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PDBsum entry 1eh2

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protein metals links
Calcium binding PDB id
1eh2
Jmol
Contents
Protein chain
95 a.a. *
Metals
_CA
* Residue conservation analysis
PDB id:
1eh2
Name: Calcium binding
Title: Structure of the second eps15 homology domain of human eps15, nmr, 20 structures
Structure: Eps15. Chain: a. Fragment: eps15 homology (eh) domain 2, residues 121-218. Synonym: eh2, epidermal growth factor receptor substrate 15. Engineered: yes. Other_details: this domain contains a calcium binding site
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: eps15. Expressed in: escherichia coli. Expression_system_taxid: 562. Plyss.
NMR struc: 20 models
Authors: T.De Beer,R.E.Carter,K.E.Lobel-Rice,A.Sorkin,M.Overduin
Key ref:
T.de Beer et al. (1998). Structure and Asn-Pro-Phe binding pocket of the Eps15 homology domain. Science, 281, 1357-1360. PubMed id: 9721102 DOI: 10.1126/science.281.5381.1357
Date:
10-Jul-98     Release date:   22-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42566  (EPS15_HUMAN) -  Epidermal growth factor receptor substrate 15
Seq:
Struc:
 
Seq:
Struc:
896 a.a.
95 a.a.
Key:    PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     calcium ion binding     1 term  

 

 
DOI no: 10.1126/science.281.5381.1357 Science 281:1357-1360 (1998)
PubMed id: 9721102  
 
 
Structure and Asn-Pro-Phe binding pocket of the Eps15 homology domain.
T.de Beer, R.E.Carter, K.E.Lobel-Rice, A.Sorkin, M.Overduin.
 
