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PDBsum entry 1ifc
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Lipid binding protein PDB id
1ifc

 

 

 

 

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Contents
Protein chain
131 a.a. *
Waters ×476
* Residue conservation analysis
PDB id:
1ifc
Name: Lipid binding protein
Title: Refinement of the structure of recombinant rat intestinal fatty acid- binding apoprotein at 1.2 angstroms resolution
Structure: Intestinal fatty acid binding protein. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116
Resolution:
1.19Å     R-factor:   0.169    
Authors: G.Scapin,J.I.Gordon,J.C.Sacchettini
Key ref: G.Scapin et al. (1992). Refinement of the structure of recombinant rat intestinal fatty acid-binding apoprotein at 1.2-A resolution. J Biol Chem, 267, 4253-4269. PubMed id: 1740465
Date:
19-Dec-91     Release date:   31-Jan-94    
PROCHECK
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 Headers
 References

Protein chain
P02693  (FABPI_RAT) -  Fatty acid-binding protein, intestinal from Rattus norvegicus
Seq:
Struc: 		132 a.a.
131 a.a.
Key:    Secondary structure  CATH domain

 

 
J Biol Chem 267:4253-4269 (1992)
PubMed id: 1740465  
 
 
Refinement of the structure of recombinant rat intestinal fatty acid-binding apoprotein at 1.2-A resolution.
G.Scapin, J.I.Gordon, J.C.Sacchettini.
 
