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Signal transduction protein PDB id
1btn
Jmol
Contents
Protein chain
106 a.a. *
Ligands
I3P
Waters ×77
* Residue conservation analysis
PDB id:
1btn
Name: Signal transduction protein
Title: Structure of the binding site for inositol phosphates in a ph domain
Structure: Beta-spectrin. Chain: a. Fragment: ph domain, residues 2199 - 2304. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organ: brain. Gene: musspna.Gbrod. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.205     R-free:   0.286
Authors: M.Wilmanns,M.Hyvoenen,M.Saraste
Key ref: M.Hyvönen et al. (1995). Structure of the binding site for inositol phosphates in a PH domain. Embo J, 14, 4676-4685. PubMed id: 7588597 Ref: Full text
Date:
23-Aug-95     Release date:   08-Mar-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q62261  (SPTB2_MOUSE) -  Spectrin beta chain, brain 1
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2363 a.a.
106 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Full text Embo J 14:4676-4685 (1995)
PubMed id: 7588597  
 
 
Structure of the binding site for inositol phosphates in a PH domain.
M.Hyvönen, M.J.Macias, M.Nilges, H.Oschkinat, M.Saraste, M.Wilmanns.
 
  ABSTRACT  
 
Phosphatidylinositol bisphosphate has been found to bind specifically to pleckstrin homology (PH) domains that are commonly present in signalling proteins but also found in cytoskeleton. We have studied the complexes of the beta-spectrin PH domain and soluble inositol phosphates using both circular dichroism and nuclear magnetic resonance spectroscopy, and X-ray crystallography. The specific binding site is located in the centre of a positively charged surface patch of the domain. The presence of 4,5-bisphosphate group on the inositol ring is critical for binding. In the crystal structure that has been determined at 2.0 A resolution, inositol-1,4,5-trisphosphate is bound with salt bridges and hydrogen bonds through these phosphate groups whereas the 1-phosphate group is mostly solvent-exposed and the inositol ring has virtually no interactions with the protein. We propose a model in which PH domains are involved in reversible anchoring of proteins to membranes via their specific binding to phosphoinositides. They could also participate in a response to a second messenger such as inositol trisphosphate, organizing cross-roads in cellular signalling.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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A Polymorphic Variant of AFAP-110 Enhances cSrc Activity.
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PDB code: 3a58
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PDB codes: 3a8n 3a8p 3a8q
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Solution solution: using NMR models for molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 57, 1457-1461.  
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  Biochim Biophys Acta, 1483, 199-216.  
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Signaling and subcellular targeting by membrane-binding domains.
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PDB codes: 1gc6 1gc7
10847681 M.A.Pearson, D.Reczek, A.Bretscher, and P.A.Karplus (2000).
Structure of the ERM protein moesin reveals the FERM domain fold masked by an extended actin binding tail domain.
  Cell, 101, 259-270.
PDB code: 1ef1
  11080629 N.Blomberg, E.Baraldi, M.Sattler, M.Saraste, and M.Nilges (2000).
Structure of a PH domain from the C. elegans muscle protein UNC-89 suggests a novel function.
  Structure, 8, 1079-1087.
PDB code: 1fho
10801429 T.Nebl, S.W.Oh, and E.J.Luna (2000).
Membrane cytoskeleton: PIP(2) pulls the strings.
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Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures.
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Pleckstrin induces cytoskeletal reorganization via a Rac-dependent pathway.
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Brain and muscle express a unique alternative transcript of alphaII spectrin.
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A conserved inositol phospholipid binding site within the pleckstrin homology domain of the Gab1 docking protein is required for epithelial morphogenesis.
  J Biol Chem, 274, 31719-31726.  
  10022866 C.R.Maroun, M.Holgado-Madruga, I.Royal, M.A.Naujokas, T.M.Fournier, A.J.Wong, and M.Park (1999).
The Gab1 PH domain is required for localization of Gab1 at sites of cell-cell contact and epithelial morphogenesis downstream from the met receptor tyrosine kinase.
  Mol Cell Biol, 19, 1784-1799.  
  10396143 G.M.Benian, A.Ayme-Southgate, and T.L.Tinley (1999).
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  Rev Physiol Biochem Pharmacol, 138, 235-268.  
10371466 H.LeVine (1999).
Structural features of heterotrimeric G-protein-coupled receptors and their modulatory proteins.
  Mol Neurobiol, 19, 111-149.  