  ABSTRACT  
 
Eps15 homology (EH) domains are eukaryotic signaling modules that recognize proteins containing Asn-Pro-Phe (NPF) sequences. The structure of the central EH domain of Eps15 has been solved by heteronuclear magnetic resonance spectroscopy. The fold consists of a pair of EF hand motifs, the second of which binds tightly to calcium. The NPF peptide is bound in a hydrophobic pocket between two alpha helices, and binding is mediated by a critical aromatic interaction as revealed by structure-based mutagenesis. The fold is predicted to be highly conserved among 30 identified EH domains and provides a structural basis for defining EH-mediated events in protein trafficking and growth factor signaling.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of EH[2]. The four helices A (amino acid residues 126 through 136), B (148 through 156), C (162 through 172), and D (182 through 197) are depicted in orange, purple, blue, and red, respectively. The mini- sheet involving residues 145 through 147 ( A) and 179 through 181 ( B) is shown in light blue, the COOH-terminal proline-rich element is shown in light green, and the calcium ion is shown as a yellow sphere. The NH[2]- and COOH-termini are labeled N and C, respectively. Figure 1, A and B, Fig. 2B, and Fig. 3, B and C, were generated with InsightII software. (A) Best-fit superposition of the backbone atoms (N, C , and C') in the secondary structure elements of the 20 structures with the lowest nuclear Overhauser effect energies (21, 22). (B) Ribbon diagram of the structure closest to the average of the 20 structures, shown in the same orientation as (A). (C) Amino acid sequence alignment for the three EH domains (residues 9 through 103, 121 through 215, and 217 through 313, respectively) of human Eps15 (11, 17). The secondary structure and solvent exposure are shown above the sequence and were determined with Procheck-NMR (20). The coloring and nomenclature of key amino acids are indicated in the inset. Phosphorylation of Eps15 at Tyr132 (shown in green) by EGFR (2) is unlikely because this residue is buried between helices A and D.
Figure 2.
Fig. 2. NPF binding site of EH[2]. (A) Superimposed regions of four 1H-13C HSQC spectra of 1 mM EH[2] with the following NPF[RAB] concentrations: 0 mM, dark blue; 0.25 mM, light blue; 0.5 mM, orange; and 2 mM, red. The inset shows the Trp169 side chain nomenclature. Observation of fast exchange on the NMR time scale is consistent with the K[D] of the EH[2]:NPF[RAB] interaction estimated by surface plasmon resonance (18). (B) Space-filling model showing the NPF binding site. Atoms are colored on the basis of 1H, 13C, and 15N chemical shift differences ( ) induced by NPF[RAB] addition. Red, orange, yellow, and light blue indicate very large, large, medium, and small differences, respectively, as listed in the inset. Dark blue indicates that the difference was not measured. (C) Ribbon diagram displaying side chains in the NPF binding site. The orientation is identical to that in (B). Leu155 (dark blue), Leu165 (yellow), and Trp169 (red) make up the base of the binding site, whereas residues Gly148 (dark green), Lys152 (magenta), Leu156 (orange), Val162 (light blue), and Gly166 (light green) form the walls of the pocket. Calcium is indicated as a yellow sphere. (D) Molecular surface of EH[2] with the same orientation and color coding as in (C) [(C)and (D) were generated with GRASP (23)].
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 281, 1357-1360) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21067929 N.Naslavsky, and S.Caplan (2011).
EHD proteins: key conductors of endocytic transport.
  Trends Cell Biol, 21, 122-131.  
20329706 G.D.Henry, D.J.Corrigan, J.V.Dineen, and J.D.Baleja (2010).
Charge effects in the selection of NPF motifs by the EH domain of EHD1.
  Biochemistry, 49, 3381-3392.  
19732400 T.Maritzen, J.Podufall, and V.Haucke (2010).
Stonins--specialized adaptors for synaptic vesicle recycling and beyond?
  Traffic, 11, 8.  
19798736 F.Kieken, M.Jović, M.Tonelli, N.Naslavsky, S.Caplan, and P.L.Sorgen (2009).
Structural insight into the interaction of proteins containing NPF, DPF, and GPF motifs with the C-terminal EH-domain of EHD1.
  Protein Sci, 18, 2471-2479.
PDB codes: 2kff 2kfg 2kfh
19369419 M.Jović, F.Kieken, N.Naslavsky, P.L.Sorgen, and S.Caplan (2009).
Eps15 homology domain 1-associated tubules contain phosphatidylinositol-4-phosphate and phosphatidylinositol-(4,5)-bisphosphate and are required for efficient recycling.
  Mol Biol Cell, 20, 2731-2743.  
19139087 N.Naslavsky, J.McKenzie, N.Altan-Bonnet, D.Sheff, and S.Caplan (2009).
EHD3 regulates early-endosome-to-Golgi transport and preserves Golgi morphology.
  J Cell Sci, 122, 389-400.  
18801062 B.D.Grant, and S.Caplan (2008).
Mechanisms of EHD/RME-1 protein function in endocytic transport.
  Traffic, 9, 2043-2052.  
18200045 J.Rumpf, B.Simon, N.Jung, T.Maritzen, V.Haucke, M.Sattler, and Y.Groemping (2008).
Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity.
  EMBO J, 27, 558-569.
PDB code: 2jxc
18502764 K.R.Doherty, A.R.Demonbreun, G.Q.Wallace, A.Cave, A.D.Posey, K.Heretis, P.Pytel, and E.M.McNally (2008).
The endocytic recycling protein EHD2 interacts with myoferlin to regulate myoblast fusion.
  J Biol Chem, 283, 20252-20260.  
18448668 L.Maldonado-Báez, M.R.Dores, E.M.Perkins, T.G.Drivas, L.Hicke, and B.Wendland (2008).
Interaction between Epsin/Yap180 adaptors and the scaffolds Ede1/Pan1 is required for endocytosis.
  Mol Biol Cell, 19, 2936-2948.  
18154663 E.Santonico, S.Panni, M.Falconi, L.Castagnoli, and G.Cesareni (2007).
Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction.
  BMC Biochem, 8, 29.  
17296314 E.Shacham, B.Sheehan, and N.Volkmann (2007).
Density-based score for selecting near-native atomic models of unknown structures.
  J Struct Biol, 158, 188-195.  
17899392 F.Kieken, M.Jović, N.Naslavsky, S.Caplan, and P.L.Sorgen (2007).
EH domain of EHD1.
  J Biomol NMR, 39, 323-329.
PDB code: 2jq6
17914359 O.Daumke, R.Lundmark, Y.Vallis, S.Martens, P.J.Butler, and H.T.McMahon (2007).
Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling.
  Nature, 449, 923-927.
PDB code: 2qpt
17050736 I.Stavrou, and T.J.O'Halloran (2006).
The monomeric clathrin assembly protein, AP180, regulates contractile vacuole size in Dictyostelium discoideum.
  Mol Biol Cell, 17, 5381-5389.  
16251358 N.Naslavsky, J.Rahajeng, M.Sharma, M.Jovic, and S.Caplan (2006).
Interactions between EHD proteins and Rab11-FIP2: a role for EHD3 in early endosomal transport.
  Mol Biol Cell, 17, 163-177.  
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
16054223 M.L.Montesinos, M.Castellano-Muñoz, P.García-Junco-Clemente, and R.Fernández-Chacón (2005).
Recycling and EH domain proteins at the synapse.
  Brain Res Brain Res Rev, 49, 416-428.  
15020713 N.Naslavsky, M.Boehm, P.S.Backlund, and S.Caplan (2004).
Rabenosyn-5 and EHD1 interact and sequentially regulate protein recycling to the plasma membrane.
  Mol Biol Cell, 15, 2410-2422.  
15520805 T.R.Dafforn, and C.J.Smith (2004).
Natively unfolded domains in endocytosis: hooks, lines and linkers.
  EMBO Rep, 5, 1046-1052.  
15260956 T.W.Koh, P.Verstreken, and H.J.Bellen (2004).
Dap160/intersectin acts as a stabilizing scaffold required for synaptic development and vesicle endocytosis.
  Neuron, 43, 193-205.  
15223314 Z.Yang, L.Shipman, M.Zhang, B.P.Anton, R.J.Roberts, and X.Cheng (2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
  J Mol Biol, 340, 695-706.
PDB code: 1t43
12176391 H.M.Kent, H.T.McMahon, P.R.Evans, A.Benmerah, and D.J.Owen (2002).
Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin.
  Structure, 10, 1139-1148.
PDB codes: 1gyu 1gyv 1gyw
11687498 F.M.Brodsky, C.Y.Chen, C.Knuehl, M.C.Towler, and D.E.Wakeham (2001).
Biological basket weaving: formation and function of clathrin-coated vesicles.
  Annu Rev Cell Dev Biol, 17, 517-568.  
  11694597 H.A.Watson, M.J.Cope, A.C.Groen, D.G.Drubin, and B.Wendland (2001).
In vivo role for actin-regulating kinases in endocytosis and yeast epsin phosphorylation.
  Mol Biol Cell, 12, 3668-3679.  
11389591 S.Kim, D.N.Cullis, L.A.Feig, and J.D.Baleja (2001).
Solution structure of the Reps1 EH domain and characterization of its binding to NPF target sequences.
  Biochemistry, 40, 6776-6785.
PDB code: 1fi6
10753805 B.M.Pearse, C.J.Smith, and D.J.Owen (2000).
Clathrin coat construction in endocytosis.
  Curr Opin Struct Biol, 10, 220-228.  
11208125 D.E.Wakeham, J.A.Ybe, F.M.Brodsky, and P.K.Hwang (2000).
Molecular structures of proteins involved in vesicle coat formation.
  Traffic, 1, 393-398.  
10873829 D.J.Owen, and J.P.Luzio (2000).
Structural insights into clathrin-mediated endocytosis.
  Curr Opin Cell Biol, 12, 467-474.  
10944104 D.J.Owen, Y.Vallis, B.M.Pearse, H.T.McMahon, and P.R.Evans (2000).
The structure and function of the beta 2-adaptin appendage domain.
  EMBO J, 19, 4216-4227.
PDB code: 1e42
10757979 J.L.Enmon, T.de Beer, and M.Overduin (2000).
Solution structure of Eps15's third EH domain reveals coincident Phe-Trp and Asn-Pro-Phe binding sites.
  Biochemistry, 39, 4309-4319.
PDB code: 1c07
10481267 A.E.Salcini, H.Chen, G.Iannolo, P.De Camilli, and P.P.Di Fiore (1999).
Epidermal growth factor pathway substrate 15, Eps15.
  Int J Biochem Cell Biol, 31, 805-809.  
10021353 B.J.Mayer (1999).
Endocytosis: EH domains lend a hand.
  Curr Biol, 9, R70-R73.  
10449404 B.Wendland, K.E.Steece, and S.D.Emr (1999).
Yeast epsins contain an essential N-terminal ENTH domain, bind clathrin and are required for endocytosis.
  EMBO J, 18, 4383-4393.  
10471276 B.Whitehead, M.Tessari, A.Carotenuto, P.M.van Bergen en Henegouwen, and G.W.Vuister (1999).
The EH1 domain of Eps15 is structurally classified as a member of the S100 subclass of EF-hand-containing proteins.
  Biochemistry, 38, 11271-11277.
PDB code: 1qjt
10611648 D.G.Myszka (1999).
Survey of the 1998 optical biosensor literature.
  J Mol Recognit, 12, 390-408.  
10380931 D.J.Owen, Y.Vallis, M.E.Noble, J.B.Hunter, T.R.Dafforn, P.R.Evans, and H.T.McMahon (1999).
A structural explanation for the binding of multiple ligands by the alpha-adaptin appendage domain.
  Cell, 97, 805-815.
PDB code: 1b9k
10430846 E.Ungewickell (1999).
Wrapping the package.
  Proc Natl Acad Sci U S A, 96, 8809-8810.  
  10436022 F.Tebar, S.K.Bohlander, and A.Sorkin (1999).
Clathrin assembly lymphoid myeloid leukemia (CALM) protein: localization in endocytic-coated pits, interactions with clathrin, and the impact of overexpression on clathrin-mediated traffic.
  Mol Biol Cell, 10, 2687-2702.  
10330371 H.T.McMahon (1999).
Endocytosis: an assembly protein for clathrin cages.
  Curr Biol, 9, R332-R335.  
10591109 K.L.Yap, J.B.Ames, M.B.Swindells, and M.Ikura (1999).
Diversity of conformational states and changes within the EF-hand protein superfamily.
  Proteins, 37, 499-507.  
9822599 S.Paoluzi, L.Castagnoli, I.Lauro, A.E.Salcini, L.Coda, S.Fre', S.Confalonieri, P.G.Pelicci, P.P.Di Fiore, and G.Cesareni (1998).
Recognition specificity of individual EH domains of mammals and yeast.
  EMBO J, 17, 6541-6550.  
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 codes are shown on the right.