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PDBsum entry 1i9z
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of inositol polyphosphate 5-phosphatase domain (ipp5c) of spsynaptojanin in complex with inositol (1,4)-bisphosphate and calcium ion
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Structure:
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Phosphatidylinositol phosphate phosphatase. Chain: a. Fragment: ipp5c domain, residues 534-880. Synonym: synaptojanin. Engineered: yes
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Source:
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Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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1.80Å
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R-factor:
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0.191
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R-free:
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0.218
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Authors:
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Y.Tsujishita,S.Guo,L.Stolz,J.D.York,J.H.Hurley
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Key ref:
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Y.Tsujishita
et al.
(2001).
Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase.
Cell,
105,
379-389.
PubMed id:
DOI:
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Date:
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21-Mar-01
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Release date:
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16-May-01
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PROCHECK
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Headers
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References
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O43001
(SYJ1_SCHPO) -
Inositol-1,4,5-trisphosphate 5-phosphatase 1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
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Seq:
Struc:
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1076 a.a.
336 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.1.3.36
- phosphoinositide 5-phosphatase.
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Pathway:
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1-Phosphatidyl-myo-inositol Metabolism
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Reaction:
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a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate) + phosphate
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1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate)
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+
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H2O
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=
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1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)
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+
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phosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Cell
105:379-389
(2001)
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PubMed id:
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Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase.
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Y.Tsujishita,
S.Guo,
L.E.Stolz,
J.D.York,
J.H.Hurley.
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ABSTRACT
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Inositol polyphosphate 5-phosphatases are central to intracellular processes
ranging from membrane trafficking to Ca(2+) signaling, and defects in this
activity result in the human disease Lowe syndrome. The 1.8 resolution structure
of the inositol polyphosphate 5-phosphatase domain of SPsynaptojanin bound to
Ca(2+) and inositol (1,4)-bisphosphate reveals a fold and an active site His and
Asp pair resembling those of several Mg(2+)-dependent nucleases. Additional
loops mediate specific inositol polyphosphate contacts. The 4-phosphate of
inositol (1,4)-bisphosphate is misoriented by 4.6 compared to the reactive
geometry observed in the apurinic/apyrimidinic endonuclease 1, explaining the
dephosphorylation site selectivity of the 5-phosphatases. Based on the
structure, a series of mutants are described that exhibit altered substrate
specificity providing general determinants for substrate recognition.
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Selected figure(s)
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Figure 1.
Figure 1. Domain Structures of Representa-
tive 5-Phosphatases
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Figure 7.
Figure 7. Membrane Docking of SPsynapto-
janin-IPP5C
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
105,
379-389)
copyright 2001.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Hichri,
J.Rendu,
N.Monnier,
C.Coutton,
O.Dorseuil,
R.V.Poussou,
G.Baujat,
A.Blanchard,
F.Nobili,
B.Ranchin,
M.Remesy,
R.Salomon,
V.Satre,
and
J.Lunardi
(2011).
From Lowe syndrome to Dent disease: correlations between mutations of the OCRL1 gene and clinical and biochemical phenotypes.
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Hum Mutat,
32,
379-388.
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X.Hou,
N.Hagemann,
S.Schoebel,
W.Blankenfeldt,
R.S.Goody,
K.S.Erdmann,
and
A.Itzen
(2011).
A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1.
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EMBO J,
30,
1659-1670.
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PDB code:
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C.A.Broberg,
L.Zhang,
H.Gonzalez,
M.A.Laskowski-Arce,
and
K.Orth
(2010).
A Vibrio effector protein is an inositol phosphatase and disrupts host cell membrane integrity.
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Science,
329,
1660-1662.
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A.Fujita,
J.Cheng,
K.Tauchi-Sato,
T.Takenawa,
and
T.Fujimoto
(2009).
A distinct pool of phosphatidylinositol 4,5-bisphosphate in caveolae revealed by a nanoscale labeling technique.
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Proc Natl Acad Sci U S A,
106,
9256-9261.
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E.L.Clayton,
and
M.A.Cousin
(2009).
The molecular physiology of activity-dependent bulk endocytosis of synaptic vesicles.
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J Neurochem,
111,
901-914.
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P.Mayinger
(2009).
Regulation of Golgi function via phosphoinositide lipids.
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Semin Cell Dev Biol,
20,
793-800.
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S.L.Bielas,
J.L.Silhavy,
F.Brancati,
M.V.Kisseleva,
L.Al-Gazali,
L.Sztriha,
R.A.Bayoumi,
M.S.Zaki,
A.Abdel-Aleem,
R.O.Rosti,
H.Kayserili,
D.Swistun,
L.C.Scott,
E.Bertini,
E.Boltshauser,
E.Fazzi,
L.Travaglini,
S.J.Field,
S.Gayral,
M.Jacoby,
S.Schurmans,
B.Dallapiccola,
P.W.Majerus,
E.M.Valente,
and
J.G.Gleeson
(2009).
Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies.
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Nat Genet,
41,
1032-1036.
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Y.Mao,
D.M.Balkin,
R.Zoncu,
K.S.Erdmann,
L.Tomasini,
F.Hu,
M.M.Jin,
M.E.Hodsdon,
and
P.De Camilli
(2009).
A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism.
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EMBO J,
28,
1831-1842.
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PDB codes:
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E.Marza,
T.Long,
A.Saiardi,
M.Sumakovic,
S.Eimer,
D.H.Hall,
and
G.M.Lesa
(2008).
Polyunsaturated Fatty Acids Influence Synaptojanin Localization to Regulate Synaptic Vesicle Recycling.
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Mol Biol Cell,
19,
833-842.
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D.Blero,
B.Payrastre,
S.Schurmans,
and
C.Erneux
(2007).
Phosphoinositide phosphatases in a network of signalling reactions.
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Pflugers Arch,
455,
31-44.
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H.M.Loovers,
A.Kortholt,
H.de Groote,
L.Whitty,
R.L.Nussbaum,
and
P.J.van Haastert
(2007).
Regulation of phagocytosis in Dictyostelium by the inositol 5-phosphatase OCRL homolog Dd5P4.
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Traffic,
8,
618-628.
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K.A.Horan,
K.Watanabe,
A.M.Kong,
C.G.Bailey,
J.E.Rasko,
T.Sasaki,
and
C.A.Mitchell
(2007).
Regulation of FcgammaR-stimulated phagocytosis by the 72-kDa inositol polyphosphate 5-phosphatase: SHIP1, but not the 72-kDa 5-phosphatase, regulates complement receptor 3 mediated phagocytosis by differential recruitment of these 5-phosphatases to the phagocytic cup.
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Blood,
110,
4480-4491.
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K.S.Erdmann,
Y.Mao,
H.J.McCrea,
R.Zoncu,
S.Lee,
S.Paradise,
J.Modregger,
D.Biemesderfer,
D.Toomre,
and
P.De Camilli
(2007).
A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway.
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Dev Cell,
13,
377-390.
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PDB code:
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M.Mani,
S.Y.Lee,
L.Lucast,
O.Cremona,
G.Di Paolo,
P.De Camilli,
and
T.A.Ryan
(2007).
The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals.
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Neuron,
56,
1004-1018.
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A.M.Kong,
K.A.Horan,
A.Sriratana,
C.G.Bailey,
L.J.Collyer,
H.H.Nandurkar,
A.Shisheva,
M.J.Layton,
J.E.Rasko,
T.Rowe,
and
C.A.Mitchell
(2006).
Phosphatidylinositol 3-phosphate [PtdIns3P] is generated at the plasma membrane by an inositol polyphosphate 5-phosphatase: endogenous PtdIns3P can promote GLUT4 translocation to the plasma membrane.
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Mol Cell Biol,
26,
6065-6081.
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B.C.Suh,
T.Inoue,
T.Meyer,
and
B.Hille
(2006).
Rapid chemically induced changes of PtdIns(4,5)P2 gate KCNQ ion channels.
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Science,
314,
1454-1457.
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D.F.Lazar,
and
A.R.Saltiel
(2006).
Lipid phosphatases as drug discovery targets for type 2 diabetes.
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Nat Rev Drug Discov,
5,
333-342.
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H.Ago,
M.Oda,
M.Takahashi,
H.Tsuge,
S.Ochi,
N.Katunuma,
M.Miyano,
and
J.Sakurai
(2006).
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
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J Biol Chem,
281,
16157-16167.
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PDB codes:
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I.S.Mian,
E.A.Worthey,
and
R.Salavati
(2006).
Taking U out, with two nucleases?
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BMC Bioinformatics,
7,
305.
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S.J.Mills,
H.Dozol,
F.Vandeput,
K.Backers,
T.Woodman,
C.Erneux,
B.Spiess,
and
B.V.Potter
(2006).
3-hydroxybenzene 1,2,4-trisphosphate, a novel second messenger mimic and unusual substrate for type-I myo-inositol 1,4,5-trisphosphate 5-phosphatase: Synthesis and physicochemistry.
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Chembiochem,
7,
1696-1706.
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T.Rowe,
C.Hale,
A.Zhou,
R.J.Kurzeja,
A.Ali,
A.Menjares,
M.Wang,
and
J.D.McCarter
(2006).
A high-throughput microfluidic assay for SH2 domain-containing inositol 5-phosphatase 2.
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Assay Drug Dev Technol,
4,
175-183.
