Structure of the Small Ubiquitin-like Modifier (SUMO)-interacting Motif of MBD1-containing Chromatin-associated Factor 1 Bound to SUMO-3

Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
Journal of Biological Chemistry (Impact Factor: 4.57). 11/2008; 283(51):35966-75. DOI: 10.1074/jbc.M802528200
Source: PubMed


Post-translational modification by small ubiquitin-like modifier (SUMO) proteins has been implicated in the regulation of
a variety of cellular events. The functions of sumoylation are often mediated by downstream effector proteins harboring SUMO-interacting
motifs (SIMs) that are composed of a hydrophobic core and a stretch of acidic residues. MBD1-containing chromatin-associated
factor 1 (MCAF1), a transcription repressor, interacts with SUMO-2/3 and SUMO-1, with a preference for SUMO-2/3. We used NMR
spectroscopy to solve the solution structure of the SIM of MCAF1 bound to SUMO-3. The hydrophobic core of the SIM forms a
parallel β-sheet pairing with strand β2 of SUMO-3, whereas its C-terminal acidic stretch seems to mediate electrostatic interactions
with a surface area formed by basic residues of SUMO-3. The significance of these electrostatic interactions was shown by
mutations of both SUMO-3 and MCAF1. The present structural and biochemical data suggest that the acidic stretch of the SIM
of MCAF1 plays an important role in the binding to SUMO-3.

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    • "For several SUMO-binding proteins the charged residues adjacent to the consensus SIM confer preferential SUMO-1 binding [4], [11]. The classical SIM forms a β-strand that inserts into a groove on SUMO-1 and SUMO-2 [4], [5], [7]–[9], [27]. Our studies revealed that the MYM-type zinc fingers of ZNF198 and ZNF261 bind preferentially to SUMO-2 using the same surface on SUMO-2 recognized by the classical SIM. "
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    ABSTRACT: SUMO-binding proteins interact with SUMO modified proteins to mediate a wide range of functional consequences. Here, we report the identification of a new SUMO-binding protein, ZNF261. Four human proteins including ZNF261, ZNF198, ZNF262, and ZNF258 contain a stretch of tandem zinc fingers called myeloproliferative and mental retardation (MYM)-type zinc fingers. We demonstrated that MYM-type zinc fingers from ZNF261 and ZNF198 are necessary and sufficient for SUMO-binding and that individual MYM-type zinc fingers function as SUMO-interacting motifs (SIMs). Our binding studies revealed that the MYM-type zinc fingers from ZNF261 and ZNF198 interact with the same surface on SUMO-2 recognized by the archetypal consensus SIM. We also present evidence that MYM-type zinc fingers in ZNF261 contain zinc, but that zinc is not required for SUMO-binding. Immunofluorescence microscopy studies using truncated fragments of ZNF198 revealed that MYM-type zinc fingers of ZNF198 are necessary for localization to PML-nuclear bodies (PML-NBs). In summary, our studies have identified and characterized the SUMO-binding activity of the MYM-type zinc fingers in ZNF261 and ZNF198.
    Full-text · Article · Aug 2014 · PLoS ONE
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    • "In the cancer cell line C33a, MCAF1, MBD1, and SETDB1 co-localize at the H3K9me3-containing heterochromatin region [8,11]. MCAF1 contains the SUMO-interacting motif (SIM) which preferentially binds to SUMO2/3 [12]. Modification of MBD1 with SUMO2/3 is considered to be required for the recruitment of the MCAF1/SETDB1 complex to DNA-methylated loci to form heterochromatin [11]. "
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    ABSTRACT: Cellular senescence is post-mitotic or oncogene-induced events combined with nuclear remodeling. MCAF1 (also known as hAM or ATF7IP), a transcriptional cofactor that is overexpressed in various cancers, functions in gene activation or repression, depending on interacting partners. In this study, we found that MCAF1 localizes to PML nuclear bodies in human fibroblasts and non-cancerous cells. Interestingly, depletion of MCAF1 in fibroblasts induced premature senescence that was characterized by cell cycle arrest, SA-β-gal activity, and senescence-associated heterochromatic foci (SAHF) formation. Under this condition, core histones and the linker histone H1 significantly decreased at both mRNA and protein levels, resulting in reduced nucleosome formation. Consistently, in activated Ras-induced senescent fibroblasts, the accumulation of MCAF1 in PML bodies was enhanced via the binding of this protein to SUMO molecules, suggesting that sequestration of MCAF1 to PML bodies promotes cellular senescence. Collectively, these results reveal that MCAF1 is an essential regulator of cellular senescence.
    Full-text · Article · Jul 2013 · PLoS ONE
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    • "K33 is one of the critical amino acids for the transcriptional inhibitory properties of SUMO2 and is likely involved in the binding to SIM-containing corepressors (Chupreta et al., 2005; Rosendorff et al., 2006). Structural data indeed demonstrate that K33 of SUMO2 forms a salt bridge with an aspartic acid in the SIM of the corepressor MCAF1 (Sekiyama et al., 2008). Consistent with these findings, the acetyl-mimicking SUMO2 K33Q variant exhibits a strongly reduced repressive potential, indicating that SUMO-dependent gene repression is directly regulated by acetylation. "
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    ABSTRACT: The attachment of the SUMO modifier to proteins controls cellular signaling pathways through noncovalent binding to SUMO-interaction motifs (SIMs). Canonical SIMs contain a core of hydrophobic residues that bind to a hydrophobic pocket on SUMO. Negatively charged residues of SIMs frequently contribute to binding by interacting with a basic surface on SUMO. Here we define acetylation within this basic interface as a central mechanism for the control of SUMO-mediated interactions. The acetyl-mediated neutralization of basic charges on SUMO prevents binding to SIMs in PML, Daxx, and PIAS family members but does not affect the interaction between RanBP2 and SUMO. Acetylation is controlled by HDACs and attenuates SUMO- and PIAS-mediated gene silencing. Moreover, it affects the assembly of PML nuclear bodies and restrains the recruitment of the corepressor Daxx to these structures. This acetyl-dependent switch thus expands the regulatory repertoire of SUMO signaling and determines the selectivity and dynamics of SUMO-SIM interactions.
    Full-text · Article · May 2012 · Molecular cell
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