PDBsum entry 3ism

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protein ligands metals Protein-protein interface(s) links
Hydrolase inhibitor/hydrolase PDB id
Protein chains
245 a.a. *
286 a.a. *
_MG ×2
Waters ×328
* Residue conservation analysis
PDB id:
Name: Hydrolase inhibitor/hydrolase
Title: Crystal structure of the endog/endogi complex: mechanism of inhibition
Structure: Cg8862. Chain: a, b. Fragment: unp residues 56-310. Synonym: endonuclease g, endog, ld35517p. Engineered: yes. Cg4930. Chain: c. Synonym: endogi, sd16985p. Engineered: yes.
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: cg8862, dmel_cg8862, endog. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: endogi, bg:ds07473.2, cg4930, dmel_cg4930.
2.20Å     R-factor:   0.186     R-free:   0.223
Authors: B.Loll,M.Gebhardt,E.Wahle,A.Meinhart
Key ref: B.Loll et al. (2009). Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition. Nucleic Acids Res, 37, 7312-7320. PubMed id: 19783821
26-Aug-09     Release date:   08-Sep-09    
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Protein chains
Pfam   ArchSchema ?
Q7JXB9  (Q7JXB9_DROME) -  Endonuclease G
310 a.a.
245 a.a.
Protein chain
Pfam   ArchSchema ?
Q9V3V9  (Q9V3V9_DROME) -  Endonuclease G inhibitor, isoform A
359 a.a.
286 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   2 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   7 terms 
  Biochemical function     nucleic acid binding     9 terms  


Nucleic Acids Res 37:7312-7320 (2009)
PubMed id: 19783821  
Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition.
B.Loll, M.Gebhardt, E.Wahle, A.Meinhart.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21113026 A.F.Moon, M.Midon, G.Meiss, A.Pingoud, R.E.London, and L.C.Pedersen (2011).
Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae.
  Nucleic Acids Res, 39, 2943-2953.
PDB code: 3owv
20846957 M.Midon, P.Schäfer, A.Pingoud, M.Ghosh, A.F.Moon, M.J.Cuneo, R.E.London, and G.Meiss (2011).
Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae.
  Nucleic Acids Res, 39, 623-634.  
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