  ABSTRACT  
 
The three-dimensional structure of the 131-residue rat intestinal fatty acid-binding protein, without bound ligand (apoI-FABP), has been refined with x-ray diffraction data to a nominal resolution of 1.19 A. The final model has a conventional crystallographic R-factor of 16.9% for 34,290 unique reflections [a root mean square (r.m.s.) deviation for bond length of 0.012 A and a r.m.s. deviation of 2.368 degrees for bond angles]. Ninety-two residues are present as components of the protein's 10 anti-parallel beta-strands while 14 residues are part of its two short alpha-helices. The beta-strands and alpha-helices are organized into two nearly orthogonal beta-sheets. Particular attention has been placed in defining solvent structure and the structures of discretely disordered groups in this protein. Two hundred thirty-seven solvent molecules have been identified; 24 are located within apoI-FABP. The refined model includes alternate conformers for 228 protein atoms (109 main-chain, 119 side-chain) and 63 solvent molecules. We have found several aromatic side-chains with multiple conformations located near, or in, the protein's ligand binding site. This observation, along with the fact that these side-chains have a temperature factor that is relatively higher than that of other aromatic residues, suggests that they may be involved in the process of noncovalent binding of fatty acid. The absence of a true hydrophobic core in I-FABP suggests that its structural integrity may be maintained primarily by a hydrogen bonding network involving protein and solvent atoms.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287616 A.Bornot, C.Etchebest, and A.G.de Brevern (2011).
Predicting protein flexibility through the prediction of local structures.
  Proteins, 79, 839-852.  
19844951 G.R.Franchini, L.M.Curto, J.J.Caramelo, and J.María Delfino (2009).
Dissection of a beta-barrel motif leads to a functional dimer: The case of the intestinal fatty acid binding protein.
  Protein Sci, 18, 2592-2602.  
18178652 J.L.Schlessman, C.Abe, A.Gittis, D.A.Karp, M.A.Dolan, and B.García-Moreno E (2008).
Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
  Biophys J, 94, 3208-3216.
PDB codes: 2pw5 2pw7 2pyk 2pzt 2pzu 2pzw
18305196 N.Juranić, J.J.Dannenberg, G.Cornilescu, P.Salvador, E.Atanasova, H.C.Ahn, S.Macura, J.L.Markley, and F.G.Prendergast (2008).
Structural dependencies of protein backbone 2JNC' couplings.
  Protein Sci, 17, 768-776.  
19018099 S.Vaezeslami, X.Jia, C.Vasileiou, B.Borhan, and J.H.Geiger (2008).
Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
  Acta Crystallogr D Biol Crystallogr, 64, 1228-1239.
PDB codes: 3cwk 3d95 3d96
17660261 M.Mihajlovic, and T.Lazaridis (2007).
Modeling fatty acid delivery from intestinal fatty acid binding protein to a membrane.
  Protein Sci, 16, 2042-2055.  
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.  
15907702 H.Xiao, and I.A.Kaltashov (2005).
Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I.
  J Am Soc Mass Spectrom, 16, 869-879.  
16080148 P.M.Dalessio, S.E.Fromholt, and I.J.Ropson (2005).
The role of Trp-82 in the folding of intestinal fatty acid binding protein.
  Proteins, 61, 176-183.  
14627737 K.Modig, E.Kurian, F.G.Prendergast, and B.Halle (2003).
Water and urea interactions with the native and unfolded forms of a beta-barrel protein.
  Protein Sci, 12, 2768-2781.  
12486725 M.Kurz, V.Brachvogel, H.Matter, S.Stengelin, H.Thüring, and W.Kramer (2003).
Insights into the bile acid transportation system: the human ileal lipid-binding protein-cholyltaurine complex and its comparison with homologous structures.
  Proteins, 50, 312-328.
PDB codes: 1o1u 1o1v
14567680 M.Rajabzadeh, J.Kao, and C.Frieden (2003).
Consequences of single-site mutations in the intestinal fatty acid binding protein.
  Biochemistry, 42, 12192-12199.  
14573874 N.Juranić, S.Macura, and F.G.Prendergast (2003).
H-bonding mediates polarization of peptide groups in folded proteins.
  Protein Sci, 12, 2633-2636.  
12237460 C.Lücke, S.Huang, M.Rademacher, and H.Rüterjans (2002).
New insights into intracellular lipid binding proteins: The role of buried water.
  Protein Sci, 11, 2382-2392.  
12001232 D.Bakowies, and W.F.Van Gunsteren (2002).
Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein.
  Proteins, 47, 534-545.  
12381795 K.Chattopadhyay, S.Saffarian, E.L.Elson, and C.Frieden (2002).
Measurement of microsecond dynamic motion in the intestinal fatty acid binding protein by using fluorescence correlation spectroscopy.
  Proc Natl Acad Sci U S A, 99, 14171-14176.  
11900547 K.Chattopadhyay, S.Zhong, S.R.Yeh, D.L.Rousseau, and C.Frieden (2002).
The intestinal fatty acid binding protein: the role of turns in fast and slow folding processes.
  Biochemistry, 41, 4040-4047.  
11170215 V.A.Likić, and F.G.Prendergast (2001).
Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments.
  Proteins, 43, 65-72.  
10806391 C.Lücke, F.Zhang, J.A.Hamilton, J.C.Sacchettini, and H.Rüterjans (2000).
Solution structure of ileal lipid binding protein in complex with glycocholate.
  Eur J Biochem, 267, 2929-2938.
PDB code: 1eio
  10933500 L.Ragona, F.Fogolari, L.Zetta, D.M.Pérez, P.Puyol, K.De Kruif, F.Löhr, H.Rüterjans, and H.Molinari (2000).
Bovine beta-lactoglobulin: interaction studies with palmitic acid.
  Protein Sci, 9, 1347-1356.  
10653776 T.B.Woolf, A.Grossfield, and M.Tychko (2000).
Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations.
  Biophys J, 78, 608-625.  
10818349 T.Holton, T.R.Ioerger, J.A.Christopher, and J.C.Sacchettini (2000).
Determining protein structure from electron-density maps using pattern matching.
  Acta Crystallogr D Biol Crystallogr, 56, 722-734.  
  10752611 V.A.Likić, N.Juranić, S.Macura, and F.G.Prendergast (2000).
A "structural" water molecule in the family of fatty acid binding proteins.
  Protein Sci, 9, 497-504.  
10231541 G.V.Richieri, P.J.Low, R.T.Ogata, and A.M.Kleinfeld (1999).
