2YVK

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis

Summary for 2YVK

• Entry DOI: 10.2210/pdb2yvk/pdb
• Related: 2YRF
• Descriptor: Methylthioribose-1-phosphate isomerase, 5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE (3 entities in total)
• Functional Keywords: isomerase, methionine salvage pathway
• Biological source: Bacillus subtilis
• Total number of polymer chains: 4
• Total formula weight: 165863.76

Authors

Tamura, H.,Inoue, T.,Kai, Y.,Matsumura, H. (deposition date: 2007-04-13, release date: 2008-01-22, Last modification date: 2023-10-25)

Primary citation

Tamura, H.,Saito, Y.,Ashida, H.,Inoue, T.,Kai, Y.,Yokota, A.,Matsumura, H.
Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism
Protein Sci., 17:126-135, 2008

PubMed Abstract: The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.

PubMed: 18156470
DOI: 10.1110/ps.073169008

Experimental method

X-RAY DIFFRACTION (2.4 Å)