3ZD8

Potassium bound structure of E. coli ExoIX in P1

Summary for 3ZD8

• Entry DOI: 10.2210/pdb3zd8/pdb
• Related: 3ZD9 3ZDA 3ZDB 3ZDC 3ZDD 3ZDE
• Descriptor: PROTEIN XNI, POTASSIUM ION (3 entities in total)
• Functional Keywords: hydrolase, flap endonuclease, dna binding
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 2
• Total formula weight: 56484.51

Authors

Anstey-Gilbert, C.S.,Hemsworth, G.R.,Flemming, C.S.,Hodskinson, M.R.G.,Zhang, J.,Sedelnikova, S.E.,Stillman, T.J.,Sayers, J.R.,Artymiuk, P.J. (deposition date: 2012-11-26, release date: 2013-07-10, Last modification date: 2024-05-08)

Primary citation

Anstey-Gilbert, C.S.,Hemsworth, G.R.,Flemming, C.S.,Hodskinson, M.R.G.,Zhang, J.,Sedelnikova, S.E.,Stillman, T.J.,Sayers, J.R.,Artymiuk, P.J.
The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases
Nucleic Acids Res., 41:8357-, 2013

PubMed Abstract: Escherichia coli Exonuclease IX (ExoIX), encoded by the xni gene, was the first identified member of a novel subfamily of ubiquitous flap endonucleases (FENs), which possess only one of the two catalytic metal-binding sites characteristic of other FENs. We have solved the first structure of one of these enzymes, that of ExoIX itself, at high resolution in DNA-bound and DNA-free forms. In the enzyme-DNA cocrystal, the single catalytic site binds two magnesium ions. The structures also reveal a binding site in the C-terminal domain where a potassium ion is directly coordinated by five main chain carbonyl groups, and we show this site is essential for DNA binding. This site resembles structurally and functionally the potassium sites in the human FEN1 and exonuclease 1 enzymes. Fluorescence anisotropy measurements and the crystal structures of the ExoIX:DNA complexes show that this potassium ion interacts directly with a phosphate diester in the substrate DNA.

PubMed: 23821668
DOI: 10.1093/NAR/GKT591

Experimental method

X-RAY DIFFRACTION (2 Å)