1Z17

Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound ligand isoleucine

Summary for 1Z17

• Entry DOI: 10.2210/pdb1z17/pdb
• Related: 1Z15 1Z16 1Z18 2LBP 2LIV
• Descriptor: Leu/Ile/Val-binding protein, ISOLEUCINE, (4R)-2-METHYLPENTANE-2,4-DIOL, ... (4 entities in total)
• Functional Keywords: periplasmic binding proteins, alpha-beta fold, aliphatic amino acid binding protein, transport protein
• Biological source: Escherichia coli
• Cellular location: Periplasm: P02917
• Total number of polymer chains: 1
• Total formula weight: 37061.74

Authors

Trakhanov, S.D.,Vyas, N.K.,Kristensen, D.M.,Ma, J.,Quiocho, F.A. (deposition date: 2005-03-03, release date: 2005-10-04, Last modification date: 2023-08-23)

Primary citation

Trakhanov, S.D.,Vyas, N.K.,Luecke, H.,Kristensen, D.M.,Ma, J.,Quiocho, F.A.
Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity.
Biochemistry, 44:6597-6608, 2005

PubMed Abstract: The leucine/isoleucine/valine-binding protein (LIVBP or LivJ) serves as the primary high-affinity receptor of the Escherichia coli ABC-type transporter for the three aliphatic amino acids. The first structure of LIVBP determined previously without bound ligand showed a molecule comprised of two domains which are far apart and bisected by a wide open, solvent-accessible cleft. Here we report the crystal structures of another ligand-free state and three complexes with the aliphatic amino acids. In the present ligand-free structure, the two domains are farther apart. In the three very similar complex structures, the two domains are in close proximity, and each desolvated ligand is completely engulfed in the cleft and bound by both domains. The two different ligand-free structures, combined with those of the very similar ligand-bound structures, indicate the trajectory and backbone torsion angle changes of the hinges that accompany domain closure and play crucial functional roles. The amino acids are bound by polar and nonpolar interactions, occurring predominantly in one domain. Consistent with the protein specificity, the aliphatic side chains of the ligands lie in a hydrophobic pocket fully formed following domain or cleft closure. Comparison of the structures of LIVBP with several different binding proteins indicates no correlations between the magnitudes of the hinge-bending angles and the protein masses, the ligand sizes, or the number of segments connecting the two domains. Results of normal-mode analysis and molecular dynamics simulations are consistent with the trajectory and intrinsic flexibility of the interdomain hinges and the dominance of one domain in ligand binding in the open state.

PubMed: 15850393
DOI: 10.1021/bi047302o

Experimental method

X-RAY DIFFRACTION (1.96 Å)