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S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
catalytic reaction mechanism, structure-function relationship, overview. Proposed reaction mechanism of M1Pi proceeds via a cis-phosphoenolate intermediate and through the following steps: (1) transfer of proton from Asp247 to the O4 atom of MTR-1-P, (2) proton abstraction from C2 atom of the substrate by the thiolate anion of Cys167 as well as cleavage of the C1-O4 bond, (3) simultaneous proton abstraction from O2 atom by the deprotonated Asp247 and transfer of proton from the thiol group of Cys167 to C1 atom, and (4) generation of the product, MTRu-1-P
S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
proposed reaction mechanism probably including residue Asp240, overview
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
S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
proposed reaction mechanism probably including residue Asp240, overview
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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
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
5-Methylthio-5-deoxy-D-ribose 1-phosphate
?
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
additional information
?
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
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r
5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-D-ribulose 1-phosphate
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
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enzyme of the pathway of the conversion of methylthioribose-1-phosphate to methionine
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
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enzyme in synthesis of methionine from 5'-S-methylthioadenosine
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
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enzyme in synthesis of methionine from 5'-S-methylthioadenosine
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
additional information
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substrate MTR-1-P is synthesized from S-adenosyl-L-methionine through hydrolysis of the adenine base by HCl, and C1 of the ribose moiety is phosphorylated by ATP via MtnK, an MTR kinase. MTR-1-P isomerase is assayed in a coupling reaction with MtnB and MtnW, previously identified as MTRu-1-P dehydratase and 2,3-diketo-5-methylthiopentyl-1-phosphate enolase respectively. In this assay, the reaction product MTRu-1-P is converted to 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P) by sequential reactions of MtnB and MtnW. NMR analysis of the MtnA reaction product, overview
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additional information
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substrate MTR-1-P is synthesized from S-adenosyl-L-methionine through hydrolysis of the adenine base by HCl, and C1 of the ribose moiety is phosphorylated by ATP via MtnK, an MTR kinase. MTR-1-P isomerase is assayed in a coupling reaction with MtnB and MtnW, previously identified as MTRu-1-P dehydratase and 2,3-diketo-5-methylthiopentyl-1-phosphate enolase respectively. In this assay, the reaction product MTRu-1-P is converted to 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P) by sequential reactions of MtnB and MtnW. NMR analysis of the MtnA reaction product, overview
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additional information
?
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substrate MTR-1-P is synthesized from S-adenosyl-L-methionine through hydrolysis of the adenine base by HCl, and C1 of the ribose moiety is phosphorylated by ATP via MtnK, an MTR kinase. MTR-1-P isomerase is assayed in a coupling reaction with MtnB and MtnW, previously identified as MTRu-1-P dehydratase and 2,3-diketo-5-methylthiopentyl-1-phosphate enolase respectively. In this assay, the reaction product MTRu-1-P is converted to 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P) by sequential reactions of MtnB and MtnW. NMR analysis of the MtnA reaction product, overview
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5-Methylthio-5-deoxy-D-ribose 1-phosphate
?
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
5-Methylthio-5-deoxy-D-ribose 1-phosphate
?
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enzyme of the pathway of the conversion of methylthioribose-1-phosphate to methionine
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?
5-Methylthio-5-deoxy-D-ribose 1-phosphate
?
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enzyme in synthesis of methionine from 5'-S-methylthioadenosine
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?
5-Methylthio-5-deoxy-D-ribose 1-phosphate
?
