Menin is a tumor suppressor protein whose loss or inactivation causes multiple endocrine neoplasia type 1 (MEN1), a hereditary autosomal dominant tumor syndrome characterized by tumorigenesis in multiple endocrine organs1. Menin interacts with a multitude of proteins and involves in a variety of cellular processes2–6. Menin binds the Jun family transcription factor JunD and inhibits its transcriptional activity7,8. Several MEN1 missense mutations disrupted the menin-JunD interaction suggestive of a correlation between menin’s tumor suppressor function and its interaction with JunD and suppression of JunD activated transcription8,9. Menin also interacts with mixed lineage leukemia protein 1 MLL1, a histone H3 lysine 4 (H3K4) methyltransferase, and functions as an oncogenic cofactor to upregulate gene (including HOX genes) transcription and promote MLL1 fusion protein (MFP)-induced leukemogenesis10–12. A recent report on menin tethering MLL1 to chromatin binding factor LEDGF indicates menin as a molecular adaptor to coordinate the functions of multiple proteins13. Despite the importance of menin, it still remains poorly understood how menin could interact with many distinct partners and control multiple functions. Here we present the crystal structures of menin, free and in complexes with MLL1 or JunD, or an MLL1-LEDGF heterodimer. These structures show that menin contains a deep pocket that binds short peptides of MLL1 or JunD in the same manner, but oppositely regulates transcription. The menin-JunD interaction blocks JNK kinase-meidated JunD phosphorylation, a crucial event for JunD activation.Moreover, menin functions as a scaffold molecule to promote gene transcription by binding MLL1 through the peptide-pocket yet interacting with LEDGF at a distinct surface.

Lysine-specific demethylase 1 (LSD1) was recently identified as the first histone demethylase that specifically demethylates monomethylated and dimethylated histone H3 at K4. It is a component of the CoREST and other corepressor complexes and plays an important role in silencing neuronal-specific genes in nonneuronal cells, but the molecular mechanisms of its action remain unclear. The 2.8-Å-resolution crystal structure of the human LSD1 reveals that LSD1 defines a new subfamily of FAD-dependent oxidases. The active center of LSD1 is characterized by a remarkable 1,245-Å 3 substrate-binding cavity with a highly negative electrostatic potential. Although the protein core of LSD1 resembles other flavoenzymes, its enzymatic activity and functions require two additional structural modules: an N-terminal SWIRM domain important for protein stability and a large insertion in the catalytic domain indispensable both for the demethylase activity and the interaction with CoREST. These results provide a framework for further probing the catalytic mechanism and the functional roles of LSD1.histone modification ͉ flavoenzyme ͉ catalysis H istone proteins are subject to a variety of posttranslational modifications, including acetylation, methylation, phosphorylation, and ubiquitination, and it is these histone modifications that function as the molecular switches that alter the state of compaction of chromatin to allow gene activation or repression (1-3). Some histone modifications (e.g., acetylation and phosphorylation) are highly dynamic, whereas others (e.g., methylation) have been regarded as ''permanent'' chromatin marks. However, the discoveries of lysine-specific demethylase 1 (LSD1) and jumonji domain C (JmjC) domain-containing histone demethylase 1 (JHDM1) have changed this picture (4, 5). Shi and colleagues demonstrated that LSD1 is a histone lysine demethylase that specifically demethylates monomethylated and dimethylated histone H3 at K4 (4). More recently, we and others have shown that many JmjC domaincontaining proteins are capable of demethylating dimethylated and trimethylated histone proteins (4-10). These findings suggest that histone methylation is a reversible modification and can be regulated under similar enzymatic control as other histone modifications (11-13).LSD1 is a component of a number of transcriptional corepressor complexes, such as CoREST, CtBP, and HDAC complexes, and plays an important role in silencing neuronal-specific genes in nonneuronal cells (14-19). The C-terminal two-thirds of LSD1 contains an amine oxidase-like (AOL) domain, which shares extensive sequence homology to FAD-dependent oxidases ( Fig. 1 A and C) (20-22). In addition, LSD1 also contains an N-terminal SWIRM domain (Fig. 1 A), which has been recently identified as a conserved motif often found in chromatin remodeling and modifying complexes with unknown function (23). Recent studies suggest that the specificity and activity of LSD1 can be modulated by its interacting factors (4, 24-26). However, the molecular mechanism by w...

