protein domains that interact with receptor tyrosine kinases: structural aspects ming-ming zhou,...
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Protein Domains That Interact with Protein Domains That Interact with Receptor Tyrosine Kinases: Receptor Tyrosine Kinases:
Structural Aspects Structural Aspects
Ming-Ming Zhou, Ph.D.MSSM Department of Pharmacology Course on
“Cell Signaling Systems”January 27, 2005
The Role of Protein Domains in Cell SignalingThe Role of Protein Domains in Cell Signaling
PLCPLC--SosSos RafRaf
PI(3)KPI(3)K MEKMEK
MAPKMAPK
c-fos, c-myc, c-junc-fos, c-myc, c-jun
Grb2Grb2
ShcShc
PP
PTBPTB
SH2SH2
CHCH
PP
PP
PP
PP
PP
PP
RTKRTK
Growth FactorsGrowth Factors
RasRas GDPGDP RasRas
GTPGTP
SH2SH2SH3SH3 SH3SH3
-pY-X-X-hy--pY-X-X-hy-
SH2SH2
-hy-X-N-P-X-(p)Y--hy-X-N-P-X-(p)Y- PhospholipidsPhospholipids
PTBPTB PHPH SH3SH3 WWWW
EHEH 14-3-314-3-3
-N-P-F--N-P-F- -R-S-X-pS-X-P--R-S-X-pS-X-P-
-P-X-X-P-X--P-X-X-P-X- -P-P-X-Y--P-P-X-Y-
PDZPDZ
-E-S/T-D/V--E-S/T-D/V-COOHCOOH--
. . .. . .
Protein Domains in Cell Signal TransductionProtein Domains in Cell Signal Transduction
Human TrkA, pY490 HIIENPQpYFSDA 280 0.053
Mouse Polyoma MT, pY250 SLLSNPTpYSVMRS 320 0.140
Human ErbB3, pY1309 SAFDNPDpYWHSRLF 230 0.020
Human ErbB2, pY1248 AENPEpYLGLDV 1290 N.D.
Human EGFR, pY1086 GSVQNPVpYHNQPLN 220 5.30
Human EGFR, pY1148 SLDNPDpYQQDFF 1000 0.200
Human EGFR, pY1114 TAVGNPEpYLNTVQ 290 0.140
Human EGFR, pY992 VADADEpYLIPQQ 130 680
Human EGFR, pY1173 TAENAEpYLRVA 60 770
Human TCR Chain, pY141 GHDGLpYQGLSTATK 50 >10000
ProteinpTyr Sites
pTyrPeptides
Shc SH2 Shc PTBKd (M) Kd (M)
Ligand Recognition of the Shc PTB and SH2 DomainsLigand Recognition of the Shc PTB and SH2 Domains
Ref: Zhou et al (1995) JBC 270, 31119-31123.
Phosphotyrosine Binding DomainsPhosphotyrosine Binding Domains
Ligand SpecificityLigand Specificity Structural Versatility Structural Versatility Functional DiversityFunctional Diversity
SH2 Domain:
---pYpYxxxx--- PTB Domain:
---xxNPNPxxpYpY---
Q:Q:
3D Structue of the Shc SH2 Domain/TCR Peptide Complex3D Structue of the Shc SH2 Domain/TCR Peptide Complex
TCR chain peptide: GHDGLpYQGLSTATK
BG
BC
A
B
N
C
pYpY+3
EF
D’
EF
CB
D
G
AR B5
BG
N
C
pY
pY+3
F
C
D
G
R B5
R A2
V C3
H D4
L D6
A BG7
L D5
T E4
I BG4
Ref: Zhou et al (1995) PNAS 92, 7784-7788.
