3G2C

Mth0212 in complex with a short ssDNA (CGTA)

3G2C の概要

• エントリーDOI: 10.2210/pdb3g2c/pdb
• 関連するPDBエントリー: 3FZI 3G00 3G0A 3G0R 3G1K 3G2D 3G38 3G3C 3G3Y 3G4T 3G8V 3G91 3GA6
• 分子名称: Exodeoxyribonuclease, 5'-D(P*CP*GP*TP*A)-3', GLYCEROL, ... (6 entities in total)
• 機能のキーワード: protein-dna complex, single-stranded dna, flipped nucleotide, po4, mg2+, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Methanothermobacter thermautotrophicus
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 65030.31

構造登録者

Lakomek, K.,Dickmanns, A.,Ficner, R. (登録日: 2009-01-31, 公開日: 2010-03-09, 最終更新日: 2023-11-01)

主引用文献

Lakomek, K.,Dickmanns, A.,Ciirdaeva, E.,Schomacher, L.,Ficner, R.
Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
J.Mol.Biol., 399:604-617, 2010

PubMed Abstract: The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.

PubMed: 20434457
DOI: 10.1016/j.jmb.2010.04.044

実験手法

X-RAY DIFFRACTION (2.3 Å)