Structural insights into the SENP6 Loop1 structure in complex with SUMO2

Abstract

The SENP proteases regulate the SUMO conjugates in the cell by cleaving SUMO from target proteins. SENP6 and SENP7 are the most divergent members of the SENP/ULP protease family in humans by the presence of insertions in their catalytic domains. Loop1 insertion is determinant for the SUMO2/3 activity and specificity on SENP6 and SENP7. To gain structural insights into the role of Loop1, we have designed a chimeric SENP2 with the insertion of Loop1 into its sequence. The structure of SENP2-Loop1 in complex with SUMO2 was solved at 2.15 Å resolution, and reveals the details of an interface exclusive to SENP6/7 and the formation of unique contacts between both proteins. Interestingly, functional data with SUMO substrates showed an increase of the proteolytic activity in the SENP2-Loop1 chimera for diSUMO2 and polySUMO2 substrates.

c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4

“…12,43 This feature is thought to contribute to its specificity for SUMO chains. 44 We found that SENP7 counteracted c-Myc SUMOylation (Fig. 4b).…”

Allosteric activation of SENP1 by SUMO1 β-grasp domain involves a dock-and-coalesce mechanism

“…Here the expectation for stronger allosteric effects is specifically supported by the observation that a pre-bound SUMO2, but not SUMO1, β-grasp domain enhanced the SENP2 catalytic activity on a peptide substrate ( Mikolajczyk et al, 2007 ). A similar causal link between strengthened exosite interactions and strengthened allosteric effects may be at play for a SENP2 mutant that was designed by grafting an insertion in the β1-β2 hairpin from SENP6 ( Alegre and Reverter, 2014 ). The insertion extended the exosite lower interface and increased the proteolytic activity of SENP2 for some SUMO2 conjugates.…”

“…Structural studies have shown that SENP catalytic domains only undergo localized conformational rearrangements upon binding SUMOs (as precursors, processed products, or SUMO conjugates), and that SENP-SUMO interactions are largely similar during precursor processing and deSUMOylation ( Reverter and Lima, 2004 , 2006 ; Shen et al, 2006a , 2006b ; Xu et al, 2006 ; Alegre and Reverter, 2014 ). In SENP1, the catalytic triad comprises residues His533, Asp550, and Cys603 ( Figure 1 ).…”

“…The β-grasp domain of SUMO1 binds into a large cleft to the side (hereafter the exosite), and makes separate contacts with the two subdomains of SENP1: the β1-β2 hairpin in the lower subdomain and the α4-α5 helices in the upper subdomain ( Figure 1 ). An insertion in the β1-β2 hairpin of SENP2 that extended the interface with SUMO2 resulted in no other change in the structure of the catalytic domain but nevertheless increased its catalytic activity ( Alegre and Reverter, 2014 ). Given that SENPs generally lack major conformational changes upon binding SUMOs, there is no simple explanation for the allosteric activation of SENPs by the β-grasp domain of SUMOs.…”

Substrate specificity of the ubiquitin and Ubl proteases

“…The crystal structure of a chimeric SENP2 fusion harboring the Loop-1 segment from SENP6 bound to SUMO2 revealed that Loop-1, an eight-residue element, extends the binding interface between the protease and SUMO2. A negative patch of amino acids unique to SUMO2 (Asn68, Asp71 and Glu77) directly contacts the SENP6 Loop-1 ( Figure 6E ) 120 . These residues are substituted to Ala, His and Gly in SUMO1, which implicates both the Loop-1 insertion in SENP6/7 and the negative patch of SUMO2 as key determinants in SUMO isoform specificity.…”