Insights into High Affinity Small Ubiquitin-like Modifier (SUMO) Recognition by SUMO-interacting Motifs (SIMs) Revealed by a Combination of NMR and Peptide Array Analysis

Namanja, Andrew T.; Li, Yijia; Shen, Yang; Wong, Steven; Lu, Jingjun; Colson, Loren; Wu, Chenggang; Li, Shawn S.‐C.; Chen, Yuan

doi:10.1074/jbc.m111.293118

Cited by 67 publications

(82 citation statements)

References 34 publications

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“…Arkadia SIM1 and SIM3 also match the previous designation of SIM subtypes, SIM-a and SIM-b, respectively, whereas SIM2 appears to be rather a bidirectional SIM than a pure SIM-r (40,41). Differences in sequence may contribute to the selectivity of individual SIMs toward different SUMO isoforms (5,35). Consistently, some of our Arkadia SIM3 mutants showed better residual interaction with SUMO1 than with SUMO2 (Fig.…”

Section: Discussionsupporting

confidence: 69%

“…3B). Our observation thus complements that of Yuan Chen and co-workers (35), where they show that only a small set of amino acids is allowed in the PIAS1 SIM for high affinity SUMO binding. Together our results indicate that a precise structure is needed for maximum SUMO affinity of the VIDLT-type SIMs, which accepts only limited perturbations.…”

Section: String Search Identified Proteins Containingsupporting

confidence: 35%

“…Novel SUMO-binding Proteins with Clustered VIDLT-type SIMs-Our data together with the recent findings by Yuan Chen and co-workers (35), strongly argue that aromatic residues Phe or Tyr may also be allowed in the first position of a pentameric VIDLT-type SIM even though they are rarely seen in reported SIMs. We thus ran another focused string search for proteins containing multiple (V/I/L/F/Y)(V/I)DLT motifs (Fig.…”

Section: String Search Identified Proteins Containingmentioning

confidence: 63%

“…3, C and D, lanes 15-17). We suggest that this reflects a subtle difference between SUMO1 and SUMO2 in the shape of their SIM docking sites at the atomic level, which accounts for the selectivity between certain SIMs (of lesser SUMO affinity) and the different SUMO isoforms (5,35). It is also remarkable that the change from VVDLT to VIDLT enhanced SUMO binding (Fig.…”

Section: String Search Identified Proteins Containingmentioning

confidence: 91%

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Poly-Small Ubiquitin-like Modifier (PolySUMO)-binding Proteins Identified through a String Search

Sun

Hunter

2012

Journal of Biological Chemistry

111

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Background: Sumoylation is recognized by proteins with SUMO-interacting motifs. Results: SUMO-interacting motifs were identified through a computational string search and validated in SUMO binding assays. Conclusion: Arkadia, FLASH, C5orf25, and SOBP all contain clustered SIMs. Significance: These proteins contain distinct SUMO binding structures responsible for the recognition of diverse forms of sumoylation.

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Section: Discussionsupporting

confidence: 69%

Section: String Search Identified Proteins Containingsupporting

confidence: 35%

Section: String Search Identified Proteins Containingmentioning

confidence: 63%

Section: String Search Identified Proteins Containingmentioning

confidence: 91%

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Poly-Small Ubiquitin-like Modifier (PolySUMO)-binding Proteins Identified through a String Search

Sun

Hunter

2012

Journal of Biological Chemistry

111

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“…SUMO, attached to cellular proteins, could also recruit other proteins through noncovalent interactions (13,14). These SIPs recognize SUMO by virtue of a short sequence motif (SUMO-interaction motif, or SIM) that is rich in hydrophobic amino acids (21,22). Variations of the SIM include "type a" SIM containing a stretch of three to four hydrophobic residues and three to four acidic residues, and "type b" SIM containing the sequence I/VDL/T (14).…”

mentioning

confidence: 99%

Identification of Arabidopsis SUMO-interacting proteins that regulate chromatin activity and developmental transitions

Elrouby

Bonequi

Porri

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Posttranslational modification of proteins by small ubiquitin-like modifier (SUMO) plays essential roles in eukaryotic growth and development. Many covalently modified SUMO targets have been identified; however, the extent and significance of noncovalent interactions of SUMO with cellular proteins is poorly understood. Here, large-scale yeast two-hybrid screens repeatedly identified a surprisingly small number of proteins that interacted with three Arabidopsis SUMO isoforms. These SUMO-interacting proteins are nuclear and fall into two main categories: six histone or DNA methyltransferses or demethylases and six proteins that we show to be the evolutionary and functional homologs of SUMOtargeted ubiquitin ligases (STUbLs). The selectivity of the screen for several methylases and demethylases suggests that SUMO interaction with these proteins has a significant impact on chromatin methylation. Furthermore, the Arabidopsis STUbLs (AT-STUbLs) complemented to varying degrees the growth defects of the Schizosaccharomyces pombe STUbL mutant rfp1/rfp2, and three of them also complemented the genome integrity defects of this mutant, demonstrating that these proteins show STUbL activity. We show that one of the AT-STUbLs least related to the S. pombe protein, AT-STUbL4, has acquired a plant-specific function in the floral transition. It reduces protein levels of CYCLING DOF FACTOR 2, hence increasing transcript levels of CONSTANS and promoting flowering through the photoperiodic pathway.SIM | Slx5/Slx8 | Nucleolus | Flowering time | CDF

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A FRET Sensor to Monitor Bivalent SUMO–SIM Interactions in SUMO Chain Binding

Kost

Mootz

2017

ChemBioChem

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The small ubiquitin-like modifier (SUMO) can be assembled into polymeric chains as part of its diverse biochemical signal pattern upon conjugation to substrate proteins. SUMO chain recognition is facilitated by receptor proteins that contain at least two SUMO-interacting motifs (SIMs). Little is known about the structure of SUMO chains, both in an unliganded form and upon complexation with multi-SIM protein partners. A FRET sensor has been developed based on a linear dimer of human SUMO-2 as a minimal SUMO chain analogue. The synthetic acceptor and donor dyes were conjugated by maleimide and copper-catalyzed click chemistry to each of the two SUMO subunits. FRET changes were only observed in the presence of di- or multi-SIM ligands. Alteration of the short linker sequence between SIMs 2 and 3 of RNF4 showed a great tolerance, and hence, structural flexibility, of the SUMO dimer for bivalent binding of adjacent SIMs. The di-SUMO FRET sensor reports on the binding of SIM clusters of the proteins C5orf25 and SOBP; this suggest that these can bind to adjacent subunits of a SUMO chain. The developed FRET sensor will be a useful tool to study the importance of SIM and linker sequences, as well as biochemical and structural properties of SUMO chains and multi-SIM proteins.

show abstract

Insights into High Affinity Small Ubiquitin-like Modifier (SUMO) Recognition by SUMO-interacting Motifs (SIMs) Revealed by a Combination of NMR and Peptide Array Analysis

Cited by 67 publications

References 34 publications

Poly-Small Ubiquitin-like Modifier (PolySUMO)-binding Proteins Identified through a String Search

Poly-Small Ubiquitin-like Modifier (PolySUMO)-binding Proteins Identified through a String Search

Identification of Arabidopsis SUMO-interacting proteins that regulate chromatin activity and developmental transitions

A FRET Sensor to Monitor Bivalent SUMO–SIM Interactions in SUMO Chain Binding

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