Crystallization (Comment) | Organism |
---|---|
purified enzyme in complex with product S-methyl-1-thio-D-ribulose 1-phosphate or a sulfate ion, sitting drop vapor diffusion method, mixing of 0.001 ml of 10 mg/ml protein in 50 mM Na HEPES, pH 7.4, and 1 mM EDTA, with or without 33 mM MTR-1-P, with 0.004-0.006 ml of reservoir solution containing 0.2 M K formate and 15% w/v PEG 3350, 20°C, X-ray diffraction structure determination and analysis at 2.4 A and 2.7 A resolution, respectively. The asymmetric unit contains two dimers for the MTRu-1-P-bound form, while one dimer is found in the asymmetric unit for the sulfate-bound form. Molecular replacement method using the crystal structure of Ypr118w (RCSB, PDB ID 1W2W) as a search model, and modeling | Bacillus subtilis |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
additional information | enzyme M1Pi does not require any metals to exhibit its catalytic activity | Bacillus subtilis |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
S-methyl-5-thio-alpha-D-ribose 1-phosphate | Bacillus subtilis | - |
S-methyl-5-thio-D-ribulose 1-phosphate | - |
r | |
S-methyl-5-thio-alpha-D-ribose 1-phosphate | Bacillus subtilis 168 | - |
S-methyl-5-thio-D-ribulose 1-phosphate | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Bacillus subtilis | O31662 | - |
- |
Bacillus subtilis 168 | O31662 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate | structure-function analysis and catalytic mechanism, overview. Two variants of isomerization mechanism are possible, the enediol and the hydride transfer mechanism, overview | Bacillus subtilis |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
S-methyl-5-thio-alpha-D-ribose 1-phosphate | - |
Bacillus subtilis | S-methyl-5-thio-D-ribulose 1-phosphate | - |
r | |
S-methyl-5-thio-alpha-D-ribose 1-phosphate | - |
Bacillus subtilis 168 | S-methyl-5-thio-D-ribulose 1-phosphate | - |
r |
Subunits | Comment | Organism |
---|---|---|
More | enzyme structure and active site structure comparisons, open/closed conformational transition of enzyme M1Pi. The structure of Bs-M1Pi shows that the active site is completely shielded from the solvent region. The substrate binding is likely to induce the large conformational changes of N- and C-terminal domains as well as the rearrangement of the hydrogen-bond network around the loops 93-98 and 290-294 to stabilize the closed state of the enzyme | Bacillus subtilis |
Synonyms | Comment | Organism |
---|---|---|
5-methylthioribose 1-phosphate isomerase | - |
Bacillus subtilis |
Bs-M1Pi | - |
Bacillus subtilis |
M1Pi | - |
Bacillus subtilis |
General Information | Comment | Organism |
---|---|---|
metabolism | the methionine salvage pathway (MSP) plays a crucial role in recycling a sulfhydryl derivative of the nucleoside. In MSP of Bacillus subtilis, the 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) | Bacillus subtilis |
additional information | enzyme structure and active site structure comparisons. The highly conserved residues at the active site, Cys160 and Asp240, are most likely to be involved in catalysis, structure-function analysis and catalytic mechanism, overview. Two variants of isomerization mechanism are possible, the enediol and the hydride transfer mechanism. M1Pi does not require any metals to exhibit its catalytic activity, which is analogous to the enzymes that proceed via a cis-enediol intermediate. On the other hand, NMR and mass spectrometry suggest the isomerase reaction of M1Pi in D2O proceeds without incorporation of deuterium from solvent into the product, resembling those measurements of xylose isomerase (XI), which adopts the hydride transfer mechanism, but which also requires two divalent cations such as Mg2+ or Mn2+. The hydrophobic interaction of the methylthio group includes the side chains of Pro54, Ala162, Ala166, and Thr167. The side chain of Asp240 is surrounded by the hydrophobic pocket formed by residues Thr96, Ala97, and Phe317, which are absolutely conserved in all M1Pis. This hydrophobic pocket appears to restrict the rotation of the Asp240 side chain, which may permit a favorable interaction with the substrate (or product). The pKa of Asp240 is likely to be increased, which might enable Asp240 to play a dual role as a proton donor/acceptor | Bacillus subtilis |
physiological function | in the methionine salvage pathway (MSP) of Bacillus subtilis, 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes an interconversion of 5-methylthioribose 1-phosphate (MTR-1-P) and 5-methylthioribulose 1-phosphate (MTRu-1-P), classified as an aldose-ketose isomerase reaction | Bacillus subtilis |