BIOC 405 Assignment 1: Dr Moore Due Friday March 1st, 2019 before 16:00 in Room 3D30.8 HSc 1. (a)In your handout for protein kinase A, there is a table of known substrate sequences, in other words sequences of peptides phosphorylated by PKA. Please do your best to align the substrate sequences provided, and from the alignment, predict what a good consensus substrate for PKA will be. To present your alignment, please use an equal width font for the protein sequences (Courier or Courier New work well). Highlight the P(0) residue, P(-1) etc. (b)The regulatory subunit (R) of protein kinase A has a short sequence (RRRRGAISA that is critical for inhibiting the activity of the kinase catalytic subunit. This short sequence of the R-subunit actually sits in the active site cleft of PKA in the crystallographically-determined structure of the inhibited RC complex. Can you deduce what the function of this sequence is? Using the answer to part (a) as a guide, please align the inhibitory sequence with the known substrate sequences to deduce how this sequence likely functions to inhibit PKA. Furthermore, using your class notes, can you make a guess at which residues on PKA might interact with specific residues from the R-inhibitory peptide? 2. For a regularly spaced 1-Dimensional array of atoms (spacing =13 Å) calculate the total number of diffraction maxima and their scattering angles (for perfect in phase scattering from the atoms in the 1-D array) between scattering angles of zero and ninety degrees Use a wavelength of d=1.25 Å. Please include a drawing to explain the diffraction condition and show your calculations. 3. Using site specific mutagenesis to change residues in the substrate binding cleft of PKA (not residues involved in catalytic roles), how would you alter PKA’s substrate specificity at P-3, and P-2 to Glu and P+1 to Asn? By this, I mean how would you specifically make mutations in the PKA enzyme amino acid sequence (not the substrate sequence) that would select for binding and phosphorylation of a peptide sequence that would clearly differ from the known substrate sequence preferred by PKA as outlined above. Be sure to clearly highlight exactly what residues in the PKA sequence you would have to change (and to what amino acid) to achieve this. 4. The following lines of data describe the atomic coordinates for an arginine residue in a protein molecule in PDB (protein data bank) format. Since proteins are three-dimensional objects, the position of each atom is specified in space by its X, Y and Z coordinates. On each line of a PDB formatted file, the atom number is given, the atom type is next (e.g. N- backbone nitrogen, backbone carbonyl oxygen etc), the residue name (here ARG 431 in chain D; in this instance the protein crystal contains four independent copies of the polypeptide chain, labelled A through D), then the X-coordinate for that atom, the Y-coordinate for that atom and the Z-coo.

1. BIOC 405 Assignment 1: Dr Moore
Due Friday March 1st, 2019 before 16:00 in Room 3D30.8 HSc
1. (a)In your handout for protein kinase A, there is a table of
known substrate
sequences, in other words sequences of peptides phosphorylated
by PKA. Please do your
best to align the substrate sequences provided, and from the
alignment, predict what a good
consensus substrate for PKA will be. To present your alignment,
please use an equal width
font for the protein sequences (Courier or Courier New work
well). Highlight the P(0)
residue, P(-1) etc.
(b)The regulatory subunit (R) of protein kinase A has a short
sequence
(RRRRGAISA that is critical for inhibiting the activity of the
kinase catalytic subunit. This
short sequence of the R-subunit actually sits in the active site
cleft of PKA in the
crystallographically-determined structure of the inhibited RC
complex. Can you deduce
what the function of this sequence is? Using the answer to part
(a) as a guide, please align
the inhibitory sequence with the known substrate sequences to
deduce how this sequence
likely functions to inhibit PKA. Furthermore, using your class
notes, can you make a guess
at which residues on PKA might interact with specific residues

2. from the R-inhibitory
peptide?
2. For a regularly spaced 1-Dimensional array of atoms (spacing
=13 Å) calculate the
total number of diffraction maxima and their scattering angles
(for perfect in phase
scattering from the atoms in the 1-D array) between scattering
angles of zero and ninety
degrees Use a wavelength of d=1.25 Å. Please include a
drawing to explain the diffraction
condition and show your calculations.
3. Using site specific mutagenesis to change residues in the
substrate binding cleft of
PKA (not residues involved in catalytic roles), how would you
alter PKA’s substrate
specificity at P-3, and P-2 to Glu and P+1 to Asn? By this, I
mean how would you
specifically make mutations in the PKA enzyme amino acid
sequence (not the substrate
sequence) that would select for binding and phosphorylation of
a peptide sequence that
would clearly differ from the known substrate sequence
preferred by PKA as outlined
above. Be sure to clearly highlight exactly what residues in the
PKA sequence you would
have to change (and to what amino acid) to achieve this.
4. The following lines of data describe the atomic coordinates
for an arginine residue in
a protein molecule in PDB (protein data bank) format. Since
proteins are three-dimensional
objects, the position of each atom is specified in space by its X,