In budding yeast, Cdc13, Stn1, and Ten1 form a heterotrimeric complex (CST) that is essential for telomere protection and maintenance. Previous bioinformatics analysis revealed a putative oligonucleotide/oligosaccharide-binding (OB) fold at the N terminus of Stn1 (Stn1N) that shows limited sequence similarity to the OB fold of Rpa2, a subunit of the eukaryotic ssDNA-binding protein complex replication protein A (RPA). Here we present functional and structural analyses of Stn1 and Ten1 from multiple budding and fission yeast. The crystal structure of the Candida tropicalis Stn1N complexed with Ten1 demonstrates an Rpa2N-Rpa3-like complex. In both structures, the OB folds of the two components pack against each other through interactions between two C-terminal helices. The structure of the C-terminal domain of Saccharomyces cerevisiae Stn1 (Stn1C) was found to comprise two related winged helix-turn-helix (WH) motifs, one of which is most similar to the WH motif at the C terminus of Rpa2, again supporting the notion that Stn1 resembles Rpa2. The crystal structure of the fission yeast Schizosaccharomyces pombe Stn1N-Ten1 complex exhibits a virtually identical architecture as the C. tropicalis Stn1N-Ten1. Functional analyses of the Candida albicans Stn1 and Ten1 proteins revealed critical roles for these proteins in suppressing aberrant telomerase and recombination activities at telomeres. Mutations that disrupt the Stn1-Ten1 interaction induce telomere uncapping and abolish the telomere localization of Ten1. Collectively, our structural and functional studies illustrate that, instead of being confined to budding yeast telomeres, the CST complex may represent an evolutionarily conserved RPA-like telomeric complex at the 39 overhangs that works in parallel with or instead of the well-characterized POT1-TPP1/TEBPa-b complex.[Keywords: Telomere; telomere-binding protein; telomerase; homologous recombination] Supplemental material is available at http://www.genesdev.org.

SummarySLX4 interacts with several endonucleases to resolve structural barriers in DNA metabolism. SLX4 also interacts with telomeric protein TRF2 in human cells. The molecular mechanism of these interactions at telomeres remains unknown. Here, we report the crystal structure of the TRF2-binding motif of SLX4 (SLX4TBM) in complex with the TRFH domain of TRF2 (TRF2TRFH) and map the interactions of SLX4 with endonucleases SLX1, XPF, and MUS81. TRF2 recognizes a unique HxLxP motif on SLX4 via the peptide-binding site in its TRFH domain. Telomeric localization of SLX4 and associated nucleases depend on the SLX4-endonuclease and SLX4-TRF2 interactions and the protein levels of SLX4 and TRF2. SLX4 assembles an endonuclease toolkit that negatively regulates telomere length via SLX1-catalyzed nucleolytic resolution of telomere DNA structures. We propose that the SLX4-TRF2 complex serves as a double-layer scaffold bridging multiple endonucleases with telomeres for recombination-based telomere maintenance.

Budding yeast Cdc13-Stn1-Ten1 (CST) complex plays an essential role in telomere protection and maintenance, and has been proposed to be a telomere-specific replication protein A (RPA)-like complex. Previous genetic and structural studies revealed a close resemblance between Stn1-Ten1 and RPA32-RPA14. However, the relationship between Cdc13 and RPA70, the largest subunit of RPA, has remained unclear. Here, we report the crystal structure of the N-terminal OB (oligonucleotide/oligosaccharide binding) fold of Cdc13. Although Cdc13 has an RPA70-like domain organization, the structures of Cdc13 OB folds are significantly different from their counterparts in RPA70, suggesting that they have distinct evolutionary origins. Furthermore, our structural and biochemical analyses revealed unexpected dimerization by the N-terminal OB fold and showed that homodimerization is probably a conserved feature of all Cdc13 proteins. We also uncovered the structural basis of the interaction between the Cdc13 N-terminal OB fold and the catalytic subunit of DNA polymerase α (Pol1), and demonstrated a role for Cdc13 dimerization in Pol1 binding. Analysis of the phenotypes of mutants defective in Cdc13 dimerization and Cdc13-Pol1 interaction revealed multiple mechanisms by which dimerization regulates telomere lengths in vivo. Collectively, our findings provide novel insights into the mechanisms and evolution of Cdc13.

Summary Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with Topoisomerase(Topo) IIIα, RMI1 and RMI2 to form the BLM complex that is essential for genome stability. The RMI1-RMI2 heterodimer stimulates the dissolution of double Holliday junction into non-crossover recombinants mediated by BLM-Topo IIIα and is essential for stabilizing the BLM complex. However, the molecular basis of these functions of RMI1 and RMI2 remains unclear. Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. Our structural and biochemical analyses revealed an unexpected insertion motif in RMI1N-OB, which is important for stimulating the dHJ dissolution. We also revealed the structural basis of the interaction between RMI1C-OB and RMI2-OB and demonstrated the functional importance of the RMI1-RMI2 interaction in genome stability maintenance.

The Fanconi anemia protein SLX4 assembles a genome and telomere maintenance toolkit, consisting of the nucleases SLX1, MUS81 and XPF. Although it is known that SLX4 acts as a scaffold for building this complex, the molecular basis underlying this function of SLX4 remains unclear. Here, we report that functioning of SLX4 is dependent on its dimerization via an oligomerization motif called the BTB domain. We solved the crystal structure of the SLX4BTB dimer, identifying key contacts (F681 and F708) that mediate dimerization. Disruption of BTB dimerization abrogates nuclear foci formation and telomeric localization of not only SLX4 but also of its associated nucleases. Furthermore, dimerization-deficient SLX4 mutants cause defective cellular response to DNA interstrand crosslinking agent and telomere maintenance, underscoring the contribution of BTB domain-mediated dimerization of SLX4 in genome and telomere maintenance.

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