1ACA

THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN ACYL-COENZYME A BINDING PROTEIN AND PALMITOYL-COENZYME A


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Three-dimensional structure of the complex between acyl-coenzyme A binding protein and palmitoyl-coenzyme A.

Kragelund, B.B.Andersen, K.V.Madsen, J.C.Knudsen, J.Poulsen, F.M.

(1993) J.Mol.Biol. 230: 1260-1277

  • DOI: 10.1006/jmbi.1993.1240
  • Also Cited By: 1NTI

  • PubMed Abstract: 
  • Multidimensional 1H, 13C and 15N nuclear magnetic resonance spectroscopy has been used to study the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein. The 1H and the 15N spectra of the holo-protein have been almost completely a ...

    Multidimensional 1H, 13C and 15N nuclear magnetic resonance spectroscopy has been used to study the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein. The 1H and the 15N spectra of the holo-protein have been almost completely assigned and so has most of the 1H spectrum of the coenzyme A part of the protein-bound ligand. The palmitoyl part of the ligand has been uniformly labelled with 13C and the nuclear magnetic resonance signals of the carbon atoms and their protons have been assigned at the two ends of the hydrocarbon chain. A total of 1251 distance restraints from nuclear Overhauser effects and 131 dihedral angle restraints from three-bond coupling constants provided the basis for the structure calculation. A comparison of 20 structures calculated from these data to the average structure showed that they could be aligned with an atomic root-mean-square deviation of 1.3(+/- 0.2) A for all C, N, O, P and S atoms in protein and ligand. The apo-protein is a four-helix protein and this structure is maintained in the holo-protein. The four alpha-helices are Ac1 of residues 3 to 15, Ac2 from residue 20 to 36, Ac3 from 51 to 62, and Ac4 from 65 to 84. For the four alpha-helices of the peptide backbone of the holo-protein the root-mean-square deviation for the C, C alpha and N atoms was 0.42(+/- 0.08) A. The binding site for the palmitoyl-chain stretches between the N-terminal end of Ac3 where the carboxyl part binds, to the N-terminal of Ac3 where the omega-end of the palmitoyl part binds. The adenosine-3'-phosphate is bound near residues of each of the four helices in an arrangement where it can form salt bridges and/or hydrogen bonds to either backbone or side-chain atoms of Ala9, Tyr28, Lys32, Lys54 and Tyr73. The polar parts of the pantetheine and the pyrophosphate are structured in the bound ligand to form an interface with the solvent. Also the ligand forms a set of non-polar intramolecular interactions where the adenine, the pantetheine, and the palmitoyl-chain are associated, so overall the structure of the bound ligand seems to be organized to protect the lipophilic palmitoyl part from the polar solvent.


    Related Citations: 
    • Amino Acid Sequence of Acyl-Coa-Binding Protein from Cow Liver
      Mikkelsen, J.,Hojrup, P.,Nielsen, P.F.,Roepstorff, P.,Knudsen, J.
      (1987) Biochem.J. 245: 857
    • Three-Dimensional Structure in Solution of Acyl-Coenzyme a Binding Protein from Bovine Liver
      Andersen, K.V.,Poulsen, F.M.
      (1992) J.Mol.Biol. 226: 1131
    • The Secondary Structure in Solution of Acyl-Coenzyme a Binding Protein from Bovine Liver Using 1H Nuclear Magnetic Resonance Spectroscopy
      Andersen, K.V.,Ludvigsen, S.,Mandrup, S.,Knudsen, J.,Poulsen, F.M.
      (1991) Biochemistry 30: 10654


    Organizational Affiliation

    Carlsberg Laboratorium, Kemisk Afdeling Gamle Carlsberg Vej 10, Valby, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACYL-COENZYME A BINDING PROTEIN
A
86Bos taurusGene Names: DBI
Find proteins for P07107 (Bos taurus)
Go to Gene View: DBI
Go to UniProtKB:  P07107
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 
  • Olderado: 1ACA Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-05-23
    Type: Other
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other