Lecture 7 - Ubiquitin Signalling 1

Question 1

Ubiquitin is covalently attached to [WHAT AMINO ACID] via [WHAT TYPE OF BOND]

Answer 1

Ubiquitin is covalently attached to Lysine via an isopeptide bond

The c-terminal end of Gly76 of Ub binds to the epsilon-amino group of Lysine’s side chain

Question 2

Ubiquitination is a far MORE/LESS complex PTM than phosphorylation

Answer 2

Ubiquitination is a far MORE complex PTM than phosphorylation

Remember: Ub = 76 Amino Acids, far larger and more complex than a phosphate)

Question 3

Isopeptide Bond vs Peptide Bond:

Answer 3

Peptide bond is in the alpha-position (i.e. the main AA chain, not in the side chains)

Isopeptide bond occurs in the side chains of the Amino Acids.

Question 4

Ubiquitin has how many Lysine residues for polyUb modification?
Plus there is one other type of Amino Acid available for polyUb modification, what is it?

Answer 4

7 Lys Residues

Additionally, Met1 can be modified

So 8 types total.

Question 5

Heterotypic polyUb:

Answer 5

Different types of polyUb modifications in the same chain (e.g. Lys63, Lys63, Lys48, Lys48)

Also get Branched Ub Chains, where the Ub modifications branch off into different directions due to different modifcations

Question 6

UBDs:

Answer 6

Ubiquitin Binding Domains:

Recognise Ubiquitin modified proteins, thus affecting downstream signalling

Question 7

DUBs:

Answer 7

Deubiquitinases: Important regulators of the Ubiquitin system involved in deubiquitination

Question 8

Different Ubiquitin linkages have the same cellular functions
TRUE OR FALSE

Answer 8

FALSE
Different Ubiquitin linkages have distinct cellular functions

e.g. Lys6: DNA damage response
Lys48: Proteasomal degradation

Question 9

Surface Hydrophobic Patches on Ubiquitin are recognised by BLANKS

What are the 3 Surface Hydrophobic Patches on Ub?

Answer 9

Surface Hydrophobic Patches on Ubiquitin are recognised by UBDs

Ile44 Patch
Ile36 Patch
Phe4 Patch

Question 10

How do UBDs differentiate between Met1 and Lys63 chains (due to their similarity)?

Answer 10

UBDs associate isopeptides bonds with Lys63 and peptide bonds with Met1

Question 11

Types of E3 ligases:

Answer 11

RING

HECT: Forms E3~thioester intermediate, while RINGs don’t

RBR: Combines properties of HECT and RING, transfers to catalytic Cys residue (causing E3~thioester intermediate formation), has RING1, RING2, and IBR (inbetween RING domains) domains. e.g. PARKIN

Question 12

Cullin RING Ligases (CRLs):

Answer 12

• Cullins are scaffold proteins that provide support for E3 ligases
• Cullins combine with RING E3 ligases to form CRLs
• SCF complex is a CRL comprised of: Skp1 (Adaptor protein), F-box (Binds substrate), RBX1 (RING E3) and Cullin 1