spacer
spacer

PDBsum entry 1lid
Go to PDB code: 
protein ligands links
Lipid binding protein PDB id
1lid

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
131 a.a. *
Ligands
OLA
Waters ×92
* Residue conservation analysis
PDB id:
1lid
Name: Lipid binding protein
Title: The adipocyte lipid-binding protein at 1.6 angstroms resolution: crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids
Structure: Adipocyte lipid-binding protein. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.60Å     R-factor:   0.172    
Authors: Z.Zu,D.A.Bernlohr,L.J.Banaszak
Key ref: Z.Xu et al. (1993). The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids. J Biol Chem, 268, 7874-7884. PubMed id: 8463311
Date:
21-Dec-93     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04117  (FABP4_MOUSE) -  Fatty acid-binding protein, adipocyte from Mus musculus
Seq:
Struc: 		132 a.a.
131 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
J Biol Chem 268:7874-7884 (1993)
PubMed id: 8463311  
 
 
The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids.
Z.Xu, D.A.Bernlohr, L.J.Banaszak.
 
  ABSTRACT  
 
Crystals of the adipocyte lipid-binding protein which diffract to near atomic resolution have been obtained in Na/K phosphate buffer/precipitant system. The structures of the apo-form and the protein with bound oleic acid and stearic acid have been determined and refined to 1.6-A resolution with R-factor around 18%. The conformations of the bound fatty acids are nearly the same. In both cases, the carboxylate group of the ligand interacts directly with Arg126 and Tyr128, indirectly with Arg106 through a water molecule. The hydrocarbon tail sticks out of the protein surface through a hydrophobic patch. Saturated and unsaturated fatty acids bind in essentially the same conformation. The remaining space of the binding pocket is filled with well ordered water molecules interacting with most of the polar side chains. Comparisons between the holo- and apostructures reveal that the hydrophobic patch on the protein surface formed by a helix and several tight turns might serve as a portal for lipid binding. Since the adipocyte lipid-binding protein is phosphorylated at Tyr19 by the insulin receptor kinase, the position of this side chain has been re-evaluated using the coordinates of the holo-forms. It appears that the position of Tyr19 does not change significantly upon the binding of either of the fatty acids.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20509169 K.Hellberg, P.A.Grimsrud, A.C.Kruse, L.J.Banaszak, D.H.Ohlendorf, and D.A.Bernlohr (2010).
X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal.
  Protein Sci, 19, 1480-1489.
PDB codes: 3js1 3jsq
  20225258 T.Young, L.Hua, X.Huang, R.Abel, R.Friesner, and B.J.Berne (2010).
Dewetting transitions in protein cavities.
  Proteins, 78, 1856-1869.  
19754198 A.V.Hertzel, K.Hellberg, J.M.Reynolds, A.C.Kruse, B.E.Juhlmann, A.J.Smith, M.A.Sanders, D.H.Ohlendorf, J.Suttles, and D.A.Bernlohr (2009).
Identification and characterization of a small molecule inhibitor of Fatty Acid binding proteins.
  J Med Chem, 52, 6024-6031.
PDB code: 3hk1
19318353 B.R.Thompson, A.M.Mazurkiewicz-Muñoz, J.Suttles, C.Carter-Su, and D.A.Bernlohr (2009).
Interaction of adipocyte fatty acid-binding protein (AFABP) and JAK2: AFABP/aP2 as a regulator of JAK2 signaling.
  J Biol Chem, 284, 13473-13480.  
19156818 C.Vasileiou, K.S.Lee, R.M.Crist, S.Vaezeslami, S.M.Goins, J.H.Geiger, and B.Borhan (2009).
Dissection of the critical binding determinants of cellular retinoic acid binding protein II by mutagenesis and fluorescence binding assay.
  Proteins, 76, 281-290.  
17761196 R.E.Gillilan, S.D.Ayers, and N.Noy (2007).
Structural basis for activation of fatty acid-binding protein 4.
  J Mol Biol, 372, 1246-1260.
PDB codes: 2q9s 2qm9
17594059 T.Janvilisri, W.Likitponrak, S.Chunchob, R.Grams, and S.Vichasri-Grams (2007).
Charge modification at conserved positively charged residues of fatty acid binding protein (FABP) from the giant liver fluke Fasciola gigantica: its effect on oligomerization and binding properties.
  Mol Cell Biochem, 305, 95.  
  16424607 A.Chmurzyńska (2006).
The multigene family of fatty acid-binding proteins (FABPs): function, structure and polymorphism.
  J Appl Genet, 47, 39-48.  
17106765 D.L.Lynch, and P.H.Reggio (2006).
Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer.
  J Comput Aided Mol Des, 20, 495-509.  
16755609 M.Careri, L.Elviri, A.Mangia, I.Zagnoni, F.Torta, D.Cavazzini, and G.L.Rossi (2006).
Mass spectrometry techniques for detection of ligand-dependent changes in the conformational flexibility of cellular retinol-binding protein type I localized by hydrogen/deuterium exchange.
  Rapid Commun Mass Spectrom, 20, 1973-1980.  
16361342 R.Friedman, E.Nachliel, and M.Gutman (2006).
Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein.
  Biophys J, 90, 1535-1545.  
15959519 T.Kuzuyama, J.P.Noel, and S.B.Richard (2005).
Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products.
