Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition

Abstract

EndoG is a ubiquitous nuclease that is translocated into the nucleus during apoptosis to participate in DNA degradation. The enzyme cleaves double- and single-stranded DNA and RNA. Related nucleases are found in eukaryotes and prokaryotes, which have evolved sophisticated mechanisms for genome protection against self-antagonizing nuclease activity. Common mechanisms of inhibition are secretion, sequestration into a separate cellular compartment or by binding to protein inhibitors. Although EndoG is silenced by compartmentalization into the mitochondrial intermembrane space, a nucleus-localized protein inhibitor protects cellular polynucleotides from degradation by stray EndoG under non-apoptotic conditions in Drosophila. Here, we report the first three-dimensional structure of EndoG in complex with its inhibitor EndoGI. Although the mechanism of inhibition is reminiscent of bacterial protein inhibitors, EndoGI has evolved independently from a generic protein-protein interaction module. EndoGI is a two-domain protein that binds the active sites of two monomers of EndoG, with EndoG being sandwiched between EndoGI. Since the amino acid sequences of eukaryotic EndoG homologues are highly conserved, this model is valid for eukaryotic dimeric EndoG in general. The structure indicates that the two active sites of EndoG occupy the most remote spatial position possible at the molecular surface and a concerted substrate processing is unlikely.

Mechanistic Insight into the Catalytic Activity of ββα‐Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case

“…The active site of Smn, NucA and Vvn is also very similar to those of apoptotic endonuclease G from Drosophila melanogaster (Dm-endoG), [16] the His-Cys box homing endonuclease, I-PpoI, from the slime mould Physarum polycephalum, [17][18][19] the DNA-entry nuclease EndA from Streptococcus pneumoniae, [20] and a recently identified endonuclease from the protozoan parasite Leishmania infantum (Li-endoG) [21] (Figure S1 in the Supporting Information). Moreover, cleavage experiments with deoxythymidine 3',5'-bis-(p-nitrophenylphosphate) as an artificial minimal substrate have indeed shown that Smn, NucA and I-PpoI follow the same mechanism of phosphodiester bond hydrolysis.…”

Role of endonuclease G in senescence-associated cell death of human endothelial cells

“…Recently, an inhibitor of EndoG (EndoGI) was found in the D. melanogaster gene cg4930 which consists of 2 homologous domains, each of them able to bind one EndoG nuclease (Temme et al, 2009). The crystal structure of the complex was resolved which supported the 2:1 stoichiometry (Loll et al, 2009). The group proposed a life insurance function for EndoGI for leakage of mitochondria by release of EndoGI from the nucleus and binding EndoG in the cytosol.…”

Structural and evolutionary versatility in protein complexes with uneven stoichiometry

“…4a shows two molecules of the Drosophila nuclease EndoG in complex with the inhibitor EndoGI 41 . EndoGI consists of repeated domains separated by a disordered linker that allows them to wrap around both sides of the EndoG homodimer, binding each EndoG subunit in a very similar manner.…”