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PDBsum entry 1hyi
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Endocytosis/exocytosis PDB id
1hyi

 

 

 

 

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Contents
Protein chain
65 a.a. *
Ligands
ITP
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1hyi
Name: Endocytosis/exocytosis
Title: Solution structure of the eea1 fyve domain complexed with inositol 1, 3-bisphosphate
Structure: Endosome-associated protein. Chain: a. Fragment: fyve domain (residues 1346-1410). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: T.Kutateladze,M.Overduin
Key ref:
T.Kutateladze and M.Overduin (2001). Structural mechanism of endosome docking by the FYVE domain. Science, 291, 1793-1796. PubMed id: 11230696 DOI: 10.1126/science.291.5509.1793
Date:
19-Jan-01     Release date:   14-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q15075  (EEA1_HUMAN) -  Early endosome antigen 1 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1411 a.a.
65 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.291.5509.1793 Science 291:1793-1796 (2001)
PubMed id: 11230696  
 
 
Structural mechanism of endosome docking by the FYVE domain.
T.Kutateladze, M.Overduin.
 
  ABSTRACT  
 
The recruitment of trafficking and signaling proteins to membranes containing is mediated by FYVE domains. Here, the solution structure of the FYVE domain of the early endosome antigen 1 protein (EEA1) in the free state was compared with the structures of the domain complexed with PtdIns(3)P and mixed micelles. The multistep binding mechanism involved nonspecific insertion of a hydrophobic loop into the lipid bilayer, positioning and activating the binding pocket. Ligation of PtdIns(3)P then induced a global structural change, drawing the protein termini over the bound phosphoinositide by extension of a hinge. Specific recognition of the 3-phosphate was determined indirectly and directly by two clusters of conserved arginines.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Solution structures of the EEA1 FYVE domain. (A) The C traces of 20 structures are shown that comprise EEA1 residues 1346 to 1410 in the lipid-free form, with the strands, helix, hinge, membrane insertion loop, and zinc ions colored green, magenta, cyan, brown, and orange, respectively. (B) Ribbon diagram of the structure closest to the average. The 1, 2, 3, and 4 strands and 1 helix consist of residues 1370 to 1372, 1379 to 1381, 1387 to 1391, 1396 to 1400, and 1402 to 1408, respectively. The two zinc ions (Zn1 and Zn2) are coordinated by eight cysteines whose side chains are shown in yellow. (C) The C traces of 20 PtdIns(3)P-bound structures are depicted as in (A). The PtdIns(3)P head group of the average structure is shown, with C and P atoms in yellow and O atoms in red. (D) Superposition of the PtdIns(3)P-bound and free structures, which are colored and gray, respectively. The view has been rotated slightly to reveal the structural differences. 		Figure 3.
Fig. 3. Phosphate group recognition by arginines. (A) The H resonances of Arg1369 and Arg1374 shift downfield upon PtdIns(3)P interaction (lower panel), indicating the formation of new hydrogen bonds. The H[2]N resonances of the Arg1370 and Arg1374 become resolved only in the presence of PtdIns(3)P (upper panel), indicating that the guanidino group rotation is impeded by PtdIns(3)P coordination. Two regions of five 1H-15N correlation spectra of the FYVE domain (1 mM) with PtdIns(3)P concentrations of 0, 0.1, 0.5, 1, and 5 mM are superimposed. Arginine's structure is shown in the upper right. (B) PtdIns(3)P moieties recognized by the FYVE domain are indicated by absolute changes in the 1H, 13C, and 31P chemical shifts of PtdIns(3)P induced by addition of equimolar FYVE domain. Atoms are numbered according to the positions indicated in (C). (C) Model of dibutanoyl PtdIns(3)P, with atom colors based on chemical shift perturbations induced by addition of equimolar FYVE domain, as indicated in (B).
 
