The Ubiquitin Proteosome pathway
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Transcript The Ubiquitin Proteosome pathway
The Ubiquitin Proteosome
Pathway
Swati Pradhan
Mayura Dange
Vidyadhar Daithankar
Overview
Background
Protein misfolding & degradation
Ubiquitin & proteosome structure
Ubiquitin Proteosome Pathway
Mechanism
Structures of enzymes involved in pathway
Pathogenic implication of defective pathway
Biological functions of pathway
Diseases & drug development
The Central Dogma
Translational Folding of a Protein
Chaperone Mediated Protein
Folding & Misfolding
Post-Translational Modification
Acetylation
Glycosylation
Phosphorylation
Ubiquitination
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmdbooks&doptcmdl/Figure+6-79
Degradation of Misfolded Proteins
Lysosomal (extracellular) protein
degradation
– Protein degraded by lysosomal enzymes
Cytosolic (intracellular) protein
degradation
– The Ubiquitin Proteosome pathway
Lysosomal degradation
Proteins delivered
via endocytosis
Lysosomes
– The cellular dustbins
– Contain many
hydrolytic enzymes
Proteases
Lipases
Glycosidases
Cytosolic protein degradation
The Ubiquitin Proteosome Pathway
www.ihf.de/forschung/ popup/ubiquitin.html
2004 Nobel Prize in Chemistry
The discovery of ubiquitin-mediated protein
degradation
– Aaron Ciechanover
– Avram Hershko
– Irwin Rose
Cells give a chemical "kiss of death" to
proteins that need to be destroyed.
Targeting by Ubiquitin
Despite help from chaperones, more than
80% fold incorrectly
Proteins are dislocated back into the cytosol
– Oligosaccharides are removed
– Deglycosylation is catalyzed by N-glycanase
One third of the newly made polypeptide
chains are selected for degradation
The Export of Misfolded Proteins
Ubiquitin
76 amino acids, 8.5 kDa
protein
Heat stable
Folds into a compact
globular structure
Found throughout the cell
Found in all eukaryotic cells
Human and yeast ubiquitin
share 96% sequence
identity
Involved in many cellular
processes
http://www.sanger.ac.uk/Users/sgj/thesis/html/node93.html
The Proteosome
Professional protein
degrading organelles
An abundant ATPdependent protease
Constitutes nearly 1% of
cellular protein
Present in many copies
throughout the cytosol and
the nucleus
Consists of a central hollow
cylinder (20S)
Ends of the cylinder are
associated with the 19S cap
http://walz.med.harvard.edu/Proteasome_Complexes/
The Structure of 20S
Proteasome
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.figgrp.3206
Types of Ubiquitination
Mono-ubiquitination
– Transcription, histone function, endocytosis and membrane trafficking
Lys48, Lys11 or Lys29 linked poly ubiquitination
– Target proteins to the proteasome
Lys63 linked poly ubiquitination
– Signaling, DNA repair, stress response, endocytosis and signal transduction
UBIQUITIN PATHWAY
UBIQUITIN PATHWAY
Covalent Attachment
molecules
of
multiple
ubiquitin
Degradation of the tagged protein
3 Enzymes : Ub – Activating enzyme E1
Ub – Conjugating enzyme E2
Ub – Ligases E3
Hierarchical structure
Several E2 transfer Ub from E1 to E3 to which substrate protein is
bound
E3s catalyze covalent attachment to the substrate and recognize
the substrate
Ubiquitin Pathway
Ubiquitin Activating Enzyme E1
Adenylation
Thio-ester bond formation
E2 association
Mechanism
E1 activates C-terminus of
Ub by forming acyl -adenylate
intermediate
Catalytic Cys residue forms
thioester bond with Ub
Another Ub is adenylated
Transfer of Ub to E2 forming
a thioester bond
Ubiquitin Conjugating enzyme E2
Carries activated Ub from E1 to the
substrate
Cys residue positioned in a shallow groove
Relatively inflexible structure
Conserved Asn may be required for Hbond network OR plays a catalytic role in
isopeptide bond formation
Ub Ligases E3
Final target selection and specificity
Place activated Ub near Lys of substrate
Isopeptide formation of Gly of Ub with the є –NH2 Lys or
to the N-terminal residue of the substrate
Categories of E3 Ligases
HECT domain: Homologous to E6-AP C terminus
RING domain: Really Interesting New Gene
HECT Ub Ligases E3
Conserved 350 amino acids
Catalytic contribution
Forms thiol ester bond with Ub before transferring it to the
substrate
N lobe and C- lobe form ‘L’ or ‘inverted T’ shape
Flexibility of hinge loop is required for catalytic activity
C lobe accepts Ub form E2 and transfers it to the substrate
Sequential addition / Indexation
L – shaped E2/E3 complex
RING Ub Ligases E3
15th most common domain in Human genome
Conserved Cys and His Zn2+ co-ordinating residues
Interact directly with E2s
Allosterically activate E2 enzymes
Acts as molecular scaffold
Brings Ub-E2 and substrate closer
Increase # Lys in the vicinity of E2
Polyubiquitination
Poly Ub chain synthesized by adding Ub moieties to
Lys of the previous Ub
Another enzyme E4 may be catalyzing this step
Deubiquitination
Thiol proteases
Ubiquitin processing (UBP) enzymes
Removes Ub from polyubiquinated proteins
Ubiquitin carboxy terminal hydrolases (UBH)
Regenerates monomeric Ub
Pathological implication of defective
ubiquitin-proteosome pathway
Ubiquitin proteasome pathway is ubiquitous & targets
many processes and substrates.
