The genomes of aerobic organisms suffer chronic oxidation of guanine to the genotoxic product 8-oxoguanine (oxoG). Replicative DNA polymerases misread oxoG residues and insert adenine instead of cytosine opposite the oxidized base. Both bases in the resulting A*oxoG mispair are mutagenic lesions, and both must undergo base-specific replacement to restore the original C*G pair. Doing so represents a formidable challenge to the DNA repair machinery, because adenine makes up roughly 25% of the bases in most genomes. The evolutionarily conserved enzyme adenine DNA glycosylase (called MutY in bacteria and hMYH in humans) initiates repair of A*oxoG to C*G by removing the inappropriately paired adenine base from the DNA backbone. A central issue concerning MutY function is the mechanism by which A*oxoG mispairs are targeted among the vast excess of A*T pairs. Here we report the use of disulphide crosslinking to obtain high-resolution crystal structures of MutY-DNA lesion-recognition complexes. These structures reveal the basis for recognizing both lesions in the A*oxoG pair and for catalysing removal of the adenine base.

Deep learning for protein interactions The use of deep learning has revolutionized the field of protein modeling. Humphreys et al . combined this approach with proteome-wide, coevolution-guided protein interaction identification to conduct a large-scale screen of protein-protein interactions in yeast (see the Perspective by Pereira and Schwede). The authors generated predicted interactions and accurate structures for complexes spanning key biological processes in Saccharomyces cerevisiae . The complexes include larger protein assemblies such as trimers, tetramers, and pentamers and provide insights into biological function. —VV

MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA. The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition. MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom. The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis. Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.The reactive byproducts of aerobic respiration oxidize DNA to generate a number of deleterious adducts, among which the most widely studied is 8-oxoguanine (oxoG). 1 Because oxoG mispairs with adenine during replication, this oxidative lesion is a source of G⅐C to T⅐A transversion mutations. Nearly all organisms possess enzymes that safeguard against the genotoxic effects of oxoG. The oxoG resistance pathway in bacteria, known as the "GO" system, comprises three components: MutT, MutY, and MutM (1-4). MutT hydrolyzes oxo-dGTP to oxodGMP and inorganic pyrophosphate so as to prevent de novo incorporation of oxoG into the genome during DNA replication. MutY initiates the repair of misreplicated oxoG⅐A pairs in DNA by catalyzing hydrolytic excision of the adenine base. MutM (also known as Fpg) is a bifunctional DNA glycosylase/lyase that catalyzes complete excision of oxoG lesion nucleosides when paired opposite C in DNA via a complex multistep reaction cascade. Most eukaryotes possess a GO system related to that in bacteria, with orthologous versions of MutT and MutY; however, in higher organisms, MutM is replaced by the functionally analogous but structurally unrelated enzyme Ogg1 (5, 6). Orthologs of MutM have been discovered in mammals, but these do not appear to be primarily involved in oxoG repair (7-10).Recent structural studies of MutM-DNA complexes have revealed the overall architecture of the protein-DNA complex. These structures have also provided insights into the general features of lesion presentation to the MutM active site, suggesting that the oxoG nucleoside is swiveled out of the DNA helix during repair, a theme common throughout the structural biology of base excision DNA repair. A segment of the protein near the active site is disordered in the DNA-bound MutM structures lacking an oxoG nucleobase, yet is ordered in the absence of DNA, thus leading to the tantalizing suggestion that induced fit might contribute to lesion base recognition. Understanding the structural determinants of lesion recognition by MutM has been hampered by the fact that none of the available high re...

Cranio-lenticulo-sutural dysplasia (CLSD) is an autosomal recessive syndrome characterized by late-closing fontanels, sutural cataracts, facial dysmorphisms and skeletal defects mapped to chromosome 14q13-q21 (ref. 1). Here we show, using a positional cloning approach, that an F382L amino acid substitution in SEC23A segregates with this syndrome. SEC23A is an essential component of the COPII-coated vesicles that transport secretory proteins from the endoplasmic reticulum to the Golgi complex. Electron microscopy and immunofluorescence show that there is gross dilatation of the endoplasmic reticulum in fibroblasts from individuals affected with CLSD. These cells also exhibit cytoplasmic mislocalization of SEC31. Cell-free vesicle budding assays show that the F382L substitution results in loss of SEC23A function. A phenotype reminiscent of CLSD is observed in zebrafish embryos injected with sec23a-blocking morpholinos. Our observations suggest that disrupted endoplasmic reticulum export of the secretory proteins required for normal morphogenesis accounts for CLSD.