PDBsum entry 1q39

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Hydrolase PDB id
Protein chain
257 a.a. *
_CA ×3
Waters ×14
* Residue conservation analysis

References listed in PDB file
Key reference
Title Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility.
Authors G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, G.Shoham.
Ref. Nucleic Acids Res, 2005, 33, 5006-5016.
PubMed id 16145054
Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme.
Figure 2.
Solvent-accessible surface of free Nei, colored according to electrostatic potential (positive in blue, negative in red and neutral in gray), demonstrating the highly positive DNA-binding cleft of the enzyme (left center). Locations of three important residues involved in DNA binding are indicated by arrows.
Figure 5.
The zinc finger motif of Nei. An electron density map is shown around the bound zinc atom [`omit' map at contour levels of 5 [220]{sigma} (blue), and 17 {sigma} (green)]. The four Cys residues (with typical Zn-S bond lengths of 2.28-2.38 ) are shown in a ball-and-stick representation and the two anti-parallel -strands are shown in a ribbon diagram (beige). Superimposed on this region is the corresponding region of the Nei-DNA complex (red), demonstrating a movement of the tip of the zinc finger between the free and the DNA-bound forms of the enzyme.
The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 5006-5016) copyright 2005.
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