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A.E.Openshaw,
P.R.Race,
H.J.Monzó,
J.A.Vázquez-Boland,
and
M.J.Banfield
(2005).
Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.
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J Biol Chem,
280,
35011-35017.
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PDB code:
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A.Koch,
A.Mancini,
O.El Bounkari,
and
T.Tamura
(2005).
The SH2-domian-containing inositol 5-phosphatase (SHIP)-2 binds to c-Met directly via tyrosine residue 1356 and involves hepatocyte growth factor (HGF)-induced lamellipodium formation, cell scattering and cell spreading.
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Oncogene,
24,
3436-3447.
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A.Weichsel,
E.M.Maes,
J.F.Andersen,
J.G.Valenzuela,
T.K.h.Shokhireva,
F.A.Walker,
and
W.R.Montfort
(2005).
Heme-assisted S-nitrosation of a proximal thiolate in a nitric oxide transport protein.
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Proc Natl Acad Sci U S A,
102,
594-599.
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PDB codes:
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M.Lowe
(2005).
Structure and function of the Lowe syndrome protein OCRL1.
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Traffic,
6,
711-719.
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M.R.Wenk
(2005).
The emerging field of lipidomics.
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Nat Rev Drug Discov,
4,
594-610.
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U.Gioia,
P.Laneve,
M.Dlakic,
M.Arceci,
I.Bozzoni,
and
E.Caffarelli
(2005).
Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis.
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J Biol Chem,
280,
18996-19002.
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O.Weichenrieder,
K.Repanas,
and
A.Perrakis
(2004).
Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
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Structure,
12,
975-986.
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PDB code:
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Y.Chi,
B.Zhou,
W.Q.Wang,
S.K.Chung,
Y.U.Kwon,
Y.H.Ahn,
Y.T.Chang,
Y.Tsujishita,
J.H.Hurley,
and
Z.Y.Zhang
(2004).
Comparative mechanistic and substrate specificity study of inositol polyphosphate 5-phosphatase Schizosaccharomyces pombe Synaptojanin and SHIP2.
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J Biol Chem,
279,
44987-44995.
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C.Venclovas
(2003).
Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance.
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Proteins,
53,
380-388.
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H.M.Loovers,
K.Veenstra,
H.Snippe,
X.Pesesse,
C.Erneux,
and
P.J.van Haastert
(2003).
A diverse family of inositol 5-phosphatases playing a role in growth and development in Dictyostelium discoideum.
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J Biol Chem,
278,
5652-5658.
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R.Gurung,
A.Tan,
L.M.Ooms,
M.J.McGrath,
R.D.Huysmans,
A.D.Munday,
M.Prescott,
J.C.Whisstock,
and
C.A.Mitchell
(2003).
Identification of a novel domain in two mammalian inositol-polyphosphate 5-phosphatases that mediates membrane ruffle localization. The inositol 5-phosphatase skip localizes to the endoplasmic reticulum and translocates to membrane ruffles following epidermal growth factor stimulation.
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J Biol Chem,
278,
11376-11385.
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C.J.Stefan,
A.Audhya,
and
S.D.Emr
(2002).
The yeast synaptojanin-like proteins control the cellular distribution of phosphatidylinositol (4,5)-bisphosphate.
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Mol Biol Cell,
13,
542-557.
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J.H.Hurley,
D.E.Anderson,
B.Beach,
B.Canagarajah,
Y.S.Ho,
E.Jones,
G.Miller,
S.Misra,
M.Pearson,
L.Saidi,
S.Suer,
R.Trievel,
and
Y.Tsujishita
(2002).
Structural genomics and signaling domains.
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Trends Biochem Sci,
27,
48-53.
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M.E.March,
and
K.Ravichandran
(2002).
Regulation of the immune response by SHIP.
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Semin Immunol,
14,
37-47.
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S.McLaughlin,
J.Wang,
A.Gambhir,
and
D.Murray
(2002).
PIP(2) and proteins: interactions, organization, and information flow.
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| |
Annu Rev Biophys Biomol Struct,
31,
151-175.
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D.Communi,
K.Gevaert,
H.Demol,
J.Vandekerckhove,
and
C.Erneux
(2001).
A novel receptor-mediated regulation mechanism of type I inositol polyphosphate 5-phosphatase by calcium/calmodulin-dependent protein kinase II phosphorylation.
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J Biol Chem,
276,
38738-38747.
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J.M.Dyson,
C.J.O'Malley,
J.Becanovic,
A.D.Munday,
M.C.Berndt,
I.D.Coghill,
H.H.Nandurkar,
L.M.Ooms,
and
C.A.Mitchell
(2001).
The SH2-containing inositol polyphosphate 5-phosphatase, SHIP-2, binds filamin and regulates submembraneous actin.
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| |
J Cell Biol,
155,
1065-1079.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
