IndraLab

"The crystal structure of the catalytic domain of AMSH-LP bound to its substrate Lys63-linked diubiquitin (PBD ID: 2ZNV) reveals the flap adopting a closed position over the active site ( xref )."

"The crystal structure of the catalytic core domain of AMSH-LP bound to K63-linked diubiquitin has provided a molecular description of this specificity xref ."

"Only recently was Lys63-linkage specificity understood from the structural analysis of the DUB domain of AMSH-LP bound Lys63-linked diubiquitin. xref This structure reveals interactions between the enzyme and both the distal and proximal ubiquitins, but the basis for specificity arises from residues in the proximal site of the enzyme interacting with the proximal ubiquitin, despite a more extensive interaction with the distal ubiquitin (a significantly more accessible surface area is buried upon interaction with distal than proximal ubiquitin). xref Overall, AMSH adopts very similar interactions when modeled according to the ubiquitin-bound structure of AMSH-LP."

"The structure of AMSH-LP bound to K63-linked diubiquitin demonstrates that the recognition of the proximal ubiquitin in diubiquitin determines AMSH-LP linkage selectivity xref ."

"However, this residue, in fact, the two-residue turn segment, Leu402-Phe403, needs to move apart relative to Thr316 to make room for the diubiquitin substrate to position itself correctly in the active site. (These observations are also true in the structure of AMSH-LP bound to diubiquitin.) It seems likely that the β-turn segment is dynamic, fluctuating between open and closed forms; the substrate binds to the open form, perhaps by conformational selection."

"Modeling of the catalytic domain of AMSH onto the structure of AMSH-LP bound to Lys63-linked diubiquitin revealed four residues within AMSH (Thr341, Phe343, Ser346, and Phe395) that could determine its specificity for Lys63-linked polyubiquitin chains by recognizing the tri-peptide sequence motif Gln62-Lys63-Glu64 within the proximal ubiquitin, which encompasses the acceptor Lys63 and its two immediate flanking residues."

"How JAMM/MPNDUBs cleave ubiquitin chains with K63-linkage specificity has been explained by the crystal structure of AMSH-LP bound to K63-linked di-ubiquitin: Two insertion loops orient the distal and proximal ubiquitin in order to place the isopeptide bond at lysine 63 in direct proximity to the active site [ xref ]."

"Recent structure determination of the K63 linked diubiquitin bound to AMSH-LP revealed specific interactions between the proximal ubiquitin and the DUB catalytic core as well as an inserted motif."

"(These observations are also true in the structure of AMSH-LP bound to diubiquitin.)"