First Class Lecture notes Dynamic Cell Module

THE UBIQUITIN PROTEASOME SYSTEM (UPS)


1. Discuss the versatility of protein ubiquitylation as a
post-translation modification and compare and contrast
with phosphorylation.
THE STUDY OF CELL BIOLOGY: see last lecture
Most of the work covered today was carried out in late 1970s and early
80s. Protein ubiquitin as a mediator of protein degradation discovered in
1980, and another prize related to this work in 2003.
UBIQUITIN CODE: see figure from last lecture
Specific membrane proteins, cytosolic proteins and large organelles (e.g
damaged mitochondria) need to be removed from cells.
Proteins/organelles tagged with ubiquitin which drives different
degradation pathways.
UBIQUITIN CHAINS are assembled between the C-terminus of a
one ubiquitin and the N-ter (NH2) or
any of the seven lysines of another
ubiquitin
Hence, ubiquitin can be assembled into
chains through 8 attachment sites.
Ubiquitin has a globular, compact
structure with extended C-terminal
‘thumb’ important for attaching to protein
targets. Can exist in isolation (just one
ubiquitin on membrane protein target –
monoubiqutin) which drives membrane recycling at the plasma
membrane. Can also exist as polymer – ubiquitin chain – which can exist in
different conformations (compact on cytosolic proteins and linear on large
protein aggregates) – drives different degradation mechanisms and
function of proteins. Lysine residues of ubiquitin are essential in attaching
to another ubiquitin monomer, thus forming chains.
LYSINE UBIQUITYLATION ONLY?
Amine group of all AA is engaged in peptide bonds, only Lysine as an
available amine group (NH2).
Hence, ubiquitination is a specific modification – cannot be added onto any
amino acid. Only targets lysine residues on protein
target, which must be exposed on the surface
rather than buried in the cell.
PROTEIN UBIQUITINATION:
An isopeptide bond is formed between the C-ter
(COOH) group of Gly76 of ubiquitin and the of the ε-
NH2 lysine on a protein target
Exposed lysine residue at the surface is attached to
ubiquitin at the C-terminal ‘thumb’ of ubiquitin via
the amino group of the free lysine residue (ATP
dependent reaction, energy needed to covalently

, label ubiquitin on protein target). Stable balanced, isopeptide bond forms
which is strong.

CAN UBIQUITIN TARGET ITSELF?
Ubiquitin has multiple lysine residues which are all exposed. These can all
receive other ubiquitin proteins. Hence, answer is yes if ubiquitin contains
lysine(s) in its peptide chain.
UBIQUITIN DNA SEQUENCE:
The human ubiquitin gene sequence contains the same sequence
repeated 3 times, producing a trimer rather than a monomer. Much
protein degradation is occurring in cells constantly, so it may be
energetically favourable to manufacture three ubiquitin proteins
simultaneously rather than translating each individually.
HOW MANY DIFFERENT
TYPES OF UBIQUITIN CHAINS
CAN BE FORMED?
Ubiquitin trimer is then cleaved
into monomers which are added
to assemble ubiquitin chains.
Each of the 3 monomers has 7
lysine residues (K) in each which
can be used to make a chain.
Hence, 7 types of ubiquitin
chains can be formed.
OTHER THAN LYSINE,
ANOTHER AMINO GROUP CAN BE USED TO ATTACH UBIQUITIN: N-
terminus of ubiquitin has a free amino group which can accept ubiquitin
monomers. Combined with lysine residues, ubiquitin can therefore make 8
chains
EXAMPLE: UBIQUITIN CHAINS
ASSEMBLED VIA LYSINE 48
Exposed lysine residue used to attach
the first molecule of ubiquitin. Then
there is a choice: can use any of the 7
lysines OR the free amino group at the
N-terminus to extend the chain. G76
attached to amino group of lysine or
N-terminus to form chain.




2. Contrast and compare between
the different types of ubiquitin