BG
A
B
N CD’
EF
C
B
D
G
ApY
pY+3
DE
pYpY+3
BG
DE
EF
D’
pY+3pY
BG
DE
EF
D’
pYpY+3
BG
DEE
F D’
Shc Lck
SypPLC-1
Structures of SH2 DomainsStructures of SH2 Domains
Shc
Lck
Syp
PLC-1
Structures of SH2 DomainsStructures of SH2 Domains
3D NMR Structure of the Shc PTB Domain/TrkA Complex3D NMR Structure of the Shc PTB Domain/TrkA Complex
Ref: Zhou et al (1995) Nature 378, 584-592.
XNPXpY Recognition by the Shc PTB DomainXNPXpY Recognition by the Shc PTB Domain
PTB Domain PTB Domain versusversus SH2 Domain SH2 Domain
Shc PTB Domain Shc PTB Domain Shc SH2 DomainShc SH2 Domain
Biological Ligands of PTB DomainsBiological Ligands of PTB Domains
PTB DomainPTB Domain Binding PartnersBinding Partners Binding Sites Binding Sites
ShcShc hTrkA, pY490hTrkA, pY490 HIHIIIEENPNPQQpYpYFSDAFSDAmPolyoma MT, pY250mPolyoma MT, pY250 SLSLLLSSNPNPTTpYpYSVMRSSVMRShErbB3, pY1309hErbB3, pY1309 SASAFFDDNPNPDDpYpYWHSRLWHSRLhEGFR, pY1148hEGFR, pY1148 ISISLLDDNPNPDDpYpYQQDFFQQDFF
IRS-1IRS-1 hIR, pY960hIR, pY960 LYALYASSSSNPNPEEpYpYLSASLSAShIL-4R, pY497hIL-4R, pY497 LVILVIAGAGNPNPAApYpYRSFSRSFShIGFIR, pY950hIGFIR, pY950 LYALYASVSVNPNPEEpYpYFSASFSAS
NumbNumb LNXLNX GGLLDDNPNPAAYYTSSV TSSV NAKNAK GGFFSSNMNMSSFFEDFP EDFP Peptide LibraryPeptide Library YIGPYIGPYYLL
X11, Fe65, Ced-6X11, Fe65, Ced-6 APPAPP GGYYEENPNPTTYYKKFFFFEE
3D Structure of the IRS-1 PTB Domain/IL-4R Complex3D Structure of the IRS-1 PTB Domain/IL-4R Complex
Ref: Zhou et al (1996) Nature Structural Biology 3, 388-393.
Ligand Recognition of the IRS-1 PTB domainLigand Recognition of the IRS-1 PTB domain
Distinct Mechanisms for NPXpY RecognitionDistinct Mechanisms for NPXpY Recognition
IRS-1 PTB Domain IRS-1 PTB Domain Shc PTB Domain Shc PTB Domain
PTB & PH Domains: A Conserved Structural FoldPTB & PH Domains: A Conserved Structural Fold
AA BB
CC DD
FGFRsFGFRs (juxtamembrane region):(juxtamembrane region):
KSDFH SQMAV HKLAK SIPLR RQVTSKSDFH SQMAV HKLAK SIPLR RQVTS
NGFRsNGFRs::•TrkA,TrkA,pY960pY960 HIIEHIIENPNPQQpYpYFSDAFSDA•TrkBTrkB PVIEPVIENPNPQQpYpYFGITFGIT•TrkCTrkC PVIEPVIENPNPQQpYpYFRQGFRQG
RETRET, pY1062pY1062
TWIETWIENNKLKLpYpYGRISGRIS
SNT/FRS2 Binding Sites in Neurotrophic ReceptorsSNT/FRS2 Binding Sites in Neurotrophic Receptors
11
33
4455
66
77
FGFRFGFR
CC
NN
NN
CC
22
11
88
’’
113344
5566
77
FGFRFGFR
CC
NN
NN
CC
22
11
88 ’’
3D Structure of the SNT-1 PTB Domain/FGFR1 3D Structure of the SNT-1 PTB Domain/FGFR1 ComplexComplex
Ref: Dhalluin et al (2000) Molecular Cell 6, 921-929.
