3G0R

Complex of Mth0212 and an 8bp dsDNA with distorted ends

Summary for 3G0R

• Entry DOI: 10.2210/pdb3g0r/pdb
• Related: 3FZI 3G00 3G0A 3G1K 3G2C 3G2D 3G38 3G3C 3G3Y 3G4T 3G8V 3G91 3GA6
• Descriptor: Exodeoxyribonuclease, 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*CP*G)-3', 5'-D(*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3', ... (7 entities in total)
• Functional Keywords: protein-dna complex, double-strand specific 3'-5' exonuclease, ap endonuclease, 2'-deoxyuridine endonuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Methanothermobacter thermautotrophicus
• Total number of polymer chains: 4
• Total formula weight: 71922.86

Authors

Lakomek, K.,Dickmanns, A.,Ficner, R. (deposition date: 2009-01-28, release date: 2010-03-09, Last modification date: 2023-11-01)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.4 Å)