how kinases work

Question 1

describe the general protein kinse structures

Answer 1

has diverse regulatory domains
then a catalytic domain (highly conserved which recognize ATP and target domain)
(regulatory domains in RTKs are the ligand binding and membrane spanning areas)

Question 2

describe how the catalytic domains of kinases are structured

Answer 2

has an n lobe and c lobe connected by a hinge region.

N lobe residues that contact ATP and 2xMg (cofactors):
1. gly-rich G group
2. Hinge reigon
3. the C helix

the C lobe contacts peptide/proteins that are targets for phosphorylation.

In the C lobe the catalytic loop:
terminal phosphate of ATP is held close to the peptide for transfer.

activation loop is part of the catalytic loop and has HRD (His, Arg, Asp) and DFG motifs.

activation loop is where autophosphorylation of the kinase occurs. tyr kinases have a Y residue here and Ser/Thr have S/T residues.

DFG motif (Asp, Phe, Gly) has an in (kinase active) and out (kinase inactive) conformation.

Has a regulatory and Catalytic spine formed of hydrophobic residues.
The c spine is completed when adenine of ATP is bound
The R spine contains the Phe in the DFG motif
C lobe has hydrophobic F helix which supports the spines.

Question 3

describe catalytic domain activation

Answer 3

1. Activation loop auto phosphorylated
2. this assembles the C helix in N lobe
3. ATP binds near C helix which completed the C spine.
4. Phosphate transferred to peptide/protein

Question 4

describe the regulation of activation in the catalytic domain.

Answer 4

Activation regulated by:
1. presence of regulatory regions in kinases where autophosphorylation can activate/inactivate (phospho switches)
2. Binding domains for second messengers (calcium binds to calmodulin, cAMP binds to PKA) or proteins (SH2 binds to src
3. Dimerization
4. Transcription factor activation.