PDBsum entry 3ez5

Transferase/DNA

PDB id: 3ez5

Contents

Protein chains

580 a.a. *

DNA/RNA

Ligands

GLC-FRU ×2

SO4 ×3

DAD ×2

Metals

_ZN ×5

Waters ×540

* Residue conservation analysis

PDB id:

3ez5

Name:

Transferase/DNA

Title:

Cocrystal structure of bacillus fragment DNA polymerase i with duplex DNA , dctp, and zinc (closed form).

Structure:

DNA polymerase i. Chain: a, d. Engineered: yes. Mutation: yes. 5'-d( Dcp Dcp Dtp Dgp Dap Dcp Dtp Dcp Dg)-3'. Chain: b, e. Engineered: yes. Other_details: DNA primer strand. 5'-d( Dap Dtp Dtp Dcp Dgp Dap Dgp Dtp Dcp Dap Dgp Dg)-3'.

Source:

Bacillus stearothermophilus. Gene: pola. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

1.90Å R-factor: 0.212 R-free: 0.244

Authors:

J.J.Warren,E.Y.Wu,A.A.Golosov,M.Karplus,L.S.Beese

Key ref:

A.A.Golosov et al. (2010). The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure, 18, 83-93. PubMed id: 20152155

Date:

22-Oct-08 Release date: 10-Nov-09

Protein chains

P52026  (DPO1_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 876 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 69 residue positions (black crosses)

DNA/RNA chains

C-C-T-G-A-C-T-C-G 9 bases

A-T-T-C-G-A-G-T-C-A-G-G 12 bases

C-C-T-G-A-C-T-C-G 9 bases

A-T-T-C-G-A-G-T-C-A-G-G 12 bases

Enzyme reactions

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

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

Added reference

Structure 18:83-93 (2010)

PubMed id: 20152155

The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.

A.A.Golosov, J.J.Warren, L.S.Beese, M.Karplus.

ABSTRACT

High-fidelity DNA polymerases copy DNA rapidly and accurately by adding correct deoxynucleotide triphosphates to a growing primer strand of DNA. Following nucleotide incorporation, a series of conformational changes translocate the DNA substrate by one base pair step, readying the polymerase for the next round of incorporation. Molecular dynamics simulations indicate that the translocation consists globally of a polymerase fingers-opening transition, followed by the DNA displacement and the insertion of the template base into the preinsertion site. They also show that the pyrophosphate release facilitates the opening transition and that the universally conserved Y714 plays a key role in coupling polymerase opening to DNA translocation. The transition involves several metastable intermediates in one of which the O helix is bent in the vicinity of G711. Completion of the translocation appears to require a gating motion of the O1 helix, perhaps facilitated by the presence of G715. These roles are consistent with the high level of conservation of Y714 and the two glycine residues at these positions. It is likely that a corresponding mechanism is applicable to other polymerases.