title: Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation.
abstract: Sumoylation is the covalent attachment of small ubiquitin-like modifier (SUMO) to a target protein. Similar to other ubiquitin-like pathways, three enzyme types are involved that act in succession: an activating enzyme (E1), a conjugating enzyme (E2), and a ligase (E3). To date, unlike other ubiquitin-like mechanisms, sumoylation of the target RanGAP1 (Target(RanGAP1)) does not absolutely require the E3 of the system, RanBP2 (E3(RanBP2)), since the presence of E2 (E2(Ubc9)) is enough to sumoylate Target(RanGAP1). However, in the presence of E3, sumoylation is more efficient. To understand the role of the target specificity of E3(RanBP2) and E2(Ubc9), we carried out molecular dynamics simulations for the structure of E2(Ubc9)-SUMO-Target(RanGAP1) with and without the E3(RanBP2) ligase. Analysis of the dynamics of E2(Ubc9)-SUMO-Target(RanGAP1) in the absence and presence of E3(RanBP2) revealed that two different allosteric sites regulate the ligase activity: (i) in the presence of E3(RanBP2), the E2(Ubc9)'s loop 2; (ii) in the absence of E3(RanBP2), the Leu65-Arg70 region of SUMO. These results provide a first insight into the question of how E3(RanBP2) can act as an intrinsic E3 for E2(Ubc9) and why, in its absence, the activity of E2(Ubc9)-SUMO-Target(RanGAP1) could still be maintained, albeit at lower efficiency.
authors.affiliation: Polymer Research Center & Chemical Engineering Department, Bogazici University, Bebek-Istanbul 34342, Turkey.
authors.forename: Ezgi
authors.initials: E
authors.lastname: Karaca
authors.forename: Melda
authors.initials: M
authors.lastname: Tozluoğlu
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.forename: Türkan
authors.initials: T
authors.lastname: Haliloğlu
mesh_terms: D000494:Allosteric Regulation; D020690:GTPase-Activating Proteins / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D018832:Molecular Chaperones / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D028861:Nuclear Pore Complex Proteins / Q000737:chemistry / Q000378:metabolism; D025841:Small Ubiquitin-Related Modifier Proteins / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity; D058207:Sumoylation; D044763:Ubiquitin-Conjugating Enzymes / Q000737:chemistry / Q000378:metabolism*; D000098843:Ubiquitin-Conjugating Enzyme UBC9
chemical_list: D020690:GTPase-Activating Proteins; D018832:Molecular Chaperones; D028861:Nuclear Pore Complex Proteins; C092317:RANGAP1 protein, human; D025841:Small Ubiquitin-Related Modifier Proteins; C094493:ran-binding protein 2; D044763:Ubiquitin-Conjugating Enzymes; D000098843:Ubiquitin-Conjugating Enzyme UBC9