1DGD

AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE

Summary for 1DGD

• Entry DOI: 10.2210/pdb1dgd/pdb
• Descriptor: DIALKYLGLYCINE DECARBOXYLASE, SODIUM ION, LITHIUM ION, ... (6 entities in total)
• Functional Keywords: lyase
• Biological source: Burkholderia cepacia
• Total number of polymer chains: 1
• Total formula weight: 46846.45

Authors

Hohenester, E.,Jansonius, J.N. (deposition date: 1994-06-29, release date: 1994-09-30, Last modification date: 2025-03-26)

Primary citation

Hohenester, E.,Keller, J.W.,Jansonius, J.N.
An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.
Biochemistry, 33:13561-13570, 1994

PubMed Abstract: The pyridoxal 5'-phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) is activated by K+ and Rb+ ions, whereas Li+ and Na+ ions are inhibitory. A binding site for alkali metal ions close to the active site (site 1) was discovered in the crystal structure of DGD, and an exchange of K+ for Na+ at this site was shown to affect the conformation of two active site residues [Toney, M. D., Hohenester, E., Cowan, S. W., & Jansonius, J. N. (1993) Science 261, 756-759]. We have investigated the effects of alkali metal ions on DGD activity and have determined the crystal structures at 2.8 A resolution of DGD with Li+ and Rb+ bound at site 1. Due to the weak scattering of the Li+ ion, its position had to be modeled using information from small molecule structures. A comparison of the DGD structures with Li+, Na+, K+, and Rb+ bound at site 1 reveals a striking correlation between active site structure and enzymatic activity. The small, inhibitory ions Li+ and Na+ are accommodated by replacing two protein-derived ligands of the larger, activating ions K+ and Rb+ by a single water molecule. This actuates a two-state structural switch between active and inactive enzyme that involves a concerted reorientation of the active site residues Ser80 and Tyr301 and a small change in the quaternary structure of the DGD tetramer. An important role of the essential K+ ion in both cofactor binding and the organization of a catalytically competent active site structure is proposed. In the structure of DGD with Rb+ bound at site 1, a second Rb+ ion has partially replaced the structural Na+ ion at metal binding site 2 on the surface of the DGD molecule, without significantly altering the protein structure. In contrast to Na+, the Rb+ ion is bound with unfavorable geometry, and it is proposed that the rigid site 2 structure results in a pronounced selectivity for Na+ ions.

PubMed: 7947767
DOI: 10.1021/bi00250a008

Experimental method

X-RAY DIFFRACTION (2.8 Å)