3LWM

Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP

Summary for 3LWM

• Entry DOI: 10.2210/pdb3lwm/pdb
• Related: 3KTQ 3LWL
• Descriptor: DNA polymerase I, thermostable, DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3'), DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... (9 entities in total)
• Functional Keywords: dna replication, dna polymerases, dna-binding, dna-directed dna polymerase, amino acid-templating mechanism, nucleotidyltransferase, transferase, transferase-dna complex, blunt-ended dna, template-independent dna synthesis, terminal deoxynucleotidyl transferase, template-independent nucleotide addition, transferase/dna
• Biological source: Thermus aquaticus; More
• Total number of polymer chains: 3
• Total formula weight: 69536.83

Authors

Marx, A.,Diederichs, K.,Obeid, S. (deposition date: 2010-02-24, release date: 2010-05-05, Last modification date: 2023-11-01)

Primary citation

Obeid, S.,Blatter, N.,Kranaster, R.,Schnur, A.,Diederichs, K.,Welte, W.,Marx, A.
Replication through an abasic DNA lesion: structural basis for adenine selectivity
Embo J., 29:1738-1747, 2010

PubMed 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.

PubMed: 20400942
DOI: 10.1038/emboj.2010.64

Experimental method

X-RAY DIFFRACTION (2.186 Å)