: 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

DOI no: 10.1093/nar/gkz248

Nucleic Acids Res 47:5712-5722 (2019)

PubMed id: 30968138

Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ϵ.

J.Ter Beek, V.Parkash, G.O.Bylund, P.Osterman, A.E.Sauer-Eriksson, E.Johansson.

ABSTRACT

DNA polymerase ϵ (Pol ϵ), the major leading-strand DNA polymerase in eukaryotes, has a catalytic subunit (Pol2) and three non-catalytic subunits. The N-terminal half of Pol2 (Pol2CORE) exhibits both polymerase and exonuclease activity. It has been suggested that both the non-catalytic C-terminal domain of Pol2 (with the two cysteine motifs CysA and CysB) and Pol2CORE (with the CysX cysteine motif) are likely to coordinate an Fe-S cluster. Here, we present two new crystal structures of Pol2CORE with an Fe-S cluster bound to the CysX motif, supported by an anomalous signal at that position. Furthermore we show that purified four-subunit Pol ϵ, Pol ϵ CysAMUT (C2111S/C2133S), and Pol ϵ CysBMUT (C2167S/C2181S) all have an Fe-S cluster that is not present in Pol ϵ CysXMUT (C665S/C668S). Pol ϵ CysAMUT and Pol ϵ CysBMUT behave similarly to wild-type Pol ϵ in in vitro assays, but Pol ϵ CysXMUT has severely compromised DNA polymerase activity that is not the result of an excessive exonuclease activity. Tetrad analyses show that haploid yeast strains carrying CysXMUT are inviable. In conclusion, Pol ϵ has a single Fe-S cluster bound at the base of the P-domain, and this Fe-S cluster is essential for cell viability and polymerase activity.