8axy

Staphylococcus aureus endonuclease IV orthorhombic crystal formStaphylococcus aureus endonuclease IV orthorhombic crystal form

Structural highlights 8axy is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.05Å Ligands: , , Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function END4_STAAR Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Publication Abstract from PubMed During Staphylococcus aureus 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 Escherichia coli, contains a catalytic site with three metal ions, previously reported to be all Zn(2+). The 1.05 A structure of Nfo from the Gram-positive organism S. aureus (SaNfo) revealed two inner Fe(2+) ions and one Zn(2+) as confirmed by dispersive anomalous difference maps. SaNfo has a previously undescribed water molecule liganded to Fe(1) 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(2+) at the corresponding site. The 1.9 A structure of E. coli Nfo (EcNfo), purified without added metals, revealed that metal 2 is Fe(2+) and not Zn(2+). Octahedral coordination for the sites occupied by Fe(2+) suggests a stereoselective mechanism for differentiating between Fe(2+) and Zn(2+) in this enzyme class. Kinetics and an inhibitor competition assay of SaNfo reveal product inhibition (or slow product release), especially at low ionic strength, caused in part by a Lys-rich DNA binding loop present in SaNfo and Gram-positive species but not in EcNfo. 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 S. aureus. Octahedral Iron in Catalytic Sites of Endonuclease IV from Staphylococcus aureus and Escherichia coli.,Kirillov S, Isupov M, Paterson NG, Wiener R, Abeldenov S, Saper MA, Rouvinski A Biochemistry. 2024 Dec 10. doi: 10.1021/acs.biochem.4c00447. PMID:39655415 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

spinqualitylabelsall models 8axy, resolution 1.05Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image