8RLY

E. coli endonuclease IV complexed with sulfate, catalytic Fe2+

Summary for 8RLY

• Entry DOI: 10.2210/pdb8rly/pdb
• Related: 8AXY 8EDD 8PKB
• Descriptor: Endonuclease 4, ZINC ION, FE (II) ION, ... (8 entities in total)
• Functional Keywords: bacterial endonuclease iv, catalytic iron, dna binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 5
• Total formula weight: 159832.53

Authors

Saper, M.A.,Paterson, N.G.,Kirillov, S.,Rouvinski, A. (deposition date: 2024-01-04, release date: 2024-12-11, Last modification date: 2025-01-15)

Primary citation

Kirillov, S.,Isupov, M.,Paterson, N.G.,Wiener, R.,Abeldenov, S.,Saper, M.A.,Rouvinski, A.
Octahedral Iron in Catalytic Sites of Endonuclease IV from Staphylococcus aureus and Escherichia coli .
Biochemistry, 64:67-82, 2025

PubMed Abstract: During infections, reactive oxygen species cause DNA damage, including nucleotide base modification. After removal of the defective base, excision repair requires an endonuclease IV (Nfo), which hydrolyzes the phosphodiester bond 5' to the abasic nucleotide. This class of enzymes, typified by the enzyme from , contains a catalytic site with three metal ions, previously reported to be all Zn. The 1.05 Å structure of Nfo from the Gram-positive organism (Nfo) revealed two inner Fe ions and one Zn as confirmed by dispersive anomalous difference maps. Nfo has a previously undescribed water molecule liganded to Fe forming an octahedral coordination geometry and hydrogen bonded to Tyr33, an active site residue conserved in many Gram-positive bacteria, but which is Phe in Gram-negative species that coordinate Zn at the corresponding site. The 1.9 Å structure of Nfo (Nfo), purified without added metals, revealed that metal 2 is Fe and not Zn. Octahedral coordination for the sites occupied by Fe suggests a stereoselective mechanism for differentiating between Fe and Zn in this enzyme class. Kinetics and an inhibitor competition assay of Nfo reveal product inhibition (or slow product release), especially at low ionic strength, caused in part by a Lys-rich DNA binding loop present in Nfo and Gram-positive species but not in Nfo. Biological significance of the slow product release is discussed. Catalytic activity in vitro is optimal at 300 mM NaCl, which is consistent with the halotolerant phenotype of .

PubMed: 39655415
DOI: 10.1021/acs.biochem.4c00447

Experimental method

X-RAY DIFFRACTION (1.9 Å)