lecture 6 and 7 Flashcards
what is ubiquitin
a small, globular, 76 amino acid, 8.5kDa protein
where is ubiquitin found
in all eukaryotes
how many human genes express preubiquitin proteins
4, each has a diff c terminal sequence
c terminal extensions are removed to generate identical ubiquitin proteins
how is ubiquitin used as a label
when it is covalently attached to other proteins
what is ubiquitylation
tagging of substrate proteins
what acts as the receptor on the substrate protein to be ubiquitinated
the epsilon amino group of the lysine residue of the substrate protein
ubiquitin has lys 6,11,27,29,33,48,63 and terminal group met 1 which can act as acceptors of further ubiquitin donors to form chains
what is the acceptor of the c terminus of the donor ubiquitin for a linear chain
the n terminal NH2 of Met1 of ubiquitin
what linkage types do heterotypic polyubiquitin chains have
different linkage types within the same chain
how are ubiquitins extended in branched polyubiquitin chains
single ubiquitin is extended at 2 or more lys residues
how does the extended chain conformation of ubiquitin come about
linking of the c terminal carboxyl of the incoming donor ubiquitin to lys63 or met1 of the acceptor ubiquitin this positions the donor opposite the c terminal gly of the acceptor
how does a compact structure of ubiquitin chain come about
the donor ubiquitin is positioned on the side of the acceptor ubiquitin because the donor is linked to lys48 of the acceptor ubiquitin
how are different linkages of ubiquitin recognised by differed ubiquitin binding domains
some UBDs require a particular ubiquitin chain length, others dock onto the substrate as well as the attached ubiquitin
what do UBDs on regulatory proteins determine
the role and fate of the ubiquitylated protein
what does the ubd K29 determine
NFkB signalling and lysosomal degradation
what does the n terminus udb determine
dna damage responses, tnf receptor signalling and innate antiviral signalling
what does k63 ubd determine
endocytosis, NFkB signalling and dna damage responses
what does k48 ubd determine
proteosomal degradation
what is the E1 enzyme and how does it work
the ubiquitin activating enzyme
it used atp to activate the carboxyl group of ubiquitins c-terminal residue
the outcome of this reaction is the formation of a thioester between gly76 of ubiquitin and a cystine residue of the e1
- can recruit 1 of 40 e2 conjugating enzymes which accept ubiquitin