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PDBsum entry 1b7a
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protein ligands Protein-protein interface(s) links
Lipid binding protein PDB id
1b7a

 

 

 

 

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Contents
Protein chains
186 a.a. *
Ligands
OPE ×2
Waters ×164
* Residue conservation analysis
PDB id:
1b7a
Name: Lipid binding protein
Title: Structure of the phosphatidylethanolamine-binding protein from bovine brain
Structure: Phosphatidylethanolamine-binding protein. Chain: a, b. Synonym: pebp
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: brain
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.208     R-free:   0.279
Authors: L.Serre,B.Vallee,N.Bureaud,F.Schoentgen,C.Zelwer
Key ref:
L.Serre et al. (1998). Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins. Structure, 6, 1255-1265. PubMed id: 9782057 DOI: 10.1016/S0969-2126(98)00126-9
Date:
21-Jan-99     Release date:   27-Jan-99    
PROCHECK
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 Headers
 References

Protein chains
P13696  (PEBP1_BOVIN) -  Phosphatidylethanolamine-binding protein 1 from Bos taurus
Seq:
Struc: 		187 a.a.
186 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(98)00126-9 Structure 6:1255-1265 (1998)
PubMed id: 9782057  
 
 
Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins.
L.Serre, B.Vallée, N.Bureaud, F.Schoentgen, C.Zelwer.
 
