PDBsum entry 6fbh

DNA binding protein

PDB id: 6fbh

Contents

Protein chain

539 a.a.

DNA/RNA

Ligands

EDO

XG4

Metals

_MN ×2

Waters ×264

PDB id:

6fbh

Name:

DNA binding protein

Title:

Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth primer nucleotide.

Structure:

DNA polymerase i, thermostable. Chain: a. Synonym: taq polymerase 1. Engineered: yes. DNA (5'-d( Gp Ap Cp Cp Cp Ap (Oh3)p Cp Gp Gp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Ap Ap Ap Cp Gp Tp Cp Cp Gp Gp Tp Gp Gp Gp Tp C)- 3').

Source:

Thermus aquaticus. Organism_taxid: 271. Gene: pola, pol1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

1.80Å R-factor: 0.198 R-free: 0.223

Authors:

H.M.Kropp,K.Diederichs,A.Marx

Key ref:

H.M.Kropp et al. (2018). Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc Natl Acad Sci U S A, 115, 9992-9997. PubMed id: 30224478 DOI: 10.1073/pnas.1811518115

Date:

19-Dec-17 Release date: 26-Sep-18

Protein chain

P19821  (DPO1_THEAQ) -  DNA polymerase I, thermostable from Thermus aquaticus

Seq: 832 a.a.

Struc: 539 a.a.

DNA/RNA chains

G-A-C-C-C-A-D4B-C-G-G-A-C 12 bases

A-A-A-C-G-T-C-C-G-G-T-G-G-G-T-C 16 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

DOI no: 10.1073/pnas.1811518115

Proc Natl Acad Sci U S A 115:9992-9997 (2018)

PubMed id: 30224478

Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.

H.M.Kropp, S.L.Dürr, C.Peter, K.Diederichs, A.Marx.

ABSTRACT

DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification "moves" from the 3'-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme's activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.