Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

PROTEIN FUNCTION
159
N
Lys63
ubiquitin
MONOUBIQUITYLATION MULTIUBIQUITYLATION POLYUBIQUITYLATION
Lys48
Lys63
Lys48
lysine side chain
of target protein
(A)
HC
C
HN
O
isopeptide
bond
histone regulation
(B)
endocytosis
proteasomal
degradation
DNA repair
Protein Complexes with Interchangeable Parts Make Efficient Use
of Genetic Information
The SCF ubiquitin ligase is a protein complex that binds different “target proteins”
at different times in the cell cycle, covalently adding polyubiquitin polypeptide
chains to these targets. Its C-shaped structure is formed from five protein subunits,
the largest of which serves as a scaffold MBoC6 on m6.93/3.64 which the rest of the complex
is built. The structure underlies a remarkable mechanism (Figure 3–71). At one
end of the C is an E2 ubiquitin-conjugating enzyme. At the other end is a substrate-binding
arm, a subunit known as an F-box protein. These two subunits are
separated by a gap of about 5 nm. When this protein complex is activated, the
F-box protein binds to a specific site on a target protein, positioning the protein
in the gap so that some of its lysine side chains contact the ubiquitin-conjugating
enzyme. The enzyme can then catalyze repeated additions of ubiquitin polypeptide
to these lysines (see Figure 3–71C), producing polyubiquitin chains that mark
the target proteins for rapid destruction in a proteasome.
Figure 3–69 The marking of proteins
by ubiquitin. (A) The three-dimensional
structure of ubiquitin, a small protein of 76
amino acids. A family of special enzymes
couples its carboxyl end to the amino
group of a lysine side chain in a target
protein molecule, forming an isopeptide
bond. (B) Some modification patterns that
have specific meanings to the cell. Note
that the two types of polyubiquitylation
differ in the way the ubiquitin molecules
are linked together. Linkage through
Lys48 signifies degradation by the
proteasome (see Figure 6–84), whereas
that through Lys63 has other meanings.
Ubiquitin markings are “read” by proteins
that specifically recognize each type of
modification.
ubiquitin
E1
SH
E1
ubiquitinactivating
enzyme
(A)
COO –
SH
ATP AMP
+
P P
E1
S C O E1 S C O
binding to
ubiquitinconjugating
enzyme
E2
SH
E2
S C O
ubiquitin-conjugating
enzyme primed with
ubiquitin
ε-amino group
on lysine
side chain
NH 2
NH 2
E2
E2
E3
E3
degradation signal
on target protein
(B)
target protein
bound to
ubiquitin ligase
first ubiquitin
chain added
to target protein
target protein with
polyubiquitin
chain
Figure 3–70 The marking of proteins with ubiquitin. (A) The C-terminus of ubiquitin is initially activated by being linked via a high-energy thioester
bond to a cysteine side chain on the E1 protein. This reaction requires ATP, and it proceeds via a covalent AMP-ubiquitin intermediate. The
activated ubiquitin on E1, also known as the ubiquitin-activating enzyme, is then transferred to the cysteine on an E2 molecule. (B) The addition of
a polyubiquitin chain to a target protein. In a mammalian cell, there are several hundred distinct E2–E3 complexes. The E2s are called ubiquitinconjugating
enzymes. The E3s are referred to as ubiquitin ligases. (Adapted from D.R. Knighton et al., Science 253:407–414, 1991.)
MBoC6 m6.92/3.65