  The above figures are reprinted by permission from the AAAs: Science (2001, 291, 1793-1796) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21166893 A.C.Schoijet, K.Miranda, L.C.Medeiros, W.de Souza, M.M.Flawiá, H.N.Torres, O.P.Pignataro, R.Docampo, and G.D.Alonso (2011).
Defining the role of a FYVE domain in the localization and activity of a cAMP phosphodiesterase implicated in osmoregulation in Trypanosoma cruzi.
  Mol Microbiol, 79, 50-62.  
20534488 A.Mishra, S.Eathiraj, S.Corvera, and D.G.Lambright (2010).
Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1).
  Proc Natl Acad Sci U S A, 107, 10866-10871.
PDB code: 3mjh
  20678208 E.Wywial, and S.M.Singh (2010).
Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana.
  BMC Plant Biol, 10, 157.  
20559318 T.G.Kutateladze (2010).
Translation of the phosphoinositide code by PI effectors.
  Nat Chem Biol, 6, 507-513.  
18618697 A.Bhunia, P.N.Domadia, H.Mohanram, and S.Bhattacharjya (2009).
NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle.
  Proteins, 74, 328-343.  
19296456 J.He, M.Vora, R.M.Haney, G.S.Filonov, C.A.Musselman, C.G.Burd, A.G.Kutateladze, V.V.Verkhusha, R.V.Stahelin, and T.G.Kutateladze (2009).
Membrane insertion of the FYVE domain is modulated by pH.
  Proteins, 76, 852-860.  
19442115 K.S.Champagne, and T.G.Kutateladze (2009).
Structural insight into histone recognition by the ING PHD fingers.
  Curr Drug Targets, 10, 432-441.  
17890395 F.Dancea, K.Kami, and M.Overduin (2008).
Lipid interaction networks of peripheral membrane proteins revealed by data-driven micelle docking.
  Biophys J, 94, 515-524.  
18657545 J.S.Saad, S.D.Ablan, R.H.Ghanam, A.Kim, K.Andrews, K.Nagashima, F.Soheilian, E.O.Freed, and M.F.Summers (2008).
Structure of the myristylated human immunodeficiency virus type 2 matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in membrane targeting.
  J Mol Biol, 382, 434-447.
PDB codes: 2k4e 2k4h 2k4i
18216767 M.A.Lemmon (2008).
Membrane recognition by phospholipid-binding domains.
  Nat Rev Mol Cell Biol, 9, 99.  
18533182 P.V.Peña, R.A.Hom, T.Hung, H.Lin, A.J.Kuo, R.P.Wong, O.M.Subach, K.S.Champagne, R.Zhao, V.V.Verkhusha, G.Li, O.Gozani, and T.G.Kutateladze (2008).
Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
  J Mol Biol, 380, 303-312.
PDB code: 2qic
17603894 A.L.Lomize, I.D.Pogozheva, M.A.Lomize, and H.I.Mosberg (2007).
The role of hydrophobic interactions in positioning of peripheral proteins in membranes.
  BMC Struct Biol, 7, 44.  
17905827 H.D.Mertens, J.M.Callaghan, J.D.Swarbrick, M.J.McConville, and P.R.Gooley (2007).
A high-resolution solution structure of a trypanosomatid FYVE domain.
  Protein Sci, 16, 2552-2559.
PDB code: 1z2q
17707914 T.G.Kutateladze (2007).
Mechanistic similarities in docking of the FYVE and PX domains to phosphatidylinositol 3-phosphate containing membranes.
  Prog Lipid Res, 46, 315-327.  
16601699 C.Stroupe, K.M.Collins, R.A.Fratti, and W.Wickner (2006).
Purification of active HOPS complex reveals its affinities for phosphoinositides and the SNARE Vam7p.
  EMBO J, 25, 1579-1589.  
16774263 J.Gajewiak, Y.Xu, S.A.Lee, T.G.Kutateladze, and G.D.Prestwich (2006).
Synthesis and molecular recognition of phosphatidylinositol-3-methylenephosphate.
  Org Lett, 8, 2811-2813.  
16689637 J.H.Hurley, and S.D.Emr (2006).
The ESCRT complexes: structure and mechanism of a membrane-trafficking network.
  Annu Rev Biophys Biomol Struct, 35, 277-298.  
16840558 J.S.Saad, J.Miller, J.Tai, A.Kim, R.H.Ghanam, and M.F.Summers (2006).
Structural basis for targeting HIV-1 Gag proteins to the plasma membrane for virus assembly.
  Proc Natl Acad Sci U S A, 103, 11364-11369.
PDB codes: 2h3f 2h3i 2h3q 2h3v 2h3z
16524465 L.McKeown, P.Robinson, S.M.Greenwood, W.Hu, and O.T.Jones (2006).
PIN-G--a novel reporter for imaging and defining the effects of trafficking signals in membrane proteins.
  BMC Biotechnol, 6, 15.  
16410353 M.J.Begley, G.S.Taylor, M.A.Brock, P.Ghosh, V.L.Woods, and J.E.Dixon (2006).
Molecular basis for substrate recognition by MTMR2, a myotubularin family phosphoinositide phosphatase.
  Proc Natl Acad Sci U S A, 103, 927-932.