3. Y and Z coordinates. On each
line of a PDB formatted file, the atom number is given, the
atom type is next (e.g. N-
backbone nitrogen, backbone carbonyl oxygen etc), the residue
name (here ARG 431 in chain
D; in this instance the protein crystal contains four independent
copies of the polypeptide
chain, labelled A through D), then the X-coordinate for that
atom, the Y-coordinate for that
atom and the Z-coordinate for that atom (given in Ångstroms =
10-10 m), a number called the
occupancy (here 1.0) and another number the B-factor that
describes the average motion of
the atom in the protein structure (units in squared Ångstroms or
Å2).
D21 = {(X2-X1)
2 + (Y2-Y1)
2 + Z2-Z1)
2}1/2
Atom Residue X Y
Z Occ B-factor
ATOM 2114 N ARG D 431 52.470 15.386 15.252 1.00
14.20
ATOM 2115 CA ARG D 431 51.319 16.197 15.632 1.00
15.27
ATOM 2116 CB ARG D 431 50.056 15.350 15.651 1.00
15.67
ATOM 2117 CG ARG D 431 49.597 14.728 14.328 1.00

4. 18.26
ATOM 2118 CD ARG D 431 48.314 13.894 14.514 1.00
21.61
ATOM 2119 NE ARG D 431 47.564 13.503 13.331 1.00
24.52
ATOM 2120 CZ ARG D 431 47.246 14.316 12.351 1.00
25.92
ATOM 2121 NH1 ARG D 431 47.643 15.558 12.409
1.00 27.74
ATOM 2122 NH2 ARG D 431 46.562 13.879 11.299
1.00 26.98
ATOM 2123 C ARG D 431 51.537 16.895 16.989 1.00
15.54
ATOM 2124 O ARG D 431 50.664 17.535 17.502 1.00
15.87
Using the coordinates provided, explicitly draw the structure of
CD, NE, CZ, NH1 and NH2
atoms of the side chain. Then calculate the bond lengths for the
CZ-NH1 and the CZ-NH2
and CZ-NE bonds of the side chain using the given atomic
positions and the provided
distance formula. Then draw the chemical structure (as you
would in organic chemistry
class) of the guanidinium group of the arginine side chain and
draw any allowable resonance
structures if you think any of the bonds are delocalized. Also
show the likely positions of the
hydrogen atoms. Hint, the bond lengths of the C-N bonds
should tell you if resonance is
occurring (a single CN bond is about 1.46 Angstroms in length,
and a double CN bond is
about 1.22 Å in length).
5. Using your knowledge of side chain torsion angles and the

5. results of question 4,
show what are the rotatable bonds for the arginine side chain.
Then please draw carefully
(using a Newman projection as demonstrated in your class
notes) the low-energy
conformations about the Chi2 and Chi4 angles of arginine. Also,
describe the hybridization
of the atoms on either side of the Chi2 and Chi4 bonds. Please
explain your results with
respect to what we covered in class.
1
Protein Kinases
Structure and Regulation:
1) Protein Kinase A (Lehninger Ch 12, pp 423-432)
2) Cyclin dependent Kinase 2 (Ch 12, pp 469-472)
3) Src Protein Kinase (Tyrosine Kinases, p 439-444)
2
Learning Objectives
• Understand Kinase Regulation across family members.

6. • Key Features of Active Site and Substrate Binding.
• Understand the Reaction Mechanism (acid base catalysis)
and structure of the Transition State.
• Know Kinase conserved sequence motifs that define
Structural components of the active site.
• Kinase Autophosphorylation and regulatory consequences.
3
Protein Kinase Families
1) Ser/Thr Kinases
2) Tyrosine Kinases
3) Requirement of effector domains and other
proteins to activate or repress catalytic activity.
4
cAMP Dependent Protein Kinase
Lecture Outline:
• Subunits and regulation of PKA.
• Substrate Specificity and Consensus Sequence
• Designing Sequence Based Inhibitors
• Three dimensional Structure – The Kinase Fold

7. • Substrate Binding Cleft
• Catalytic Mechanism and Sequence Motifs
• Activation/Regulation by Phosphorylation
• Transition State Geometry and Inhibitors
5
Cyclic AMP-Dependent Protein Kinase:
Signaling and Regulation
6
7
PKA (cAMP-dependent Protein Kinase)
Catalytic Domain and Inhibitor
N-domain is Blue (1-126).
C-domain is Orange
(127-159; and 204-322).
Inhibitor Peptide is Red.
Active Site loop and Activation
Segment are (161-202).
Thr197 is Phosphorylated.

