1KFV

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

Summary for 1KFV

• Entry DOI: 10.2210/pdb1kfv/pdb
• Related: 1EE8
• Descriptor: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3', 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3', Formamido-pyrimidine DNA glycosylase, ... (6 entities in total)
• Functional Keywords: dna repair enzyme, abasic site, dna, n-glycosylase, ap lyase, hydrolase-dna complex, hydrolase/dna
• Biological source: Lactococcus lactis
• Total number of polymer chains: 6
• Total formula weight: 78342.62

Authors

Serre, L.,Pereira de Jesus, K.,Boiteux, S.,Zelwer, C.,Castaing, B. (deposition date: 2001-11-23, release date: 2002-06-14, Last modification date: 2024-10-30)

Primary citation

Serre, L.,Pereira de Jesus, K.,Boiteux, S.,Zelwer, C.,Castaing, B.
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
EMBO J., 21:2854-2865, 2002

PubMed Abstract: The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged DNA. The structure of a non-covalent complex between the Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site analogue-containing DNA has been solved. Through an asymmetric interaction along the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg pushes out the Pr site from the DNA double helix, recognizing the cytosine opposite the lesion and inducing a 60 degrees bend of the DNA. The specific recognition of this cytosine provides some structural basis for understanding the divergence between Fpg and its structural homologue endo nuclease VIII towards their substrate specificities. In addition, the modelling of the 8-oxoguanine residue allows us to define an enzyme pocket that may accommodate the extrahelical oxidized base.

PubMed: 12065399
DOI: 10.1093/emboj/cdf304

Experimental method

X-RAY DIFFRACTION (2.55 Å)