PDBsum entry 1eii

Transport protein

PDB id: 1eii

Contents

Protein chain

134 a.a. *

Ligands

RTL

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Binding of retinol induces changes in rat cellular retinol-Binding protein ii conformation and backbone dynamics.

Authors

J.Lu, C.L.Lin, C.Tang, J.W.Ponder, J.L.Kao, D.P.Cistola, E.Li.

Ref.

J Mol Biol, 2000, 300, 619-632. [DOI no: 10.1006/jmbi.2000.3883]

PubMed id

10884357

Abstract

The structure and backbone dynamics of rat holo cellular retinol-binding protein II (holo-CRBP II) in solution has been determined by multidimensional NMR. The final structure ensemble was based on 3980 distance and 30 dihedral angle restraints, and was calculated using metric matrix distance geometry with pairwise Gaussian metrization followed by simulated annealing. The average RMS deviation of the backbone atoms for the final 25 structures relative to their mean coordinates is 0.85(+/-0.09) A. Comparison of the solution structure of holo-CRBP II with apo-CRBP II indicates that the protein undergoes conformational changes not previously observed in crystalline CRBP II, affecting residues 28-35 of the helix-turn-helix, residues 37-38 of the subsequent linker, as well as the beta-hairpin C-D, E-F and G-H loops. The bound retinol is completely buried inside the binding cavity and oriented as in the crystal structure. The order parameters derived from the (15)N T(1), T(2) and steady-state NOE parameters show that the backbone dynamics of holo-CRBP II is restricted throughout the polypeptide. The T(2) derived apparent backbone exchange rate and amide (1)H exchange rate both indicate that the microsecond to second timescale conformational exchange occurring in the portal region of the apo form has been suppressed in the holo form.

Figure 3.
Figure 3. (a) A stereodiagram of the final 25 NMR structures of holo-CRBP II in C a trace (in cyan) that are superim- posed on the four molecules of the X-ray structure of holo-CRBP II (in yellow). The bound retinol is highlighted in green and red in the NMR and X-ray structures, respectively. (b) A ribbon diagram of the mean NMR structure of CRBP II-retinol (ball/stick model) complex. These molecular images and the subsequent ones were generated using MOLMOL v.2.6 (Koradi et al., 1996).

Figure 5.
Figure 5. A stereodiagram of the bound retinols in the NMR ensemble (in green) superimposed on those in the crystal structures (in red). Residues that have NOE contacts with the ligand are shown in cyan along with the respective residues in the crystal structure (in yellow). Residues 20, 21, 24 (underneath the b-ionone ring of the bound retinol), 41, 59, 60 (above the b-ionone ring) and 63 (above the polyene chain) are omitted to allow a clear view of the ligand and the binding cavity.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 619-632) copyright 2000.

Secondary reference #1

Title

The structure and dynamics of rat apo-Cellular retinol-Binding protein ii in solution: comparison with the X-Ray structure.

Authors

J.Lu, C.L.Lin, C.Tang, J.W.Ponder, J.L.Kao, D.P.Cistola, E.Li.

Ref.

J Mol Biol, 1999, 286, 1179-1195. [DOI no: 10.1006/jmbi.1999.2544]

PubMed id

10047490

Figure 4.
Figure 4. (a) Distribution of the distance restraints for the final 25 NMR structures. The CSI-derived secondary

Figure 5.
Figure 5. A ribbon diagram of the mean coordinates for the NMR ensemble of apo-CRBP II (left) compared with the ribbon diagrams of the X-ray crystal structures of apo-CRBP II[a](helix, red and yellow; strand, cyan; coil, gray) and apo-CRBP II[b](helix, purple and yellow; strand, aquamarine; coil, sky blue). The secondary structural elements for the NMR structure are defined by the CSI.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Crystal structures of holo and apo-Cellular retinol-Binding protein ii.

Authors

N.S.Winter, J.M.Bratt, L.J.Banaszak.

Ref.

J Mol Biol, 1993, 230, 1247-1259.

PubMed id

8487303

Secondary reference #3

Title

Lipid-Binding proteins: a family of fatty acid and retinoid transport proteins.

Authors

L.Banaszak, N.Winter, Z.Xu, D.A.Bernlohr, S.Cowan, T.A.Jones.

Ref.

Adv Protein Chem, 1994, 45, 89.

PubMed id

8154375

Secondary reference #4

Title

The nmr solution structure of intestinal fatty acid-Binding protein complexed with palmitate: application of a novel distance geometry algorithm.

Authors

M.E.Hodsdon, J.W.Ponder, D.P.Cistola.

Ref.

J Mol Biol, 1996, 264, 585-602. [DOI no: 10.1006/jmbi.1996.0663]

PubMed id

8969307

Figure 5.
Figure 5. The ensemble of 20 final NMR structures emphasizing the bound fatty acid and several selected side-chains. The position of the protein backbone is indicated by a single C a trace taken from Figure 3. The bound palmitate is located near the center of the Figure with its carboxyl end pointing toward the lower right and its methyl end toward the upper left. Starting at the top of the Figure and proceeding clockwise around the structure, the displayed side-chains are Lys27, Phe128, Arg106, Leu64, and Tyr70.

Figure 9.
Figure 9. The progress of the iterative procedure for NOE cross-peak assignment and structure calculation. The y-axis displays the total number of interproton distance restraints (squares) and the average pairwise C a RMSD values for the ensemble of 20 structures (triangles) at each major step of the iterative procedure.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #5

Title

Ligand binding alters the backbone mobility of intestinal fatty acid-Binding protein as monitored by 15n nmr relaxation and 1h exchange.

Authors

M.E.Hodsdon, D.P.Cistola.

Ref.

Biochemistry, 1997, 36, 2278-2290. [DOI no: 10.1021/bi962018l]

PubMed id

9047330