Literature summary for 5.3.1.23 extracted from

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 (2008), Protein Sci., 17, 126-135 .

Crystallization (Commentary)

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

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

Metals/Ions	Comment	Organism	Structure
additional information	enzyme M1Pi does not require any metals to exhibit its catalytic activity	Bacillus subtilis

Natural Substrates/ Products (Substrates)

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

Organism	UniProt	Comment	Textmining
Bacillus subtilis	O31662	-	-
Bacillus subtilis 168	O31662	-	-

Reaction

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	a

Substrates and Products (Substrate)

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

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

Synonyms	Comment	Organism
5-methylthioribose 1-phosphate isomerase	-	Bacillus subtilis
Bs-M1Pi	-	Bacillus subtilis
M1Pi	-	Bacillus subtilis

General Information

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