8. From PDB coordinates 1APM.
What side chains are shown in
this picture?
8
Protein Kinase A R-subunit Binding
This is rotated ~90 deg ccw from previous
views and also shows binding of R-subunit
9
Active Form of Protein
Kinase A with Inhibitor + ATP
and Mn cations.
N-domain is Blue.
C-domain is Orange.
Inhibitor Peptide is Red.
Active Site loop and Activation
Segment are .
From PDB coordinates 1ATP.
What side chains are shown in
this picture?

9. 10
Closeup View of Activation Segment
and Active Site Loop
The Mn2+ cations
(green) mimic Mg2+.
The inhibitor
peptide has been
removed for clarity.
Can you describle
the roles of the
residues shown in
this figure?
PDB entry: 1ATP
Lys 72
Glu 91
ATP
Lys 168
Asp 166
Arg 165
Thr 201
Phospho-
Thr197

10. Lys 189
Asn 171
Asp 184
Hairpin in middle
of activation loop,
located between N-
and C-domains at
back of molecule.
N-Domain
Activation
Segment
11
Closeup View of Glycine-Rich
Hairpin and ATP
The β-hairpin from
residues 49-57 acts as a
flexible lid that sits over
the ATP phosphate
groups.
GTGSFGRV
The backbone N-H
groups of residues 53, 54
and 55 make N-H ...O

11. hydrogen bonds with
the two terminal
phosphates of ATP.
PDB entry: 1ATP
Flexible hairpin
Glu127
Lys168
Glu91
Phe54
Val57
Asp184
Gly52
Gly55
Gly50 Lys72
12
Mus musculus PKA 12
QESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTG
SFGRVMLVKHKESGNHYAMKILDKQKVVK--- 81
C. elegans PKA 42
AEETHMKLSITPTRESFSLSQLERIITIGKGTFGRVELARDKIT
GAHYALKVLNIRRVVD--- 101
S. cerevisiae PKA 65 EEQYKQFIAQAR---------

12. VTGGKYSLQDFQILRTLGTGSFGRVHLIRSRHNGRYYAMKV
LKKEIVVR--- 125
H. sapiens CDK2 2
ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETE
--- 42
H. sapiens CDK7 10
KRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSE
AKD 53
H. sapiens LCK 258
DEWEVPRETLKLVERLGAGQFGEVWMGY-
YNGHTKVAVKSLKQGSMS---- 303
G. gallus cSRC 258
DAWEIPRESLRLEVKLGQGCFGEVWMGT-
WNGTTRVAIKTLKPGNMS---- 303
* * * * * *
Mus musculus PKA 82
LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY
VAGGEMFSHLRRIGRFSEP 141
C. elegans PKA 102
MRQTQHVHNEKRVLLQLKHPFIVKMYASEKDSNHLYMIME
FVPGGEMFSYLRASRSFSNS 161
S. cerevisiae PKA 126
LKQVEHTNDERLMLSIVTHPFIIRMWGTFQDAQQIFMIMDYI
EGGELFSLLRKSQRFPNP 185
H. sapiens CDK2 43 -
GVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ
DLKKFMDASALTGIPL 100
H. sapiens CDK7 54 -
GINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMET
DLEVIIKDNSLVLTP- 111
H. sapiens LCK 304 ---
PDAFLAEANLMKQLQHQRLVRLYAVVTQ-
EPIYIITEYMENGSLVDFLKTPSGIKLT 359
G. gallus cSRC 304 ---
PEAFLQEAQVMKKLRHEKLVQLYAVVSE-