  ABSTRACT  
 
BACKGROUND: Phosphatidylethanolamine-binding protein (PEBP) is a basic protein found in numerous tissues from a wide range of species. The screening of gene and protein data banks defines a family of PEBP-related proteins that are present in a variety of organisms, including Drosophila and inferior eukaryotes. PEBP binds to phosphatidylethanolamine and nucleotides in vitro, but its biological function in vivo is not yet known. The expression of PEBP and related proteins seems to be correlated with development and cell morphogenesis, however. To obtain new insights into the PEBP family and its potential functions, we initiated a crystallographic study of bovine brain PEPB. RESULTS: The X-ray crystal structure of bovine brain PEBP has been solved using multiple isomorphous replacement methods, and refined to 1.84 A resolution. The structure displays a beta fold and exhibits one nonprolyl cis peptide bond. Analysis of cavities within the structure and sequence alignments were used to identify a putative ligand-binding site. This binding site is defined by residues of the C-terminal helix and the residues His85, Asp69, Gly109 and Tyr119. This site also corresponds to the binding site of phosphorylethanolamine, the polar head group of phosphatidylethanolamine. CONCLUSIONS: This study shows that PEBP is not related to the G-protein family nor to known lipid-binding proteins, and therefore defines a novel structural family of phospholipid-binding proteins. The PEBP structure contains no internal hydrophobic pocket, as described for lipocalins or small phospholipid-transfer proteins. Nevertheless, in PEBP, a small cavity close to the protein surface has a high affinity for anions, such as phosphate and acetate, and also phosphorylethanolamine. We suggest that this cavity corresponds to the binding site of the polar head group of phosphatidylethanolamine.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The electrostatic surface potential of PEBP. The bound phosphorylethanolamine is shown in the cavity in ball-and-stick representation. Regions of negative potential are shown in red; regions of positive potential are in blue. The strip of basic residues is labeled in yellow. CR1 and CR2 represent strand-connecting regions 1 and 2, respectively. (The figure was created using the program GRASP [25].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1255-1265) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20463977 A.N.Shemon, G.L.Heil, A.E.Granovsky, M.M.Clark, D.McElheny, A.Chimon, M.R.Rosner, and S.Koide (2010).
Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands.
  PLoS One, 5, e10479.  
19103740 A.E.Granovsky, M.C.Clark, D.McElheny, G.Heil, J.Hong, X.Liu, Y.Kim, G.Joachimiak, A.Joachimiak, S.Koide, and M.R.Rosner (2009).
Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism.
  Mol Cell Biol, 29, 1306-1320.  
17706925 J.Klysik, S.J.Theroux, J.M.Sedivy, J.S.Moffit, and K.Boekelheide (2008).
Signaling crossroads: the function of Raf kinase inhibitory protein in cancer, the central nervous system and reproduction.
  Cell Signal, 20, 1-9.  
17367210 G.Hu, B.R.Steen, T.Lian, A.P.Sham, N.Tam, K.L.Tangen, and J.W.Kronstad (2007).
Transcriptional regulation by protein kinase A in Cryptococcus neoformans.
  PLoS Pathog, 3, e42.  
17227760 Y.Yamada, N.N.Suzuki, T.Hanada, Y.Ichimura, H.Kumeta, Y.Fujioka, Y.Ohsumi, and F.Inagaki (2007).
The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation.
  J Biol Chem, 282, 8036-8043.
PDB code: 2dyt
16424903 J.H.Ahn, D.Miller, V.J.Winter, M.J.Banfield, J.H.Lee, S.Y.Yoo, S.R.Henz, R.L.Brady, and D.Weigel (2006).
A divergent external loop confers antagonistic activity on floral regulators FT and TFL1.
  EMBO J, 25, 605-614.
PDB codes: 1wko 1wkp
17076703 J.Mima, H.Fukada, M.Nagayama, and M.Ueda (2006).
Specific membrane binding of the carboxypeptidase Y inhibitor I(C), a phosphatidylethanolamine-binding protein family member.
  FEBS J, 273, 5374-5383.  
16456706 M.C.Clark, D.McElheny, J.Wojcik, J.Kurutz, M.R.Rosner, and S.Koide (2006).
NMR assignment of rat Raf kinase inhibitor protein.
  J Biomol NMR, 36, 4.  
16170456 F.Chardon, and C.Damerval (2005).
Phylogenomic analysis of the PEBP gene family in cereals.
  J Mol Evol, 61, 579-590.  
15686621 N.Trakul, and M.R.Rosner (2005).
Modulation of the MAP kinase signaling cascade by Raf kinase inhibitory protein.
  Cell Res, 15, 19-23.  
