The bacterial RecA protein participates in a remarkably diverse set of functions, all of which are involved in the maintenance of genomic integrity. RecA is a central component in both the catalysis of recombinational DNA repair and the regulation of the cellular SOS response. Despite the mechanistic differences of its functions, all require formation of an active RecA/ATP/DNA complex. RecA is a classic allosterically regulated enzyme, and ATP binding results in a dramatic increase in DNA binding affinity and a cooperative assembly of RecA subunits to form an ordered, helical nucleoprotein filament. The molecular events that underlie this ATP-induced structural transition are becoming increasingly clear. This review focuses on descriptions of our current understanding of the molecular design and allosteric regulation of RecA. We present a comprehensive list of all published recA mutants and use the results of various genetic and biochemical studies, together with available structural information, to develop ideas regarding the design of RecA functional domains and their catalytic organization.

No abstract

IMP dehydrogenase (IMPDH) catalyzes the pivotal step in guanine nucleotide biosynthesis. Here we show that both IMPDH type 1 (IMPDH1) and IMPDH type 2 are associated with polyribosomes, suggesting that these housekeeping proteins have an unanticipated role in translation regulation. This interaction is mediated by the subdomain, a region of disputed function that is the site of mutations that cause retinal degeneration. The retinal isoforms of IMPDH1 also associate with polyribosomes. The most common disease-causing mutation, D226N, disrupts the polyribosome association of at least one retinal IMPDH1 isoform. Finally, we find that IMPDH1 is associated with polyribosomes containing rhodopsin mRNA. Because any perturbation of rhodopsin expression can trigger apoptosis in photoreceptor cells, these observations suggest a likely pathological mechanism for IMPDH1-mediated hereditary blindness. We propose that IMPDH coordinates the translation of a set of mRNAs, perhaps by modulating localization or degradation. IMP dehydrogenase (IMPDH)2 catalyzes the reaction that controls the entry of purines into the guanine nucleotide pool, and thus controls proliferation (1). The enzyme is a homotetramer; each monomer is composed of a catalytic (␤/␣) 8 barrel and a subdomain containing two CBS domains (named for the related domain in cystathionine ␤-synthase) (Fig. 1). Deletion of the subdomain has no effect on enzymatic activity (2, 3), and the function of the subdomain in IMPDH is currently under debate. CBS domains act as adenosine nucleotide-binding modules in several proteins (4 -9), and a similar role has been proposed for the CBS domains of IMPDH (5), but we and others have been unable to confirm this function in IMPDH (10 -13). Notably, the CBS domains of IMPDH share little sequence identity with the other proteins, so it would not be surprising if their function has diverged. The subdomain does appear to coordinately regulate the adenine and guanine nucleotide pool in Escherichia coli, although the molecular mechanism of this process has not yet been elucidated (11). We have discovered that IMPDH binds single-stranded nucleic acids and that the subdomain mediates this interaction (10, 15). IMPDH associates with RNA in tissue culture cells, which suggests that this housekeeping enzyme is involved in translation, splicing, or some other feature of RNA metabolism (10, 15). Others report that IMPDH binds DNA and may be involved in gene expression (16, 17). These observations suggest that IMPDH has a "moonlighting" function involving nucleic acid that is mediated by the subdomain.Mammals have two IMPDH genes, encoding IMPDH1 and IMPDH2, and most tissues express both isozymes (18,19). In contrast, only IMPDH1 appears to be expressed in the retina; in addition, retina contains distinct IMPDH1 isoforms generated by alternative mRNA splicing as follows: IMPDH1(546) (major) and IMPDH1(595) (minor) ( Fig. 1; these proteins are also known as IMPDH1␣/IMPDH1(13b) and IMPDH␥/IMPDH1(Aϩ13b), respectively; the canonical enzyme is hereaft...

The human Rad51 protein requires ATP for the catalysis of DNA strand exchange, as do all Rad51 and RecA-like recombinases. However, understanding the specific mechanistic requirements for ATP binding and hydrolysis has been complicated by the fact that ATP appears to have distinctly different effects on the functional properties of human Rad51 versus yeast Rad51 and bacterial RecA. Here we use RNAi methods to test the function of two ATP binding site mutants, K133R and K133A, in human cells. Unexpectedly, we find that the K133A mutant is functional for repair of DNA double-strand breaks when endogenous Rad51 is depleted. We also find that the K133A protein maintains wild-type-like DNA binding activity and interactions with Brca2 and Xrcc3, properties that undoubtedly promote its DNA repair capability in the cell-based assay used here. Although a Lys to Ala substitution in the Walker A motif is commonly assumed to prevent ATP binding, we show that the K133A protein binds ATP, but with an affinity approximately 100-fold lower than that of wild-type Rad51. Our data suggest that ATP binding and release without hydrolysis by the K133A protein act as a mechanistic surrogate in a catalytic process that applies to all RecA-like recombinases. ATP binding promotes assembly and stabilization of a catalytically active nucleoprotein filament, while ATP hydrolysis promotes filament disassembly and release from DNA.

IMPDH has a function in the retina, apparently independent of its enzymatic activity, mediated by retina-specific variants. This moonlighting activity may involve the posttranscriptional regulation of rhodopsin mRNA. The adRP mutation D226N has reduced binding to nucleic acids and reduced association with polyribosomes. If this mutation perturbs the biosynthesis of rhodopsin in some way, this would explain a link between IMPDH and the mechanism of retinal degeneration.