PDBsum entry 3lwl

Transferase/DNA

PDB id: 3lwl

Contents

Protein chain

534 a.a. *

DNA/RNA

Ligands

DDS

ACT ×5

GOL ×7

Metals

_NA ×4

_MG

Waters ×161

* Residue conservation analysis

PDB id:

3lwl

Name:

Transferase/DNA

Title:

Structure of klenow fragment of taq polymerase in complex with an abasic site

Structure:

DNA polymerase i, thermostable. Chain: a. Fragment: klenow fragment, unp residues 293-832. Synonym: taq polymerase 1. Engineered: yes. DNA (5'-d( Gp Ap Cp Cp Ap Cp Gp Gp Cp Gp Cp (2Da))-3'). Chain: b. Engineered: yes. Other_details: DNA primer.

Source:

Thermus aquaticus. Organism_taxid: 271. Gene: pol1, pola. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA

Resolution:

2.25Å R-factor: 0.191 R-free: 0.234

Authors:

A.Marx,K.Diederichs,S.Obeid

Key ref:

S.Obeid et al. (2010). Replication through an abasic DNA lesion: structural basis for adenine selectivity. Embo J, 29, 1738-1747. PubMed id: 20400942

Date:

24-Feb-10 Release date: 05-May-10

Protein chain

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

Seq: 832 a.a.

Struc: 534 a.a.

DNA/RNA chains

G-A-C-C-A-C-G-G-C-G-C-2DA 12 bases

A-3DR-T-G-C-G-C-C-G-T-G-G-T-C 14 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

Embo J 29:1738-1747 (2010)

PubMed id: 20400942

Replication through an abasic DNA lesion: structural basis for adenine selectivity.

S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, A.Marx.

ABSTRACT

Abasic sites represent the most frequent DNA lesions in the genome that have high mutagenic potential and lead to mutations commonly found in human cancers. Although these lesions are devoid of the genetic information, adenine is most efficiently inserted when abasic sites are bypassed by DNA polymerases, a phenomenon termed A-rule. In this study, we present X-ray structures of a DNA polymerase caught while incorporating a nucleotide opposite an abasic site. We found that a functionally important tyrosine side chain directs for nucleotide incorporation rather than DNA. It fills the vacant space of the absent template nucleobase and thereby mimics a pyrimidine nucleobase directing for preferential purine incorporation opposite abasic residues because of enhanced geometric fit to the active site. This amino acid templating mechanism was corroborated by switching to pyrimidine specificity because of mutation of the templating tyrosine into tryptophan. The tyrosine is located in motif B and highly conserved throughout evolution from bacteria to humans indicating a general amino acid templating mechanism for bypass of non-instructive lesions by DNA polymerases at least from this sequence family.