PMID:18981218

Citation	Hsiao, YY, Nakagawa, A, Shi, Z, Mitani, S, Xue, D and Yuan, HS (2009) Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation. Mol. Cell. Biol. 29:448-57
Abstract	Cell death related nuclease 4 (CRN-4) is one of the apoptotic nucleases involved in DNA degradation in Caenorhabditis elegans. To understand how CRN-4 is involved in apoptotic DNA fragmentation, we analyzed CRN-4's biochemical properties, in vivo cell functions, and the crystal structures of CRN-4 in apo-form, Mn(2+)-bound active form, and Er(3+)-bound inactive form. CRN-4 is a dimeric nuclease with the optimal enzyme activity in cleaving double-stranded DNA in apoptotic salt conditions. Both mutational studies and the structures of the Mn(2+)-bound CRN-4 revealed the geometry of the functional nuclease active site in the N-terminal DEDDh domain. The C-terminal domain, termed the Zn-domain, contains basic surface residues ideal for nucleic acid recognition and is involved in DNA binding, as confirmed by deletion assays. Cell death analysis in C. elegans further demonstrated that both the nuclease active site and the Zn-domain are required for crn-4's function in apoptosis. Combining all of the data, we suggest a structural model where chromosomal DNA is bound at the Zn-domain and cleaved at the DEDDh nuclease domain in CRN-4 when the cell is undergoing apoptosis.
Links	PubMed PMC2612515 Online version:10.1128/MCB.01006-08
Keywords	Amino Acid Motifs; Animals; Apoptosis/physiology; Caenorhabditis elegans/metabolism; Caenorhabditis elegans Proteins/chemistry; Caenorhabditis elegans Proteins/metabolism; Calcium/metabolism; Catalytic Domain; Crystallography, X-Ray; DNA Fragmentation; DNA, Helminth/metabolism; Dimerization; Endodeoxyribonucleases/chemistry; Endodeoxyribonucleases/metabolism; Endonucleases/chemistry; Endonucleases/metabolism; Hydrogen-Ion Concentration; Magnesium/metabolism; Models, Molecular; Protein Conformation; Protein Structure, Tertiary; Zinc/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
CAEEL:CRN4	enables	GO:0003697: single-stranded DNA binding	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
CAEEL:CRN4	enables	GO:0008408: 3'-5' exonuclease activity	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
CAEEL:CRN4	enables	GO:0004520: endodeoxyribonuclease activity	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
CAEEL:CRN4	enables	GO:0004540: ribonuclease activity	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
CAEEL:CRN4	involved_in	GO:0006401: RNA catabolic process	ECO:0000314: direct assay evidence used in manual assertion		P		Seeded From UniProt	complete
CAEEL:CRN4	involved_in	GO:0000737: DNA catabolic process, endonucleolytic	ECO:0000314: direct assay evidence used in manual assertion		P		Seeded From UniProt	complete
CAEEL:CRN4	involved_in	GO:0000738: DNA catabolic process, exonucleolytic	ECO:0000314: direct assay evidence used in manual assertion		P		Seeded From UniProt	complete

References

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