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- PDB-1kzx: Solution structure of human intestinal fatty acid binding protein... -

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Basic information

Entry
Database: PDB / ID: 1kzx
TitleSolution structure of human intestinal fatty acid binding protein with a naturally-occurring single amino acid substitution (A54T)
ComponentsINTESTINAL FATTY ACID-BINDING PROTEIN (T54)
KeywordsLIPID BINDING PROTEIN / NMR spectroscopy / 15N isotope labelling / Fatty acid binding / Type 2 diabetes / Single base polymorphism / Holo-form
Function / homology
Function and homology information


intestinal lipid absorption / apical cortex / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / microvillus / fatty acid transport / fatty acid binding / fatty acid metabolic process / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, energy minimization
AuthorsZhang, F. / Luecke, C. / Baier, L.J. / Sacchettini, J.C. / Hamilton, J.A.
Citation
Journal: Biochemistry / Year: 2003
Title: Solution structure of human intestinal fatty acid binding protein with a naturally-occurring single amino acid substitution (A54T) that is associated with altered lipid metabolism
Authors: Zhang, F. / Luecke, C. / Baier, L.J. / Sacchettini, J.C. / Hamilton, J.A.
#1: Journal: J.Biomol.NMR / Year: 1997
Title: SOLUTION STRUCTURE OF HUMAN INTESTINAL FATTY ACID BINDING PROTEIN: IMPLICATIONS FOR LIGAND ENTRY AND EXIT
Authors: Zhang, F. / Luecke, C. / Baier, L.J. / Sacchettini, J.C. / Hamilton, J.A.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: A POLYMORPHISM IN THE HUMAN INTESTINAL FATTY ACID BINDING PROTEIN ALTERS FATTY ACID TRANSPORT ACROSS CACO-2 CELLS
Authors: Baier, L.J. / Bogardus, C. / Sacchettini, J.C.
#3: Journal: J.Clin.Invest. / Year: 1995
Title: AN AMINO ACID SUBSTITUTION IN THE HUMAN INTESTINAL FATTY ACID BINDING PROTEIN IS ASSOCIATED WITH INCREASED FATTY ACID BINDING, INCREASED FAT OXIDATION, AND INSULIN RESISTANCE
Authors: Baier, L.J. / Sacchettini, J.C. / Knowler, W.C. / Eads, J. / Paolisso, G. / Tataranni, P.A. / Mochizuki, H. / Bennet, H.P. / Bogardus, C. / Prochazka, M.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The mutation is due to a naturally occuring polymorphism in the human genome. This ...SEQUENCE The mutation is due to a naturally occuring polymorphism in the human genome. This polymorphism at codon 54, which changes ALA-54 (0.71 allele frequency in a population of native americans) to THR-54 (0.29 allelle frequency), has been associated with type-2 diabetes and insulin resistance.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTESTINAL FATTY ACID-BINDING PROTEIN (T54)


Theoretical massNumber of molelcules
Total (without water)15,1281
Polymers15,1281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300target function
Representative

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Components

#1: Protein INTESTINAL FATTY ACID-BINDING PROTEIN (T54) / I-FABP / FABPI


Mass: 15128.069 Da / Num. of mol.: 1 / Mutation: A54T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP2 / Plasmid: PET-3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12104

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H TOCSY, 1H-1H NOESY
1221H-15N HSQC, 1H-15N HTQC, 3D 1H-15N TOCSY-HMQC, 3D 1H-15N NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM T54 I-FABP, 20mM phosphate buffer, 0.05% sodium azide95% H2O/5% D2O
23mM T54 I-FABP U-15N, 20mM phosphate buffer, 0.05% sodium azide95% H2O/5% D2O
Sample conditionsIonic strength: 20mM phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
nmr2st2.05P. Pristovsekdata analysis
DYANA1.5P. Guentertstructure solution
Discover97MSIrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, energy minimization
Software ordinal: 1
Details: the structures are based on a total number of 2497 distance restraints
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 20

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