15894619 Y.Hanzawa, T.Money, and D.Bradley (2005).
A single amino acid converts a repressor to an activator of flowering.
  Proc Natl Acad Sci U S A, 102, 7748-7753.  
15075275 H.Chautard, M.Jacquet, F.Schoentgen, N.Bureaud, and H.Bénédetti (2004).
Tfs1p, a member of the PEBP family, inhibits the Ira2p but not the Ira1p Ras GTPase-activating protein in Saccharomyces cerevisiae.
  Eukaryot Cell, 3, 459-470.  
15333936 J.Mima, M.Hayashida, T.Fujii, Y.Hata, R.Hayashi, and M.Ueda (2004).
Crystallization and preliminary X-ray analysis of carboxypeptidase Y inhibitor IC complexed with the cognate proteinase.
  Acta Crystallogr D Biol Crystallogr, 60, 1622-1624.  
15302887 X.Wang, N.Li, B.Liu, H.Sun, T.Chen, H.Li, J.Qiu, L.Zhang, T.Wan, and X.Cao (2004).
A novel human phosphatidylethanolamine-binding protein resists tumor necrosis factor alpha-induced apoptosis by inhibiting mitogen-activated protein kinase pathway activation and phosphatidylethanolamine externalization.
  J Biol Chem, 279, 45855-45864.  
12492898 B.S.Vallée, G.Coadou, H.Labbé, D.Sy, F.Vovelle, and F.Schoentgen (2003).
Peptides corresponding to the N- and C-terminal parts of PEBP are well-structured in solution: new insights into their possible interaction with partners in vivo.
  J Pept Res, 61, 47-57.  
12791700 J.Mima, Y.Narita, H.Chiba, and R.Hayashi (2003).
The multiple site binding of carboxypeptidase Y inhibitor (IC) to the cognate proteinase. Implications for the biological roles of the phosphatidylethanolamine-binding protein.
  J Biol Chem, 278, 29792-29798.  
12551925 K.C.Corbit, N.Trakul, E.M.Eves, B.Diaz, M.Marshall, and M.R.Rosner (2003).
Activation of Raf-1 signaling by protein kinase C through a mechanism involving Raf kinase inhibitory protein.
  J Biol Chem, 278, 13061-13068.  
12839983 K.Takeda, H.Miyatake, N.Yokota, S.Matsuyama, H.Tokuda, and K.Miki (2003).
Crystal structures of bacterial lipoprotein localization factors, LolA and LolB.
  EMBO J, 22, 3199-3209.
PDB codes: 1iwl 1iwm 1iwn 1ua8
12037323 P.C.Simister, M.J.Banfield, and R.L.Brady (2002).
The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family.
  Acta Crystallogr D Biol Crystallogr, 58, 1077-1080.
PDB code: 1kn3
11722570 B.S.Vallée, P.Tauc, J.C.Brochon, R.Maget-Dana, D.Lelièvre, M.H.Metz-Boutigue, N.Bureaud, and F.Schoentgen (2001).
Behaviour of bovine phosphatidylethanolamine-binding protein with model membranes. Evidence of affinity for negatively charged membranes.
  Eur J Biochem, 268, 5831-5841.  
11585904 K.C.Yeung, D.W.Rose, A.S.Dhillon, D.Yaros, M.Gustafsson, D.Chatterjee, B.McFerran, J.Wyche, W.Kolch, and J.M.Sedivy (2001).
Raf kinase inhibitor protein interacts with NF-kappaB-inducing kinase and TAK1 and inhibits NF-kappaB activation.
  Mol Cell Biol, 21, 7207-7217.  
11318875 N.Mimida, K.Goto, Y.Kobayashi, T.Araki, J.H.Ahn, D.Weigel, M.Murata, F.Motoyoshi, and W.Sakamoto (2001).
Functional divergence of the TFL1-like gene family in Arabidopsis revealed by characterization of a novel homologue.
  Genes Cells, 6, 327-336.  
11514577 T.Kroslak, T.Koch, E.Kahl, and V.Höllt (2001).
Human phosphatidylethanolamine-binding protein facilitates heterotrimeric G protein-dependent signaling.
  J Biol Chem, 276, 39772-39778.  
11114512 J.H.Hurley, Y.Tsujishita, and M.A.Pearson (2000).
Floundering about at cell membranes: a structural view of phospholipid signaling.
  Curr Opin Struct Biol, 10, 737-743.  
10726774 Y.Kuramitsu, M.Fujimoto, T.Tanaka, J.Ohata, and K.Nakamura (2000).
Differential expression of phosphatidylethanol-amine-binding protein in rat hepatoma cell lines: analyses of tumor necrosis factor-alpha-resistant cKDH-8/11 and -sensitive KDH-8/YK cells by two-dimensional gel electrophoresis.
  Electrophoresis, 21, 660-664.  
10542049 B.Vallée, C.Teyssier, R.Maget-Dana, J.Ramstein, N.Bureaud, and F.Schoentgen (1999).
Stability and physicochemical properties of the bovine brain phosphatidylethanolamine-binding protein.
  Eur J Biochem, 266, 40-52.  
10583961 I.Kardailsky, V.K.Shukla, J.H.Ahn, N.Dagenais, S.K.Christensen, J.T.Nguyen, J.Chory, M.J.Harrison, and D.Weigel (1999).
Activation tagging of the floral inducer FT.
  Science, 286, 1962-1965.  
10583960 Y.Kobayashi, H.Kaya, K.Goto, M.Iwabuchi, and T.Araki (1999).
A pair of related genes with antagonistic roles in mediating flowering signals.
  Science, 286, 1960-1962.  
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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