PDBsum entry 1lls

Sugar binding protein

PDB id: 1lls

Contents

Protein chain

370 a.a. *

Metals

_XE

Waters ×171

* Residue conservation analysis

PDB id:

1lls

Name:

Sugar binding protein

Title:

Crystal structure of unliganded maltose binding protein with xenon

Structure:

Maltose-binding periplasmic protein. Chain: a. Synonym: maltodextrin-binding protein, mmbp. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.204 R-free: 0.226

Authors:

S.M.Rubin,S.-Y.Lee,E.J.Ruiz,A.Pines,D.E.Wemmer

Key ref:

S.M.Rubin et al. (2002). Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy. J Mol Biol, 322, 425-440. PubMed id: 12217701 DOI: 10.1016/S0022-2836(02)00739-8

Date:

30-Apr-02 Release date: 18-Sep-02

Protein chain

P0AEX9  (MALE_ECOLI) -  Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 370 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0022-2836(02)00739-8

J Mol Biol 322:425-440 (2002)

PubMed id: 12217701

Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy.

S.M.Rubin, S.Y.Lee, E.J.Ruiz, A.Pines, D.E.Wemmer.

ABSTRACT

Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered.

Selected figure(s)

Figure 2.
Figure 2. Stereo diagram of MBP with bound xenon. The density shown in magenta marks the difference Fourier map (contoured at 5s) generated from the previously published native data set and the data set presented here for MBP crystals pressurized with 8 atm xenon. The xenon-binding cavity is located in the N-terminal domain of the protein below the surface of the sugar binding cleft.

Figure 3.
Figure 3. Stereo view of the xenon-binding cavity in MBP. The electron density in cyan corresponds to a 2F[obs] -F[calc] map contoured at 2s. The xenon is localized in the cavity away from the lysine and water that mark the end of the cavity at the protein surface. While the presence of many hydrophobic side-chains is often observed in xenon-binding cavities, the proximity of the cavity to the surface is less common.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 425-440) copyright 2002.

Figures were selected by an automated process.