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ClpX (423 amino acids), a member of the Clp/Hsp100 family of molecular chaperones and the protease, ClpP, comprise a multimeric complex supporting targeted protein degradation in Escherichia coli. The ClpX sequence consists of an NH 2 -terminal zinc binding domain (ZBD) and a COOH-terminal ATPase domain. Earlier, we have demonstrated that the zinc binding domain forms a constitutive dimer that is essential for the degradation of some ClpX substrates such as O and MuA but is not required for the degradation of other substrates such as green fluorescent protein-SsrA. In this report, we present the NMR solution structure of the zinc binding domain dimer. The monomer fold reveals that ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions. However, the dimeric ZBD structure is not related to any protein structure in the Protein Data Bank. A trimer-of-dimers model of ZBD is presented, which might reflect the closed state of the ClpX hexamer.Molecular chaperones and proteases are part of an essential quality control machinery in the cell, which ensures the conformational integrity of proteins under conditions of normal growth as well as under stress (1). In Escherichia coli, the chaperone ClpX, a member of the Hsp100 family (2-4), associates with the serine protease ClpP (5) to form a cylindrical structure that is similar to the 26 S proteasome (6, 7). Hexameric ClpX binds on one or both ends of tetradecameric ClpP (8). Specific biological processes mediated by ClpX include remodeling of bacteriophage MuA-DNA transposase complexes (9, 10), degradation of the O replication protein (11), degradation of the UmuDЈ subunit of error-prone DNA polymerase (12), and removal of LexA repressor protein fragments after RecA processing (13). Using an inactive ClpP mutant as a trap for native E. coli substrates, Flynn et al. (14) defined five classes of recognition sequences that are bound by ClpX. A more general class of substrates are directed to ClpXP via an SsrA tag (15-17), which is typically placed by a tmRNA at the COOH terminus of nascent chains stalled on the ribosomes. Additional specificity and regulation are provided by the accessory factors SspB (18,19) and RssB (20), which promote interactions between ClpX and specific substrates.ClpX sequence consists of an NH 2 -terminal zinc binding domain (ZBD) 1 followed by one AAA ATPase domain (21-23). AAA domains are characterized by specific sequence motifs such as the Walker A and Walker B motifs (21). ClpX binds and, subsequently, unfolds and translocates substrate proteins into the ClpP chamber in an ATP-dependent manner. Other Clp/Hsp100 chaperones in E. coli include ClpA and ClpB. Both ClpA and ClpB have an NH 2 -terminal domain followed by two AAA domains. ClpA also binds as a hexamer to ClpP oligomer, while ClpB does not seem to associate with any proteases. The N-domain of ClpA has been shown to be important for substrate binding (24) as well as for the binding of the cofactor Cl...

Defects in the nonhomologous end-joining (NHEJ) pathway of double-stranded DNA break repair severely impair V(D)J joining and selectively predispose mice to the development of lymphoid neoplasia. This connection was first noted in mice with the severe combined immune deficient (SCID) mutation in the DNA-dependent protein kinase (DNA-PK). SCID mice spontaneously develop thymic lymphoma with low incidence and long latency. However, we and others showed that low-dose irradiation of SCID mice dramatically increases the frequency and decreases the latency of thymic lymphomagenesis, but irradiation does not promote the development of other tumors. We have used this model to explore the mechanistic basis by which defects in NHEJ confer selective and profound susceptibility to lymphoid oncogenesis. Here, we show that radiation quantitatively and qualitatively improves V(D)J joining in SCID cells, in the absence of T-cell receptor-mediated cellular selection. Furthermore, we show that the lymphocyte-specific endonuclease encoded by the recombinaseactivating genes (RAG-1 and RAG-2) is required for radiation-induced thymic lymphomagenesis in SCID mice. Collectively, these data suggest that irradiation induces a DNA-PK-independent NHEJ pathway that facilitates V(D)J joining, but also promotes oncogenic misjoining of RAG-1/2-induced breaks in SCID T-cell precursors.Lymphocytes require the faithful execution of DNA repair processes to generate a highly diverse repertoire of antigen receptors. The variable region exon of each T-cell receptor (TCR) and B-cell antigen receptor (BCR) gene is assembled by site-specific cleavage and rejoining of variable (V), diversity (D), and joining (J) gene segments in developing T and B lymphocytes. Tandem genomic arrays of dozens to hundreds of V, D, or J gene segments allow combinatorial diversification of the available germline repertoire during lymphocyte development to create a large number of clonally distinct VDJ or VJ genes. In addition, terminal deoxynucleotidal transferase (TdT), a lymphocyte-specific polymerase, inserts non-germline-encoded nucleotides at V(D)J junctions, providing additional somatic diversification of the available germline repertoire (30,44,67). Thus, V(D)J recombination endows T and B lymphocytes with the capacity to specifically recognize and destroy an almost infinite array of pathogens. However, DNA breaks are highly recombinogenic and must be repaired efficiently to maintain genomic stability and minimize the risk of oncogenic transformation (31,33,43,49,90,104). A high frequency of lymphoid tumors have chromosomal translocations involving antigen receptor genes (reviewed in reference 101), raising the question as to whether the V(D)J recombination process threatens genomic stability in lymphoid lineages.The molecular mechanism of V(D)J cleavage has recently been elucidated by elegant biochemical studies (reviewed in references 93 and 106). This process is mediated by the lymphoid-specific RAG-1 and RAG-2 proteins, which bind recombination signal sequences fl...