  Nature, 435, 983-987.
PDB codes: 1zb6 1zcw 1zdw 1zdy
14696180 K.Gunasekaran, A.T.Hagler, and L.M.Gierasch (2004).
Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions.
  Proteins, 54, 179-194.  
14673826 M.Careri, L.Elviri, I.Zagnoni, D.Cavazzini, and G.L.Rossi (2003).
Acid-induced denaturation of cellular retinol-binding proteins types I and II studied by electrospray mass spectrometry.
  Rapid Commun Mass Spectrom, 17, 2773-2780.  
11965396 M.van Dongen, J.Weigelt, J.Uppenberg, J.Schultz, and M.Wikström (2002).
Structure-based screening and design in drug discovery.
  Drug Discov Today, 7, 471-478.  
11106780 P.H.Reggio, and H.Traore (2000).
Conformational requirements for endocannabinoid interaction with the cannabinoid receptors, the anandamide transporter and fatty acid amidohydrolase.
  Chem Phys Lipids, 108, 15-35.  
10026291 P.Penzes, and J.L.Napoli (1999).
Holo-cellular retinol-binding protein: distinction of ligand-binding affinity from efficiency as substrate in retinal biosynthesis.
  Biochemistry, 38, 2088-2093.  
9719561 H.Vorum, P.Madsen, I.Svendsen, J.E.Cells, and B.Honoré (1998).
Expression of recombinant psoriasis-associated fatty acid binding protein in Escherichia coli: gel electrophoretic characterization, analysis of binding properties and comparison with human serum albumin.
  Electrophoresis, 19, 1793-1802.  
9533682 T.B.Woolf (1998).
Simulations of fatty acid-binding proteins suggest sites important for function. I. Stearic acid.
  Biophys J, 74, 681-693.  
9533683 T.B.Woolf, and M.Tychko (1998).
Simulations of fatty acid-binding proteins. II. Sites for discrimination of monounsaturated ligands.
  Biophys J, 74, 694-707.  
9849941 V.J.LiCata, and D.A.Bernlohr (1998).
Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins.
  Proteins, 33, 577-589.  
9240929 D.A.Bernlohr, M.A.Simpson, A.V.Hertzel, and L.J.Banaszak (1997).
Intracellular lipid-binding proteins and their genes.
  Annu Rev Nutr, 17, 277-303.  
9063893 M.E.Hodsdon, and D.P.Cistola (1997).
Discrete backbone disorder in the nuclear magnetic resonance structure of apo intestinal fatty acid-binding protein: implications for the mechanism of ligand entry.
  Biochemistry, 36, 1450-1460.  
8608126 C.D.Kane, N.R.Coe, B.Vanlandingham, P.Krieg, and D.A.Bernlohr (1996).
Expression, purification, and ligand-binding analysis of recombinant keratinocyte lipid-binding protein (MAL-1), an intracellular lipid-binding found overexpressed in neoplastic skin cells.
  Biochemistry, 35, 2894-2900.  
8808741 D.M.van Aalten, R.Bywater, J.B.Findlay, M.Hendlich, R.W.Hooft, and G.Vriend (1996).
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.
  J Comput Aided Mol Des, 10, 255-262.  
8573586 F.M.Herr, J.Aronson, and J.Storch (1996).
Role of portal region lysine residues in electrostatic interactions between heart fatty acid binding protein and phospholipid membranes.
  Biochemistry, 35, 1296-1303.  
9082452 J.F.Glatz, and G.J.van der Vusse (1996).
Cellular fatty acid-binding proteins: their function and physiological significance.
  Prog Lipid Res, 35, 243-282.  
8634281 M.R.Rich, and J.S.Evans (1996).
Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation.
  Biochemistry, 35, 1506-1515.  
8718858 W.Minor, J.Steczko, B.Stec, Z.Otwinowski, J.T.Bolin, R.Walter, and B.Axelrod (1996).
Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution.
  Biochemistry, 35, 10687-10701.
PDB code: 1yge
  8829367 D.Mangroo, B.L.Trigatti, and G.E.Gerber (1995).
Membrane permeation and intracellular trafficking of long chain fatty acids: insights from Escherichia coli and 3T3-L1 adipocytes.
  Biochem Cell Biol, 73, 223-234.  
7644552 J.H.Veerkamp, and R.G.Maatman (1995).
Cytoplasmic fatty acid-binding proteins: their structure and genes.
  Prog Lipid Res, 34, 17-52.  
7588781 M.Fujita, H.Fujii, T.Kanda, E.Sato, K.Hatakeyama, and T.Ono (1995).
Molecular cloning, expression, and characterization of a human intestinal 15-kDa protein.
  Eur J Biochem, 233, 406-413.  
7595283 R.L.Londraville, and B.D.Sidell (1995).
Purification and characterization of fatty acid-binding protein from aerobic muscle of the Antarctic icefish Chaenocephalus aceratus.
  J Exp Zool, 273, 190-203.  
7922029 A.C.Young, G.Scapin, A.Kromminga, S.B.Patel, J.H.Veerkamp, and J.C.Sacchettini (1994).
Structural studies on human muscle fatty acid binding protein at 1.4 A resolution: binding interactions with three C18 fatty acids.
  Structure, 2, 523-534.
PDB codes: 1hmr 1hms 1hmt
8174560 R.G.Maatman, M.Degano, H.T.Van Moerkerk, W.J.Van Marrewijk, D.J.Van der Horst, J.C.Sacchettini, and J.H.Veerkamp (1994).
Primary structure and binding characteristics of locust and human muscle fatty-acid-binding proteins.
  Eur J Biochem, 221, 801-810.  
8281930 D.Ricquier, and A.M.Cassard-Doulcier (1993).
The biochemistry of white and brown adipocytes analysed from a selection of proteins.
  Eur J Biochem, 218, 785-796.  
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.

 

spacer
spacer