Binding kinetics of engineered mutants provide insight about the pathway for entering and exiting the intestinal fatty acid binding protein.
  Biochemistry, 38, 5888-5895.  
10570238 G.Zanotti (1999).
Muscle fatty acid-binding protein.
  Biochim Biophys Acta, 1441, 94.  
  10452609 V.A.Likić, and F.G.Prendergast (1999).
Structure and dynamics of the fatty acid binding cavity in apo rat intestinal fatty acid binding protein.
  Protein Sci, 8, 1649-1657.  
9770459 B.Corsico, D.P.Cistola, C.Frieden, and J.Storch (1998).
The helical domain of intestinal fatty acid binding protein is critical for collisional transfer of fatty acids to phospholipid membranes.
  Proc Natl Acad Sci U S A, 95, 12174-12178.  
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.  
  10082380 K.Kim, and C.Frieden (1998).
Turn scanning by site-directed mutagenesis: application to the protein folding problem using the intestinal fatty acid binding protein.
  Protein Sci, 7, 1821-1828.  
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.  
9214305 I.J.Ropson, and P.M.Dalessio (1997).
Fluorescence spectral changes during the folding of intestinal fatty acid binding protein.
  Biochemistry, 36, 8594-8601.  
  9041638 K.Kim, R.Ramanathan, and C.Frieden (1997).
Intestinal fatty acid binding protein: a specific residue in one turn appears to stabilize the native structure and be responsible for slow refolding.
  Protein Sci, 6, 364-372.  
9047330 M.E.Hodsdon, and D.P.Cistola (1997).
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
  Biochemistry, 36, 2278-2290.
PDB code: 1ael
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.  
8805562 C.Lücke, F.Zhang, H.Rüterjans, J.A.Hamilton, and J.C.Sacchettini (1996).
Flexibility is a likely determinant of binding specificity in the case of ileal lipid binding protein.
  Structure, 4, 785-800.
PDB code: 1eal
8652536 D.P.Cistola, K.Kim, H.Rogl, and C.Frieden (1996).
Fatty acid interactions with a helix-less variant of intestinal fatty acid-binding protein.
  Biochemistry, 35, 7559-7565.  
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.  
8652535 K.Kim, D.P.Cistola, and C.Frieden (1996).
Intestinal fatty acid-binding protein: the structure and stability of a helix-less variant.
  Biochemistry, 35, 7553-7558.  
8770188 W.R.Kirk, E.Kurian, and F.G.Prendergast (1996).
Characterization of the sources of protein-ligand affinity: 1-sulfonato-8-(1')anilinonaphthalene binding to intestinal fatty acid binding protein.
  Biophys J, 70, 69-83.  
8541331 B.Rolf, E.Oudenampsen-Krüger, T.Börchers, N.J.Faergeman, J.Knudsen, A.Lezius, and F.Spener (1995).
Analysis of the ligand binding properties of recombinant bovine liver-type fatty acid binding protein.
  Biochim Biophys Acta, 1259, 245-253.  
7601110 D.Lassen, C.Lücke, M.Kveder, A.Mesgarzadeh, J.M.Schmidt, B.Specht, A.Lezius, F.Spener, and H.Rüterjans (1995).
Three-dimensional structure of bovine heart fatty-acid-binding protein with bound palmitic acid, determined by multidimensional NMR spectroscopy.
  Eur J Biochem, 230, 266-280.
PDB code: 1bwy
7705793 H.J.Verkade, R.J.Vonk, and F.Kuipers (1995).
New insights into the mechanism of bile acid-induced biliary lipid secretion.
  Hepatology, 21, 1174-1189.  
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.  
7597071 N.Shani, P.A.Watkins, and D.Valle (1995).
PXA1, a possible Saccharomyces cerevisiae ortholog of the human adrenoleukodystrophy gene.
  Proc Natl Acad Sci U S A, 92, 6012-6016.  
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.  
8054470 E.Schievano, D.Quarzago, P.Spadon, H.L.Monaco, G.Zanotti, and E.Peggion (1994).
Conformational and binding properties of chicken liver basic fatty acid binding protein in solution.
  Biopolymers, 34, 879-887.  
7704533 G.J.Kleywegt, T.Bergfors, H.Senn, P.Le Motte, B.Gsell, K.Shudo, and T.A.Jones (1994).
Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid.
  Structure, 2, 1241-1258.
PDB codes: 1cbq 1cbr 1cbs
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.  
8232257 D.Lassen, C.Lücke, A.Kromminga, A.Lezius, F.Spener, and H.Rüterjans (1993).
Solution structure of bovine heart fatty acid-binding protein (H-FABPc).
  Mol Cell Biochem, 123, 15-22.  
8265560 E.Freire, D.T.Haynie, and D.Xie (1993).
Molecular basis of cooperativity in protein folding. IV. CORE: a general cooperative folding model.
  Proteins, 17, 111-123.  
8232270 F.Schroeder, J.R.Jefferson, D.Powell, S.Incerpi, J.K.Woodford, S.M.Colles, S.Myers-Payne, T.Emge, T.Hubbell, and D.Moncecchi (1993).
Expression of rat L-FABP in mouse fibroblasts: role in fat absorption.
  Mol Cell Biochem, 123, 73-83.  
8232266 G.Scapin, A.C.Young, A.Kromminga, J.H.Veerkamp, J.I.Gordon, and J.C.Sacchettini (1993).
High resolution X-ray studies of mammalian intestinal and muscle fatty acid-binding proteins provide an opportunity for defining the chemical nature of fatty acid: protein interactions.
  Mol Cell Biochem, 123, 3.  
  8358295 J.J.Van Beeumen, B.V.Devreese, S.M.Van Bun, W.D.Hoff, K.J.Hellingwerf, T.E.Meyer, D.E.McRee, and M.A.Cusanovich (1993).
Primary structure of a photoactive yellow protein from the phototrophic bacterium Ectothiorhodospira halophila, with evidence for the mass and the binding site of the chromophore.
  Protein Sci, 2, 1114-1125.  
8488555 S.Petrou, R.W.Ordway, J.J.Singer, and J.V.Walsh (1993).
A putative fatty acid-binding domain of the NMDA receptor.
  Trends Biochem Sci, 18, 41-42.  
1483473 C.Lücke, D.Lassen, H.J.Kreienkamp, F.Spener, and H.Rüterjans (1992).
Sequence-specific 1H-NMR assignment and determination of the secondary structure of bovine heart fatty-acid-binding protein.
  Eur J Biochem, 210, 901-910.  
1496015 I.J.Ropson, and C.Frieden (1992).
Dynamic NMR spectral analysis and protein folding: identification of a highly populated folding intermediate of rat intestinal fatty acid-binding protein by 19F NMR.
  Proc Natl Acad Sci U S A, 89, 7222-7226.  
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.

 

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