  10454216 I.Galetic, M.Andjelkovic, R.Meier, D.Brodbeck, J.Park, and B.A.Hemmings (1999).
Mechanism of protein kinase B activation by insulin/insulin-like growth factor-1 revealed by specific inhibitors of phosphoinositide 3-kinase--significance for diabetes and cancer.
  Pharmacol Ther, 82, 409-425.  
10607674 J.D.Forman-Kay, and T.Pawson (1999).
Diversity in protein recognition by PTB domains.
  Curr Opin Struct Biol, 9, 690-695.  
10585959 J.Dai, and M.P.Sheetz (1999).
Membrane tether formation from blebbing cells.
  Biophys J, 77, 3363-3370.  
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Activation of phospholipase C delta1 through C2 domain by a Ca(2+)-enzyme-phosphatidylserine ternary complex.
  J Biol Chem, 274, 21995-22001.  
10391917 L.Yao, P.Janmey, L.G.Frigeri, W.Han, J.Fujita, Y.Kawakami, J.R.Apgar, and T.Kawakami (1999).
Pleckstrin homology domains interact with filamentous actin.
  J Biol Chem, 274, 19752-19761.  
10419454 M.H.Hu, E.M.Bauman, R.L.Roll, N.Yeilding, and C.S.Abrams (1999).
Pleckstrin 2, a widely expressed paralog of pleckstrin involved in actin rearrangement.
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The PH superfold: a structural scaffold for multiple functions.
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10089391 S.Gourinath, A.Srinivasan, and T.P.Singh (1999).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.9 A resolution.
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PDB code: 1jfo
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The Vav-Rac1 pathway in cytotoxic lymphocytes regulates the generation of cell-mediated killing.
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The solution structure and dynamics of the pleckstrin homology domain of G protein-coupled receptor kinase 2 (beta-adrenergic receptor kinase 1). A binding partner of Gbetagamma subunits.
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PDB code: 1bak
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Replacements of single basic amino acids in the pleckstrin homology domain of phospholipase C-delta1 alter the ligand binding, phospholipase activity, and interaction with the plasma membrane.
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G protein-coupled receptor kinases.
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Specificity and promiscuity in phosphoinositide binding by pleckstrin homology domains.
  J Biol Chem, 273, 30497-30508.  
9712908 J.M.Stevenson, I.Y.Perera, and W.F.Boss (1998).
A phosphatidylinositol 4-kinase pleckstrin homology domain that binds phosphatidylinositol 4-monophosphate.
  J Biol Chem, 273, 22761-22767.  
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Specific binding of phosphatidylinositol 4,5-bisphosphate to calcium-dependent activator protein for secretion (CAPS), a potential phosphoinositide effector protein for regulated exocytosis.
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9581500 M.Chabre, B.Antonny, and S.Paris (1998).
PIP2: activator ... or terminator of small G proteins?
  Trends Biochem Sci, 23, 98.  
9430633 M.Falasca, S.K.Logan, V.P.Lehto, G.Baccante, M.A.Lemmon, and J.Schlessinger (1998).
Activation of phospholipase C gamma by PI 3-kinase-induced PH domain-mediated membrane targeting.
  EMBO J, 17, 414-422.  
9838094 M.J.Bottomley, K.Salim, and G.Panayotou (1998).
Phospholipid-binding protein domains.
  Biochim Biophys Acta, 1436, 165-183.  
9646876 M.J.Rebecchi, and S.Scarlata (1998).
Pleckstrin homology domains: a common fold with diverse functions.
  Annu Rev Biophys Biomol Struct, 27, 503-528.  
9442060 M.Mosior, D.A.Six, and E.A.Dennis (1998).
Group IV cytosolic phospholipase A2 binds with high affinity and specificity to phosphatidylinositol 4,5-bisphosphate resulting in dramatic increases in activity.
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9825957 M.Steel, J.Moss, K.A.Clark, I.R.Kearns, C.H.Davies, R.G.Morris, W.C.Skarnes, and R.Lathe (1998).
Gene-trapping to identify and analyze genes expressed in the mouse hippocampus.
  Hippocampus, 8, 444-457.  
9665728 R.P.Johnson, V.Niggli, P.Durrer, and S.W.Craig (1998).
A conserved motif in the tail domain of vinculin mediates association with and insertion into acidic phospholipid bilayers.
  Biochemistry, 37, 10211-10222.  
9552154 S.Alberti (1998).
A phosphoinositide-binding sequence is shared by PH domain target molecules--a model for the binding of PH domains to proteins.
