Tyrosine Protein
Kinase ABL1
Mira Patel
H Molecular Human Anatomy
Kinases


Attach a phosphate group to an amino acid residue of a protein
Result is usually a conformational change that activates the
substrate protein

Activation allows proteins to take part in chemical reactions

Over 500 different types of kinases

Function is shared, so it can safely be assumed that structure
will also be highly conserved
c-abl Protein

Named as a homolog of the v-abl oncogene, found in the Abelson
murine leukemia virus

Human c-abl tyrosine kinase is a product of the Abelson (abl) gene,
located on the 9th chromosome

Non-receptor tyrosine kinase

Transfers a phosphate group from ATP to a tyrosine residue in a
protein

Located in both cell cytoplasm and the nucleus

Functions are altered depending on its location in the cell

protein is thought to move from one location to the other,
depending on which of its functions are needed in the cell
N lobe
SH3 domain
SH3-SH2 linker
SH2-kinase linker
Kinase Domain
SH2 domain
Myristoyl group
C lobe
ribbon view of abl tyrosine kinase (PDB 1opk X-RAY)
Structure: N-terminal half

N terminal cap
~80 amino acid residues

Src Homology 2 (SH2) domain
~100 amino acid residues

Src Homology 3 (SH3) domain
~50 amino acid residues

Kinase domain
encloses the ATP-binding site
ATP Binding
Pocket of
Kinase Domain
Kinase domain
of c-abl
(PDB 2v7a X-Ray)
Phosphate Binding Loop
Activation Loop
Phosphate Binding Loop
Activation Loop
ribbon and surface views of hydrophobic ATP-binding cleft (PDB 1opk X-RAY)
Structure: C-terminal half

Binding elements for the SH3 domain

Three nuclear localization signals

Export signal

DNA binding domain

Actin-binding domain
Cellular Function: Cytoplasm



cytoskeleton remodeling
actin binding domain
suggests that c-abl can
anchor actin filaments
a similar domain is seen in
proteins with cytoskeletal
associations
N terminus
C terminus
f-actin binding domain of c-abl
(PBD 1zzp NMR)
Cellular Function: Nucleus





Cell is exposed to ionizing radiation
c-abl phosphorylates p73 on Y99 
Activation of p73
Induction of p21 gene
p21 inhibits Cdk kinase activity

Conclusion: c-abl can be involved in G1/S
checkpoint, in a pathway independent of p53
ABL 1a




and
1b
Two variants of the abl protein—abl 1a and abl
1b
Only difference is that form 1b has a posttranslational modification that form 1a lacks
abl 1b is myristoylated
For reasons that are not known, abl 1b is found
in larger amounts in cells than abl 1a
Abl and Src Kinases



Many structural similarities between abl and src
family kinases
N-terminal half, minus the cap, is almost identical to
an Src family kinase protein
However, abl kinases differ in their C-terminal half,
the domains of which are absent in Src family
proteins
Ribbon view of c-abl , c-src overlap
N lobe
SH3 domain
Human tyrosine
kinase c-abl
(PDB 1opk X-RAY)
Kinase Domain
Human tyrosine
kinase c-src
(PDB 2src X-RAY)
SH2-kinase linker
SH3-SH2 linker
SH2 domain
Y527
C lobe
http://jkweb.berkeley.edu/external/pdb/2003/hlabl/C0301076_Nagar_etal_fig2.jpg
ClustalW between c-abl and c-src kinases
(SH2, SH3, and kinase domains)
_c-abl_
_c-src_
MGQQPGK-VLGDQRRPSLPALHFIKGAG----KKESSRHGGPHCNVFVEHEALQRPVASD
MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAE
**.: .*
..*** ** . . ::***
..:
. .: .
.*
*.*::
_c-abl_
_c-src_
FEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHN
PKLFGGFNSSDTVTSP-QRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEG
: * :::
:.
*** .. . ******: : :. **:.***:*:::. ...
_c-abl_
_c-src_
GEWCEAQTKNGQ-GWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGIN--GSFLVRE
DWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRE
. *
. ..** *::****::* :*:: ..**.* ::*. :* ** .. * *:*****
_c-abl_
_c-src_
SESSPGQRSISLRYEG-----RVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADG
SETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADG
**:: * .:*:
.
.* **:*.. ..* :*::*.::**:* :** ::*. ***
_c-abl_
_c-src_
LITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTV
LCHRLTTVCP-TSKPQTQGLAK--DAWEIPRESLRLEVKLGQGCFGEVWMGTWNG-TTRV
*
*
.* .** . *::
* **: * .: :: *** * :***: *.*: : *
_c-abl_
_c-src_
AVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLR
AIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEP-IYIVTEYMSKGSLLDFLK
*:**** .**. * **:** ***:::* :**** .* :.** :**:**:*: *.***:*:
_c-abl_
_c-src_
ECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLM
GETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLI
. : :.
*: **:**:*.* *:*: *::**** * * ***** : *******:**:
_c-abl_
_c-src_
TGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQV
EDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREV
.: ***: ************: *.:*:******:**:** *::* * ****:
:*
_c-abl_
_c-src_
YELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAF
LDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFL
: :*:.*** * ***.:::** **: :*.:**:* :: :
* sequence identity
: strong conservation
. weaker conservation
35.93% identity
http://align.genome.jp/sit-bin/clustalw
Regulation and Activity