13. EPIYIVTEYMSKGSLLDFLKGEMGKYLR 359
* *(P-2)
Mus musculus PKA 142 HARFYAAQIVL--
TFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR
TWTLCGT 201
C. elegans PKA 162 MARFYASEIVC--
ALEYIHSLGIVYRDLKPENLMLSKEGHIKMADFGFAKELRD
RTYTICGT 221
S. cerevisiae PKA 186 VAKFYAAEVCL--
ALEYLHSKDIIYRDLKPENILLDKNGHIKITDFGFAKYVPDV
TYTLCGT 245
H. sapiens CDK2 101 -
PLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKL
ADFGLARAFGVPVRTYTHE 162
H. sapiens CDK7 112 -
SHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVL
KLADFGLAKSFGSPNRAYTHQ 172
H. sapiens LCK 360
INKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCK
IADFGLARLIEDNEYTAREG 421
G. gallus cSRC 360
LPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLV
CKVADFGLGRLIEDNEYTARQG 421
** * * *** * **
Mus musculus PKA 202 -----PEYLAPEIILSKGYNK-
AVDWWALGVLIYEMAA-
GYPPFFADQPIQIYEKIVSGKVRFPSHF 261
C. elegans PKA 222 -----PDYLAPESLARTGHNK-
GVDWWALGILIYEMMV-
GKPPFRGKTTSEIYDAIIEHKLKFPRSF 281
S. cerevisiae PKA 246 -----PDYIAPEVVSTKPYNK-
SIDWWSFGILIYEMLA-
GYTPFYDSNTMKTYEKILNAELRFPPFF 306
H. sapiens CDK2 163 --

14. VVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVT-
RRALFPGDSEIDQLFRIFRTLGTPDEVV 226
H. sapiens CDK7 173 --
VVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLL-
RVPFLPGDSDLDQLTRIFETLGTPTEEQ 236
H. sapiens LCK 422 -AKFPIKWTAPEAINY-
GTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGY
RMVRPDN 485
G. gallus cSRC 422 -AKFPIKWTAPEAALY-
GRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVER
GYRMPCPPE 485
* **(P-6) *
P+1 pocket P-2 pocket
N-domain
C-domain Part 1
Catalytic Loop Act. Segment
C-domain Part 2
13
Mechanism of Activation of PKA
Asp166 functions as a general base.
Lys72 binds α and β phosphates of ATP.
Glu91 positions Lys 72 (how?).
Asp184 binds Mg2+

15. Mg2+ binds ATP β and γ PO4 oxygen atoms.
Arg165 and Lys189 bind Thr197-PO4
14
Function Protein Kinase A CDK2 cSRC
Binds ATP αβPO4 Lys 72 Lys 33 Lys 295
Salt Bridge to Lys 72 Glu 91 Glu 51 Glu 310
ATP Ribose H-bond Glu 127 Asp 86 None
General Base Asp 166 Asp 127 Asp 386
Orients Asp 166 Asn 171 Asn 132 Asn 391
Orients Asp 166 Thr 201 Thr 165 None
Binds Thr /Tyr PO4 Arg 165 Arg 126 Arg 385
Binds ATP γPO4 Lys 168 Lys 129 Arg 388
Phosphorylated Thr 197 Thr 160 Tyr 416
Binds Thr/Tyr PO4 Lys 189 Arg 150 Arg 409
Binds Mg2+ Asp 184 Asp 145 Asp 404
Conserved Residues Important for
Protein Kinase Function
15
Inhibitor Binding to Protein Kinase A
Serine-Based Peptide L R R A S L G KM = 16.0
µM

16. Ala-Based Peptide L R R A A L G Ki = 490 µM
PKI(5-24) T T Y A D F I A S G R T G R R N A I H D Ki =
2.3 nM
12 10 9 8 7 6 5 4 3 2 1 0 1 2 3
- +
Helix Turn Extended
Note the conservation of Arg residues at positions P-2, P-3 and
P-6 on the inhibitor peptide.
Arg at P-2 makes a strong salt bridge to Glu170 (plus a weaker
one to Glu230) on the Kinase.
The side chain of Glu170 also H-bonds the backbone NH of the
inhibitor peptide at residue P-2.
Arg at P-3 makes a strong salt bridge to Glu127. Glu127 also H-
bonds to the ATP ribose and is
moderately conserved in Ser/Thr Kinases.
Arg at P-6 makes a salt bridge to Glu203, part of the activation
loop.
16
Substrate Binding Surface in Protein Kinase A
17