  Proteins, 31, 1-9.  
9736615 S.J.Isakoff, T.Cardozo, J.Andreev, Z.Li, K.M.Ferguson, R.Abagyan, M.A.Lemmon, A.Aronheim, and E.Y.Skolnik (1998).
Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast.
  EMBO J, 17, 5374-5387.  
9891784 T.F.Martin (1998).
Phosphoinositide lipids as signaling molecules: common themes for signal transduction, cytoskeletal regulation, and membrane trafficking.
  Annu Rev Cell Dev Biol, 14, 231-264.  
9417097 T.Iglesias, and E.Rozengurt (1998).
Protein kinase D activation by mutations within its pleckstrin homology domain.
  J Biol Chem, 273, 410-416.  
9651677 T.P.Levine, and S.Munro (1998).
The pleckstrin homology domain of oxysterol-binding protein recognises a determinant specific to Golgi membranes.
  Curr Biol, 8, 729-739.  
9614087 W.Nagel, L.Zeitlmann, P.Schilcher, C.Geiger, J.Kolanus, and W.Kolanus (1998).
Phosphoinositide 3-OH kinase activates the beta2 integrin adhesion pathway and induces membrane recruitment of cytohesin-1.
  J Biol Chem, 273, 14853-14861.  
  9693361 W.Nagel, P.Schilcher, L.Zeitlmann, and W.Kolanus (1998).
The PH domain and the polybasic c domain of cytohesin-1 cooperate specifically in plasma membrane association and cellular function.
  Mol Biol Cell, 9, 1981-1994.  
9060471 A.D.Ma, L.F.Brass, and C.S.Abrams (1997).
Pleckstrin associates with plasma membranes and induces the formation of membrane projections: requirements for phosphorylation and the NH2-terminal PH domain.
  J Cell Biol, 136, 1071-1079.  
9034331 A.Lambrechts, J.L.Verschelde, V.Jonckheere, M.Goethals, J.Vandekerckhove, and C.Ampe (1997).
The mammalian profilin isoforms display complementary affinities for PIP2 and proline-rich sequences.
  EMBO J, 16, 484-494.  
  9260159 B.K.Saha, S.K.Curtis, L.B.Vogler, and M.Vihinen (1997).
Molecular and structural characterization of five novel mutations in the Bruton's tyrosine kinase gene from patients with X-linked agammaglobulinemia.
  Mol Med, 3, 477-485.  
9130701 C.R.Artalejo, M.A.Lemmon, J.Schlessinger, and H.C.Palfrey (1997).
Specific role for the PH domain of dynamin-1 in the regulation of rapid endocytosis in adrenal chromaffin cells.
  EMBO J, 16, 1565-1574.  
9188725 E.Tall, G.Dormán, P.Garcia, L.Runnels, S.Shah, J.Chen, A.Profit, Q.M.Gu, A.Chaudhary, G.D.Prestwich, and M.J.Rebecchi (1997).
Phosphoinositide binding specificity among phospholipase C isozymes as determined by photo-cross-linking to novel substrate and product analogs.
  Biochemistry, 36, 7239-7248.  
9066302 G.D.Prestwich, G.Dormán, J.T.Elliott, D.M.Marecak, and A.Chaudhary (1997).
Benzophenone photoprobes for phosphoinositides, peptides and drugs.
  Photochem Photobiol, 65, 222-234.  
  9372970 J.N.Davis, C.O.Rock, M.Cheng, J.B.Watson, R.A.Ashmun, H.Kirk, R.J.Kay, and M.F.Roussel (1997).
Complementation of growth factor receptor-dependent mitogenic signaling by a truncated type I phosphatidylinositol 4-phosphate 5-kinase.
  Mol Cell Biol, 17, 7398-7406.  
9297972 J.Pascual, J.Castresana, and M.Saraste (1997).
Evolution of the spectrin repeat.
  Bioessays, 19, 811-817.  
9374522 J.Zheng, R.H.Chen, S.Corblan-Garcia, S.M.Cahill, D.Bar-Sagi, and D.Cowburn (1997).
The solution structure of the pleckstrin homology domain of human SOS1. A possible structural role for the sequential association of diffuse B cell lymphoma and pleckstrin homology domains.
  J Biol Chem, 272, 30340-30344.
PDB code: 1awe
9164454 K.Djinovic Carugo, S.Bañuelos, and M.Saraste (1997).
Crystal structure of a calponin homology domain.
  Nat Struct Biol, 4, 175-179.