Several complex processes are mediated via degradation
or processing of specific proteins.
Aberrations in these systems associates with pathogenic
conditions either directly or indirectly.
Biological function of Ubiquitin
Proteosome pathway
Consequences of Defects in
Ubiquitination
Pathological Conditions Associated with
Ubiquitin Proteosome Pathway
– Malignancies
– Neurodegenerative disorders
– Genetic disease
Cystic fibrosis, Angelman’s syndrome & Liddle’s
syndrome
– Immune and inflammatory responses
Malignancies
Oncoproteins like NMyc, c-Myc, c-Fos, are substrates of U-P pathway.
Destabilization of tumor suppressor genes like p53 and p27.
Extremely low levels of p53 in uterine cervical carcinoma.
Prostate, Colorectal and breast cancer:
– Tumor suppressor protein p27 is CDK inhibitor of the cell cycle.
– Healthy individuals have high levels of p27. Mitogenic stimuli
rapidly degrades the protein.
– Cancer patients has low levels of p27 in quiescent cells.
–
Defects in ubiquitin system accelerates degradation of suppressor.
– Strong correlation of low levels of p27 and aggressiveness of cancer.
Skp2
Polyubiquitination
Degradation of P27
Cell Cycle Regulators and Cancer
Defect in ubiquitin
pathway ( Skp2)
Neurodegenerative disorders
Alzheimer's disease
Parkinson's disease
Huntington’s disease
Formation of
inclusion bodies
Spinocerebellar ataxias
Spinobulbar muscular dystrophy (Kennedy’s syndrome)
(Ref: http://w3.dbb.su.se/~oliveberg/images/bildstrat1.jpg)
Accumulation of ubiquitin may be secondary reflecting unsuccessful
attempts of ubiquitination.
Abnormal protein associate with each other forming aggregates.
Hypothesis: Aggregated proteins inhibit ubiquitin proteosome pathway.
Parkinson’s disease and Lewy Bodies
( Ref: http://www.neurodegeneration.uni-goettingen.de/index.html?/en/p311.html)
Liddle’s Syndrome
Hereditary form of hypertension.
Caused due to deletion of proline rich (PY) region in the β and γ subunits of
epithelial Na+ channel (hENaC).
HECT domain of E3 binds to PY motif of hENaC.
Mutation in PY motif leads to stabilization of channel complex and E3 ligase
cannot bind to PY motif.
Increased expression of hENaC channel causing excessive reabsorption of
sodium and water.
Stabilization of channel
Angleman syndrome
Ubiquitin system is considered to be involved in brain development.
Defective synthesis of gene coding for E3 ligase E6-AP
Characteristic symptoms involve mental retardation, seizures, out of
context frequent smiling and laughter.
Brain proteins that could be stabilized by mutation have not been
identified.
Cystic fibrosis
Gene codes for a protein, CFTR, which is chloride ion channel.
Small fraction of protein matures to the cell surface.
Mutation in protein ΔF508, CFTRΔF508 doesn't reach the cell surface.
Ubiquitination degrades mutant CFTRΔF508, resulting in complete
lack of cell surface expression.
Immune and inflammatory responses
Ubiqutin proteosome pathway is involved in processing of antigenic proteins.
Epitopes are presented on class I MHC molecule generating T cell immune
response.
Ubiquitin proteosome
pathway
Native protein
Foreign protein
CLASS I MHC molecule
No immune response
Immune response
Drug Development for Ubiquitin
Dysfunction
Inhibition of enzymes common to entire pathway would target the
process non- specifically.
Narrow window between benefits and toxicity needs to be
identified.
Develop completely specific E3 ligase inhibitors that would affect
the pathways of interests.
Better approach would be development of small molecules that
would be specific for substrates.
Conclusions
Ubiquitylation plays a fundamental role of protein degradation at cellular level.
(Levels of proteins in nucleus, cytoplasm, ER lumen and transmembrane protein are
kept in check by ubiquitin proteosome pathway.)
Ubiquitylation is highly complex, temporally controlled and tightly regulated process.
Enzymologically Ubiquitination is more complex pathway compared to other post
translational modification.
Mechanism of catalysis by E3 ligase still remains unclear.
Elucidation of complete catalytic mechanism of ubiquitylation will provide considerable
insight on cellular functions.
Questions
extra
Extra
www.mekentosj.com/ubiquitin/proteasome.html
Extra (The Central
Dogma)