3EXS

Crystal structure of KGPDC from Streptococcus mutans in complex with D-R5P

Summary for 3EXS

• Entry DOI: 10.2210/pdb3exs/pdb
• Related: 3EXR 3EXT
• Descriptor: RmpD (Hexulose-6-phosphate synthase), RIBULOSE-5-PHOSPHATE (3 entities in total)
• Functional Keywords: beta barrel, lyase
• Biological source: Streptococcus mutans
• Total number of polymer chains: 4
• Total formula weight: 95861.14

Authors

Li, G.L.,Liu, X.,Wang, K.T.,Li, L.F.,Su, X.D. (deposition date: 2008-10-17, release date: 2009-08-25, Last modification date: 2023-11-01)

Primary citation

Li, G.L.,Liu, X.,Nan, J.,Brostromer, E.,Li, L.F.,Su, X.D.
Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans
Biochem.Biophys.Res.Commun., 381:429-433, 2009

PubMed Abstract: The 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC) catalyses the decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose in the presence of magnesium ions. The enzyme is involved in L-ascorbate metabolism and plays an essential role in the pathway of glucuronate interconversion. Crystal structures of Streptococcus mutans KGPDC were determined in the absence and presence of the product analog D-ribulose 5-phosphate. We have observed an 8 A alphaB-helix movement and other structural rearrangements around the active site between the apo-structures and product analog bound structure. These drastic conformational changes upon ligand binding are the first observation of this kind for the KGPDC family. The flexibilities of both the alpha-helix lid and the side chains of Arg144 and Arg197 are associated with substrate binding and product releasing. The open-closed conformational changes of the active site, through the movements of the alpha-helix lid and the arginine residues are important for substrate binding and catalysis.

PubMed: 19222992
DOI: 10.1016/j.bbrc.2009.02.049

Experimental method

X-RAY DIFFRACTION (2.5 Å)