Pathways used to regulate abl activity are not clear
Key structural differences between abl and src kinases lead to
different regulatory mechanisms for the two proteins
 Activation of src kinase controlled by phosphotyrosine
residue, Y527
 This residue is absent in abl kinase
Both kinases exist in an autoinhibited form
 Kinase domains are controlled negatively by other domains
on the protein

Mutations in or deletion of SH3 domain result in an active abl
kinase that cannot otherwise be inactivated

This suggests that the SH3 domain regulates the activity of the
kinase domain in c-abl
c-abl Proto-oncogene

Translocation, t(9;22)(q34;q11), between abl (Abelson) and bcr
(breakpoint cluster region) genes results in Philadelphia chromosome

Fusion bcr/abl gene encodes altered kinase (bcr/abl kinase) that allows
cell proliferation without regulation

Philadelphia chromosome is directly responsible for chronic myeloid
leukemia (CML), although individuals with acute myeloid leukemia (AML)
or acute lymphoblastic leukemia (ALL) can also have this chromosome
Chronic Myelogenous Leukemia



Unnecessary and dangerous increase in the
production of immature granulocytes
Blood tissue becomes so packed with nonfunctional white blood cells that healthy
blood cells can no longer be produced
Leads to anemia, a dysfunctional immune
system, and dangerous infections
CML Treatment



Kinase inhibitors designed bind to hydrophobic ATP-binding
pocket of kinase
 ATP cleft is small and requires a small inhibitor molecule
FDA approved kinase inhibitors to fight CML:
 Imatinib, marketed as Gleevec in 2001 by Novartis
Pharmaceuticals Corporation
 Dasatinib, marketed as Sprycel in 2006 by Bristol-Myers
Squibb Company
 Nilotinib, marketed as Tasigna in 2007 by Novartis
Pharmaceuticals Corporation
Patients diagnosed with CML must immediately begin taking
kinase inhibitors in addition to chemotherapy treatment
1st generation inhibitor
Gleevec
Binds to only inactive conformations of bcr/abl
Many mutation sites cause resistance
A surface view of Gleevec in the
hydrophobic ATP-binding pocket
of the abl kinase domain
(PDB 2hyy X-RAY)
2nd generation inhibitor
Sprycel
Binds to both active and inactive
conformations of bcr/abl
Overcomes many imatinib mutation sites
A surface view of Sprycel in the
hydrophobic ATP-binding pocket
of the abl kinase domain
(PDB 2gqg X-RAY)
Gleevec: Mutation Sites
Gleevec in the hydrophobic ATP-binding pocket of the
abl kinase domain (PDB 1iep X-RAY)
F317L
Q252H/R
Y253F/H
E255K
L387M
T315I
V379I
M351T
M244V
Sprycel: Mutation Sites
Sprycel in the hydrophobic ATP-binding pocket of
the abl kinase domain (PDB 2gqg X-RAY)
F317L
T315I
T315I
GLEEVEC
F317L
SPRYCEL
Activation Loop
Phosphate Binding Loop
Overlap of Gleevec and Sprycel in the
hydrophobic ATP-binding pocket of the abl kinase
domain (PDB 1iep X-RAY, 2gqg X-RAY)
Drug Resistance
• Mutation in T315, the “gatekeeper residue,” leads to
resistance to Gleevec, Sprycel, and Tasigna
• To combat this problem, another class of inhibitors must
be used
• SGX Pharmaceuticals is currently working with Novartis
to produce a generation of abl-bcr kinase inhibitors that
can overcome T315 mutation
• Testing of this new drug, SGX393, is expected to be
complete by June 2008, after which the developers may
seek FDA approval for the drug
T315I Mutation
T315
I315
H Bonds
GLEEVEC
GLEEVEC
SPRYCEL
SPRYCEL
(c-abl in complex with imatinib PDB 1iep X-RAY)
(c-abl in complex with dasatinib PDB 2gqg X-RAY)
(mutated c-abl kinase domain PDB 2v7a X-Ray)
Conclusion

Understanding structure of a protein
can lead to structure-based drug
designs, which have proven to be very
effective

Individuals afflicted with cancer are
able to live normal and productive lives
References
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Nagar, et al. Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-486WNCND&_user=526750&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000023759&
_version=1&_urlVersion=0&_userid=526750&md5=3c430835fc17373b68b770c1da093d1f
Shaul, Y. c-Abl: activation and nuclear targets.
http://www.nature.com/cdd/journal/v7/n1/full/4400626a.html
Pendergast, Anne Marie. Nuclear tyrosine kinases: from Abl to WEE1.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRW-4547875C7&_user=6824479&_coverDate=04%2F30%2F1996&_rdoc=1&_fmt=summary&_orig=ar
ticle&_cdi=6245&_sort=v&_docanchor=&view=c&_ct=29845&_acct=C000023759&_versio
n=1&_urlVersion=0&_userid=6824479&md5=4feed9094a9b76b1ac3d8372c4e9c766
Hantschel, et al. Structural Basis for the Cytoskeletal Association of Bcr-Abl/c-Abl.
http://www.cemm.oeaw.ac.at/downloads/MolecularCell19p461to473.pdf
Shah, et al. Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the
tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid
leukemia. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WWK-46KR83D7&_user=6824479&_origUdi=B6WWK-4D4KPHG4&_fmt=high&_coverDate=08%2F31%2F2002&_rdoc=1&_orig=article&_acct=C00002375
9&_version=1&_urlVersion=0&_userid=6824479&md5=72adfb4aa21d767908ef62e79d2ac
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