PDB codes: 1zsq 1zvr
16585509 R.Alvarez-Venegas, M.Sadder, A.Hlavacka, F.Baluska, Y.Xia, G.Lu, A.Firsov, G.Sarath, H.Moriyama, J.G.Dubrovsky, and Z.Avramova (2006).
The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes.
  Proc Natl Acad Sci U S A, 103, 6049-6054.  
16984909 S.A.Lee, J.Kovacs, R.V.Stahelin, M.L.Cheever, M.Overduin, T.G.Setty, C.G.Burd, W.Cho, and T.G.Kutateladze (2006).
Molecular mechanism of membrane docking by the Vam7p PX domain.
  J Biol Chem, 281, 37091-37101.  
16554828 T.E.Rusten, and H.Stenmark (2006).
Analyzing phosphoinositides and their interacting proteins.
  Nat Methods, 3, 251-258.  
16644267 T.G.Kutateladze (2006).
Phosphatidylinositol 3-phosphate recognition and membrane docking by the FYVE domain.
  Biochim Biophys Acta, 1761, 868-877.  
16943433 Y.J.Sun, K.Nishikawa, H.Yuda, Y.L.Wang, H.Osaka, N.Fukazawa, A.Naito, Y.Kudo, K.Wada, and S.Aoki (2006).
Solo/Trio8, a membrane-associated short isoform of Trio, modulates endosome dynamics and neurite elongation.
  Mol Cell Biol, 26, 6923-6935.  
16417379 Y.Xu, S.A.Lee, T.G.Kutateladze, D.Sbrissa, A.Shisheva, and G.D.Prestwich (2006).
Chemical synthesis and molecular recognition of phosphatase-resistant analogues of phosphatidylinositol-3-phosphate.
  J Am Chem Soc, 128, 885-897.  
16331966 R.Brunecky, S.Lee, P.W.Rzepecki, M.Overduin, G.D.Prestwich, A.G.Kutateladze, and T.G.Kutateladze (2005).
Investigation of the binding geometry of a peripheral membrane protein.
  Biochemistry, 44, 16064-16071.  
16141328 S.A.Lee, R.Eyeson, M.L.Cheever, J.Geng, V.V.Verkhusha, C.Burd, M.Overduin, and T.G.Kutateladze (2005).
Targeting of the FYVE domain to endosomal membranes is regulated by a histidine switch.
  Proc Natl Acad Sci U S A, 102, 13052-13057.  
15869386 W.Cho, and R.V.Stahelin (2005).
Membrane-protein interactions in cell signaling and membrane trafficking.
  Annu Rev Biophys Biomol Struct, 34, 119-151.  
15473838 D.J.Owen, B.M.Collins, and P.R.Evans (2004).
Adaptors for clathrin coats: structure and function.
  Annu Rev Cell Dev Biol, 20, 153-191.  
15170460 M.A.De Matteis, and A.Godi (2004).
PI-loting membrane traffic.
  Nat Cell Biol, 6, 487-492.  
15576038 M.D.Tibbetts, E.N.Shiozaki, L.Gu, E.R.McDonald, W.S.El-Deiry, and Y.Shi (2004).
Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2.
  Structure, 12, 2257-2263.
PDB code: 1y02
15359279 T.C.Cronin, J.P.DiNitto, M.P.Czech, and D.G.Lambright (2004).
Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains.
  EMBO J, 23, 3711-3720.
PDB codes: 1u27 1u29 1u2b
12471164 H.L.Yin, and P.A.Janmey (2003).
Phosphoinositide regulation of the actin cytoskeleton.
  Annu Rev Physiol, 65, 761-789.  
  12694559 M.A.Lemmon (2003).
Phosphoinositide recognition domains.
  Traffic, 4, 201-213.  
12612640 M.González-Gaitán (2003).
Signal dispersal and transduction through the endocytic pathway.
  Nat Rev Mol Cell Biol, 4, 213-224.  
12859901 O.Gozani, P.Karuman, D.R.Jones, D.Ivanov, J.Cha, A.A.Lugovskoy, C.L.Baird, H.Zhu, S.J.Field, S.L.Lessnick, J.Villasenor, B.Mehrotra, J.Chen, V.R.Rao, J.S.Brugge, C.G.Ferguson, B.Payrastre, D.G.Myszka, L.C.Cantley, G.Wagner, N.Divecha, G.D.Prestwich, and J.Yuan (2003).
The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor.
  Cell, 114, 99.  
11906837 B.K.Drøbak, and B.Heras (2002).
Nuclear phosphoinositides could bring FYVE alive.
  Trends Plant Sci, 7, 132-138.  
11454456 A.Simonsen, A.E.Wurmser, S.D.Emr, and H.Stenmark (2001).
The role of phosphoinositides in membrane transport.
  Curr Opin Cell Biol, 13, 485-492.  
11684018 J.Bravo, D.Karathanassis, C.M.Pacold, M.E.Pacold, C.D.Ellson, K.E.Anderson, P.J.Butler, I.Lavenir, O.Perisic, P.T.Hawkins, L.Stephens, and R.L.Williams (2001).
The crystal structure of the PX domain from p40(phox) bound to phosphatidylinositol 3-phosphate.
  Mol Cell, 8, 829-839.
PDB code: 1h6h
11741531 J.J.Dumas, E.Merithew, E.Sudharshan, D.Rajamani, S.Hayes, D.Lawe, S.Corvera, and D.G.Lambright (2001).
Multivalent endosome targeting by homodimeric EEA1.
  Mol Cell, 8, 947-958.
PDB code: 1joc
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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