PDB code: 1aa2
  9271429 K.S.Ravichandran, M.M.Zhou, J.C.Pratt, J.E.Harlan, S.F.Walk, S.W.Fesik, and S.J.Burakoff (1997).
Evidence for a requirement for both phospholipid and phosphotyrosine binding via the Shc phosphotyrosine-binding domain in vivo.
  Mol Cell Biol, 17, 5540-5549.  
9268346 L.E.Rameh, A.Arvidsson, K.L.Carraway, A.D.Couvillon, G.Rathbun, A.Crompton, B.VanRenterghem, M.P.Czech, K.S.Ravichandran, S.J.Burakoff, D.S.Wang, C.S.Chen, and L.C.Cantley (1997).
A comparative analysis of the phosphoinositide binding specificity of pleckstrin homology domains.
  J Biol Chem, 272, 22059-22066.  
  17708952 L.M A, F.M, S.J, and F.K (1997).
Regulatory recruitment of signalling molecules to the cell membrane by pleckstrinhomology domains.
  Trends Cell Biol, 7, 237-242.  
9148913 L.Yao, H.Suzuki, K.Ozawa, J.Deng, C.Lehel, H.Fukamachi, W.B.Anderson, Y.Kawakami, and T.Kawakami (1997).
Interactions between protein kinase C and pleckstrin homology domains. Inhibition by phosphatidylinositol 4,5-bisphosphate and phorbol 12-myristate 13-acetate.
  J Biol Chem, 272, 13033-13039.  
9218782 M.Hyvönen, and M.Saraste (1997).
Structure of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia.
  EMBO J, 16, 3396-3404.
PDB code: 1btk
9016530 M.Vihinen, B.H.Belohradsky, R.N.Haire, E.Holinski-Feder, S.P.Kwan, I.Lappalainen, H.Lehväslaiho, T.Lester, A.Meindl, H.D.Ochs, J.Ollila, I.Vorechovsky, M.Weiss, and C.I.Smith (1997).
BTKbase, mutation database for X-linked agammaglobulinemia (XLA)
  Nucleic Acids Res, 25, 166-171.  
9135150 R.H.Chen, S.Corbalan-Garcia, and D.Bar-Sagi (1997).
The role of the PH domain in the signal-dependent membrane targeting of Sos.
  EMBO J, 16, 1351-1359.  
9376220 R.M.Scaife, and R.L.Margolis (1997).
The role of the PH domain and SH3 binding domains in dynamin function.
  Cell Signal, 9, 395-401.  
  9667855 S.E.Shoelson (1997).
SH2 and PTB domain interactions in tyrosine kinase signal transduction.
  Curr Opin Chem Biol, 1, 227-234.  
  9032245 S.Giorgetti-Peraldi, E.Ottinger, G.Wolf, B.Ye, T.R.Burke, and S.E.Shoelson (1997).
Cellular effects of phosphotyrosine-binding domain inhibitors on insulin receptor signaling and trafficking.
  Mol Cell Biol, 17, 1180-1188.  
8999863 T.J.Kubiseski, Y.M.Chook, W.E.Parris, M.Rozakis-Adcock, and T.Pawson (1997).
High affinity binding of the pleckstrin homology domain of mSos1 to phosphatidylinositol (4,5)-bisphosphate.
  J Biol Chem, 272, 1799-1804.  
9242915 W.D.Singer, H.A.Brown, and P.C.Sternweis (1997).
Regulation of eukaryotic phosphatidylinositol-specific phospholipase C and phospholipase D.
  Annu Rev Biochem, 66, 475-509.  
8952464 A.Dietrich, D.Brazil, O.N.Jensen, M.Meister, M.Schrader, J.F.Moomaw, M.Mann, D.Illenberger, and P.Gierschik (1996).
Isoprenylation of the G protein gamma subunit is both necessary and sufficient for beta gamma dimer-mediated stimulation of phospholipase C.
  Biochemistry, 35, 15174-15182.  
8791400 A.Viel, and D.Branton (1996).
Spectrin: on the path from structure to function.
  Curr Opin Cell Biol, 8, 49-55.  
8810277 C.S.Abrams, J.Zhang, C.P.Downes, X.Tang, W.Zhao, and S.E.Rittenhouse (1996).
Phosphopleckstrin inhibits gbetagamma-activable platelet phosphatidylinositol-4,5-bisphosphate 3-kinase.
  J Biol Chem, 271, 25192-25197.  
  8805586 D.Cowburn (1996).
Adaptors and integrators.
