A Zinc Site in the C-Terminal Domain of RAG1 Is Essential for DNA Cleavage Activity

• Published in: Journal of molecular biology Vol. 390; no. 5; pp. 863 - 878
• Main Authors: Gwyn, Lori M., Peak, Mandy M., De, Pallabi, Rahman, Negar S., Rodgers, Karla K.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 31.07.2009
• Subjects: atomic absorption spectroscopy; Binding Sites; Biocatalysis; Chromatography, Gel; Conserved Sequence; Cysteine - metabolism; DNA Cleavage; DNA double-strand breaks; Histidine - metabolism; Homeodomain Proteins - chemistry; Homeodomain Proteins - metabolism; inductively coupled plasma mass spectrometry; Ions; Ligands; Mutagenesis; Mutation - genetics; Protein Binding; Protein Folding; Protein Structure, Tertiary; Recombination, Genetic - genetics; site-specific recombination; Zinc - metabolism; zinc-binding motif; CD; DTPA; GST; inductively coupled plasma mass spectrometry; EDTA; DNA double-strand breaks; FAAS; ds; SEC; atomic absorption spectroscopy; DSB; CTD; RSS; MHMN; site-specific recombination; zinc-binding motif; mbp; ICP-MS; WT
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2009.05.076

The recombination-activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn2+ ions in its catalytically required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well resolved. To address this issue, we determined the stoichiometry of Zn2+ ions bound to the catalytically active core region of RAG1 under various conditions. Using metal quantitation methods, we determined that core RAG1 can bind up to four Zn2+ ions. Stripping the full complement of bound Zn2+ ions to produce apoprotein abrogated DNA cleavage activity. Moreover, even partial removal of zinc-binding equivalents resulted in a significant diminishment of DNA cleavage activity, as compared to holo-Zn2+ core RAG1. Mutants of the intact core RAG1 and the isolated core RAG1 domains were studied to identify the location of zinc-binding sites. Significantly, the C-terminal domain in core RAG1 binds at least two Zn2+ ions, with one zinc-binding site containing C902 and C907 as ligands (termed the CC zinc site) and H937 and H942 coordinating a Zn2+ ion in a separate site (HH zinc site). The latter zinc-binding site is essential for DNA cleavage activity, given that the H937A and H942A mutants were defective in both in vitro DNA cleavage assays and cellular recombination assays. Furthermore, as mutation of the active-site residue E962 reduces Zn2+ coordination, we propose that the HH zinc site is located in close proximity to the DDE active site. Overall, these results demonstrate that Zn2+ serves an important auxiliary role for RAG1 DNA cleavage activity. Furthermore, we propose that one of the zinc-binding sites is linked to the active site of core RAG1 directly or indirectly by E962.