SNT-1 SNT-1 versusversus IRS-1 PTB domains IRS-1 PTB domains
R78
FGFR
11
33
4488
55
6677
C
N
22
11
R63
’’
N
C
R212
IL-4R
11
33
44
55
6677
C
N
22
11
R227
N
C
pY-3
pY-6
pY-8
pY
A
B
SNT-1SNT-1
IRS-1IRS-1
Sequence Alignment of the SNT & IRS PTB DomainsSequence Alignment of the SNT & IRS PTB Domains
R78R78
11
33
44
88
5566
77
FGFRFGFR
CC NN NN
CC
22
11
R63R63
’’
Vec
tor
Vec
tor
SN
T-1
PT
B
SN
T-1
PT
B
D
om
ain
Do
mai
n S
NT
-1 P
TB
S
NT
-1 P
TB
D
om
ain
D
om
ain
88
HisHis--, Leu, Leu--, Trp, Trp--LeuLeu--, Trp, Trp--HisHis--, Leu, Leu--, Trp, Trp--LeuLeu--, Trp, Trp--HisHis--, Leu, Leu--, Trp, Trp--LeuLeu--, Trp, Trp--
TRKBTRKBhFGFR1hFGFR1VectorVector
SNT-1 Truncation Effect on FGFR & TRK BindingSNT-1 Truncation Effect on FGFR & TRK Binding
w/FGFRw/FGFR
Yeast Two-Hybrid Binding AssayYeast Two-Hybrid Binding Assay
11
33
44
5566
77 NN
22
11
pYpY
pY-5pY-5
R78R78
R63R63
TrkBTrkB
CC
CC
w/TrkBw/TrkB
Unifying Features of PTB DomainsUnifying Features of PTB Domains
Ref: Yan & Zhou (2002) FEBS Lett. 513, 67-70.
Structure & Function of the SH3 DomainStructure & Function of the SH3 Domain
Ref: Zarrinpar (2003) Sci. STKE 2003(179), re8
CCAA
BB
RTKs: Activation by Receptor Dimerization
Ref: Hubbard, et al (1998) JBC 273, 11987-11990.
Autoinhibition of Insulin and FGF ReceptorsAutoinhibition of Insulin and FGF Receptors
IRKIRK FGFR1KFGFR1K
Unphosphorylated IRK (IRK0P)Unphosphorylated IRK (IRK0P)
Tris-phosphorylated IRK (IRK3P)Tris-phosphorylated IRK (IRK3P)
Unphosphorylated FGFR1KUnphosphorylated FGFR1K
Tris-phosphorylated IRK (IRK3P)Tris-phosphorylated IRK (IRK3P)
- Cis-inhibition & Trans-activation- Cis-inhibition & Trans-activation
AutoRegulation & Activation of AutoRegulation & Activation of SrcSrc Tyrosine Kinase Tyrosine Kinase
3D Structure of Protein Tyrosine Kinase 3D Structure of Protein Tyrosine Kinase HckHck
Ref: Xu, et al (1997) Nature 385, 595-602; Sicheri, et al (1997) Nature 385, 602-609.
Rational Design of Nonpeptide Inhibitors of Rational Design of Nonpeptide Inhibitors of SrcSrc SH2 Domain SH2 Domain
Ref: Sundaramoorthi et al (2003) Biopolymers 71, 717-729.
3D Structure of the Abl Kinase Domain/Drug Complex3D Structure of the Abl Kinase Domain/Drug Complex
Ref: Daub, H. et al (2004) Nature Review Drug Discovery 3, 1001-1010.
Summary
Structure-Function of Protein Domains in RTKs
Conserved 3D structural fold with divergent sequences
Conserved structural fold with different functions
Single protein domain with multiple functions
Cooperative regulation of RTK activity in cell signaling