3CM6

Crystal structure of cell-death related nuclease 4 (CRN-4) bound with Er

Summary for 3CM6

• Entry DOI: 10.2210/pdb3cm6/pdb
• Related: 3CG7 3CM5
• Descriptor: Cell death-related nuclease 4, ZINC ION, ERBIUM (III) ION, ... (4 entities in total)
• Functional Keywords: hydrolase, apoptosis, apoptotic nuclease, 3'-5' exonuclease, dedd family
• Biological source: Caenorhabditis elegans
• Total number of polymer chains: 2
• Total formula weight: 71650.59

Authors

Hsiao, Y.-Y.,Yuan, H.S. (deposition date: 2008-03-21, release date: 2008-12-30, Last modification date: 2023-11-01)

Primary citation

Hsiao, Y.-Y.,Nakagawa, A.,Shi, Z.,Mitani, S.,Xue, D.,Yuan, H.S.
Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation
Mol.Cell.Biol., 29:448-457, 2009

PubMed 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.

PubMed: 18981218
DOI: 10.1128/MCB.01006-08

Experimental method

X-RAY DIFFRACTION (2.6 Å)