  Structure, 4, 1005-1008.  
  8978681 D.R.Alessi, M.Andjelkovic, B.Caudwell, P.Cron, N.Morrice, P.Cohen, and B.A.Hemmings (1996).
Mechanism of activation of protein kinase B by insulin and IGF-1.
  EMBO J, 15, 6541-6551.  
8663526 F.Yoshikawa, M.Morita, T.Monkawa, T.Michikawa, T.Furuichi, and K.Mikoshiba (1996).
Mutational analysis of the ligand binding site of the inositol 1,4,5-trisphosphate receptor.
  J Biol Chem, 271, 18277-18284.  
8603916 G.M.Benian, T.L.Tinley, X.Tang, and M.Borodovsky (1996).
The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains.
  J Cell Biol, 132, 835-848.  
8593162 G.Shaw (1996).
The pleckstrin homology domain: an intriguing multifunctional protein module.
  Bioessays, 18, 35-46.  
8755528 H.Konishi, H.Matsuzaki, M.Tanaka, Y.Ono, C.Tokunaga, S.Kuroda, and U.Kikkawa (1996).
Activation of RAC-protein kinase by heat shock and hyperosmolarity stress through a pathway independent of phosphatidylinositol 3-kinase.
  Proc Natl Acad Sci U S A, 93, 7639-7643.  
8663537 J.Font de Mora, C.Guerrero, D.Mahadevan, J.J.Coque, J.M.Rojas, L.M.Esteban, M.Rebecchi, and E.Santos (1996).
Isolated Sos1 PH domain exhibits germinal vesicle breakdown-inducing activity in Xenopus oocytes.
  J Biol Chem, 271, 18272-18276.  
8810295 J.W.Lomasney, H.F.Cheng, L.P.Wang, Y.Kuan, S.Liu, S.W.Fesik, and K.King (1996).
Phosphatidylinositol 4,5-bisphosphate binding to the pleckstrin homology domain of phospholipase C-delta1 enhances enzyme activity.
  J Biol Chem, 271, 25316-25326.  
  8947047 K.Salim, M.J.Bottomley, E.Querfurth, M.J.Zvelebil, I.Gout, R.Scaife, R.L.Margolis, R.Gigg, C.I.Smith, P.C.Driscoll, M.D.Waterfield, and G.Panayotou (1996).
Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase.
  EMBO J, 15, 6241-6250.  
8646770 M.A.Lemmon, K.M.Ferguson, and J.Schlessinger (1996).
PH domains: diverse sequences with a common fold recruit signaling molecules to the cell surface.
  Cell, 85, 621-624.  
8702543 M.Fukuda, and K.Mikoshiba (1996).
Structure-function relationships of the mouse Gap1m. Determination of the inositol 1,3,4,5-tetrakisphosphate-binding domain.
  J Biol Chem, 271, 18838-18842.  
8691724 M.J.Lohse, C.Krasel, R.Winstel, and F.Mayor (1996).
G-protein-coupled receptor kinases.
  Kidney Int, 49, 1047-1052.  
8913683 M.Nilges (1996).
Structure calculation from NMR data.
  Curr Opin Struct Biol, 6, 617-623.  
8594569 M.Vihinen, T.Iwata, C.Kinnon, S.P.Kwan, H.D.Ochs, I.Vorechovský, and C.I.Smith (1996).
BTKbase, mutation database for X-linked agammaglobulinemia (XLA).
  Nucleic Acids Res, 24, 160-165.  
8885720 P.T.Mattsson, M.Vihinen, and C.I.Smith (1996).
X-linked agammaglobulinemia (XLA): a genetic tyrosine kinase (Btk) disease.
  Bioessays, 18, 825-834.  
8702475 S.C.Hwang, D.Y.Jhon, Y.S.Bae, J.H.Kim, and S.G.Rhee (1996).
Activation of phospholipase C-gamma by the concerted action of tau proteins and arachidonic acid.
  J Biol Chem, 271, 18342-18349.  
8798423 S.K.DebBurman, J.Ptasienski, J.L.Benovic, and M.M.Hosey (1996).
G protein-coupled receptor kinase GRK2 is a phospholipid-dependent enzyme that can be conditionally activated by G protein betagamma subunits.
  J Biol Chem, 271, 22552-22562.  
8521504 K.M.Ferguson, M.A.Lemmon, J.Schlessinger, and P.B.Sigler (1995).
Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain.
  Cell, 83, 1037-1046.
PDB code: 1mai
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