17. Mus musculus PKA 12
QESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTG
SFGRVMLVKHKESGNHYAMKILDKQKVVK--- 81
C. elegans PKA 42
AEETHMKLSITPTRESFSLSQLERIITIGKGTFGRVELARDKIT
GAHYALKVLNIRRVVD--- 101
S. cerevisiae PKA 65 EEQYKQFIAQAR---------
VTGGKYSLQDFQILRTLGTGSFGRVHLIRSRHNGRYYAMKV
LKKEIVVR--- 125
H. sapiens CDK2 2
ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETE
--- 42
H. sapiens CDK7 10
KRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSE
AKD 53
H. sapiens LCK 258
DEWEVPRETLKLVERLGAGQFGEVWMGY-
YNGHTKVAVKSLKQGSMS---- 303
G. gallus cSRC 258
DAWEIPRESLRLEVKLGQGCFGEVWMGT-
WNGTTRVAIKTLKPGNMS---- 303
* * * * * *
Mus musculus PKA 82
LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY
VAGGEMFSHLRRIGRFSEP 141
C. elegans PKA 102
MRQTQHVHNEKRVLLQLKHPFIVKMYASEKDSNHLYMIME
FVPGGEMFSYLRASRSFSNS 161
S. cerevisiae PKA 126
LKQVEHTNDERLMLSIVTHPFIIRMWGTFQDAQQIFMIMDYI
EGGELFSLLRKSQRFPNP 185
H. sapiens CDK2 43 -
GVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ
DLKKFMDASALTGIPL 100

18. H. sapiens CDK7 54 -
GINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMET
DLEVIIKDNSLVLTP- 111
H. sapiens LCK 304 ---
PDAFLAEANLMKQLQHQRLVRLYAVVTQ-
EPIYIITEYMENGSLVDFLKTPSGIKLT 359
G. gallus cSRC 304 ---
PEAFLQEAQVMKKLRHEKLVQLYAVVSE-
EPIYIVTEYMSKGSLLDFLKGEMGKYLR 359
* *(P-2)
Mus musculus PKA 142 HARFYAAQIVL--
TFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR
TWTLCGT 201
C. elegans PKA 162 MARFYASEIVC--
ALEYIHSLGIVYRDLKPENLMLSKEGHIKMADFGFAKELRD
RTYTICGT 221
S. cerevisiae PKA 186 VAKFYAAEVCL--
ALEYLHSKDIIYRDLKPENILLDKNGHIKITDFGFAKYVPDV
TYTLCGT 245
H. sapiens CDK2 101 -
PLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKL
ADFGLARAFGVPVRTYTHE 162
H. sapiens CDK7 112 -
SHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVL
KLADFGLAKSFGSPNRAYTHQ 172
H. sapiens LCK 360
INKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCK
IADFGLARLIEDNEYTAREG 421
G. gallus cSRC 360
LPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLV
CKVADFGLGRLIEDNEYTARQG 421
** * * *** * **
P+1 Pocket
Mus musculus PKA 202 -----PEYLAPEIILSKGYNK-

19. AVDWWALGVLIYEMAA-
GYPPFFADQPIQIYEKIVSGKVRFPSHF 261
C. elegans PKA 222 -----PDYLAPESLARTGHNK-
GVDWWALGILIYEMMV-
GKPPFRGKTTSEIYDAIIEHKLKFPRSF 281
S. cerevisiae PKA 246 -----PDYIAPEVVSTKPYNK-
SIDWWSFGILIYEMLA-
GYTPFYDSNTMKTYEKILNAELRFPPFF 306
H. sapiens CDK2 163 --
VVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVT-
RRALFPGDSEIDQLFRIFRTLGTPDEVV 226
H. sapiens CDK7 173 --
VVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLL-
RVPFLPGDSDLDQLTRIFETLGTPTEEQ 236
H. sapiens LCK 422 -AKFPIKWTAPEAINY-
GTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGY
RMVRPDN 485
G. gallus cSRC 422 -AKFPIKWTAPEAALY-
GRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVER
GYRMPCPPE 485
* **(P-6) *
P+1 pocket P-2 pocket
N-domain
C-domain Part 1
Catalytic Loop Act. Segment
C-domain Part 2
18
Representation of Transition State in

20. Phosphoryl Transfer
Here, a phosphate would be undergoing
inversion of configuration, so phosphorous
would be where the carbon is located.
19
Protein Kinase A with Bound AlF3
ADP and Substrate Peptide
AlF3 mimics the transition state,
exactly ½ way along the
“umbrella” flipping pathway of
PO4 group inversion.
(SN2 reaction)