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enzyme in synthesis of methionine from 5'-S-methylthioadenosine
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-methyl-5-thio-D-ribulose 1-phosphate
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r
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evolution
the enzyme is a member of the family PF01008. The open and closed states of the proteins belonging to the family PF01008 are usually demarcated by the degree of angle formed owing to the bend in the longest helix alpha5
metabolism
the enzyme is part of the methionine salvage pathway (MSP) is a metabolic pathway for recovery of the reduced sulfur in 5-methylthioribose (MTR), which is formed in the synthesis of polyamines, as methionine
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)
metabolism
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the enzyme is part of the methionine salvage pathway (MSP) is a metabolic pathway for recovery of the reduced sulfur in 5-methylthioribose (MTR), which is formed in the synthesis of polyamines, as methionine
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metabolism
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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)
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physiological function
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MRDI is induced in metastatic cells by constitutive RhoA activation and promotes cell invasion
physiological function
enzyme MtnA of Bacillus subtilis catalyzes the isomerization of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). The reaction is an isomerization of an aldose phosphate harboring a phosphate group on the hemiacetal group
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
physiological function
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enzyme MtnA of Bacillus subtilis catalyzes the isomerization of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). The reaction is an isomerization of an aldose phosphate harboring a phosphate group on the hemiacetal group
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physiological function
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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
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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
additional information
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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
additional information
transition from an open to closed state creates a hydrophobic active site environment. The active-site pocket of M1Pi is optimized to follow a reaction mechanism via the formation of a cis-phosphoenolate intermediate, structural transition, overview
additional information
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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
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dimer
x-ray crystallography
homodimer
2 * 38900, detagged recombinant enzyme, SDS-PAGE
homodimer
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2 * 38900, detagged recombinant enzyme, SDS-PAGE
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homodimer
2 * 40000, about, recombinant enzyme, SDS-PAGE
additional information
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
additional information
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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
additional information
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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
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additional information
enzyme three-dimensional structure analysis and structure comparisons. The most visible difference between the open and closed conformation can be perceived in the position of the loop connecting the helices alpha3 and alpha4 of the NTD. In the open state, the loop is away from the active-site pocket, whereas in the closed state the loop moves toward the active-site pocket with a forward shift of about 24 A
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cocrystallized with the substrate 5-methylthio-5-deoxy-D-ribose 1-phosphate, sitting drop vapour diffusion method, using 0.2 M K formate and 15% (w/v) polyethylene glycol 3350, at 20°C
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
sitting-drop vapour-diffusion method. Crystals diffract to 2.5 A at 100 K using synchrotron radiation and belong to the tetragonal space group P4(1), with unit-cell parameters a = b = 69.2 A, c = 154.7 A
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hanging drop vapor diffusion method, using 0.7 M sodium citrate and 100 mM imidazole, pH 8.0
in silico analysis of conserved residues and molecular modeling of structure. Residues of the enzymic activity of methylthioribose-1-phosphate isomerase that interact with the substrate are absolutely conserved. Residues essential for the hydrophobic stabilization of the substrate/product in the active site are conserved as well
purified recombinant enzyme in two different forms of crystals belonging to space groups P3221 and P1, that are obtained at 4°C and 20°C, respectively. The crystal belonging to space group P3221 grows in a microbatch-under-oil set up by mixing 0.002 ml of protein solution and 0.002 ml of 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 2.5 M 1,6-hexanediol. Initial crystals belonging to space group P1 are obtained by hanging-drop vapor-diffusion method, mixing of 0.003 ml of protein solution with 0.001 ml of resevoir solution containing 0.05 M ammonium acetate, 0.1 M Tris, pH 8.0, 16% PEG 10000 and 0.05 M sodium acetate, method optimization, X-ray diffraction structure determination analysis at 2.30-2.65 A resolution, molecular replacement method using the three-dimensional atomic coordinates of M1Pi from Archaeoglobus fulgidus (PDB ID 1T5O) as the search model, modeling
sitting-drop vapour-diffusion method
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Trackman, P.C.; Abeles, R.H.
Methionine synthesis from 5'-S-methylthioaenosine. Resolution of enzyme activities and identification of 1-phospho-5-S-methylthioribulose
J. Biol. Chem.
258
6717-6720
1983
Rattus norvegicus
brenda
Furfine, E.S.; Abeles, R.H.
Intermediates in the conversion of 5'-S-methylthioadenosine to methionine in Klebsiella pneumoniae
J. Biol. Chem.
263
9598-9606
1988
Klebsiella pneumoniae
brenda
Ghoda, L.Y.; Savarese, T.M.; Dexter, D.L.; Parks, R.E.; Trackman, P.C.; Abeles, R.H.
Characterization of a defect in the pathway for converting 5'-deoxy-5'-methylthioadenosine to methionine in a subline of a cultured heterogeneous human colon carcinoma
J. Biol. Chem.
259
6715-6719
1984
Homo sapiens
brenda
Tamura, H.; Matsumura, H.; Inoue, T.; Ashida, H.; Saito, Y.; Yokota, A.; Kai, Y.
Crystallization and preliminary X-ray analysis of methylthioribose-1-phosphate isomerase from Bacillus subtilis
Acta Crystallogr. Sect. F
F61
595-598
2005
Bacillus subtilis
brenda
Bumann, M.; Djafarzadeh, S.; Oberholzer, A.E.; Bigler, P.; Altmann, M.; Trachsel, H.; Baumann, U.
Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits
J. Biol. Chem.
279
37087-37094
2004
Saccharomyces cerevisiae
brenda
Pirkov, I.; Norbeck, J.; Gustafsson, L.; Albers, E.
A complete inventory of all enzymes in the eukaryotic methionine salvage pathway
FEBS J.
275
4111-4120
2008
Saccharomyces cerevisiae
brenda
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
Bacillus subtilis (O31662), Bacillus subtilis
brenda
Kabuyama, Y.; Litman, E.S.; Templeton, P.D.; Metzner, S.I.; Witze, E.S.; Argast, G.M.; Langer, S.J.; Polvinen, K.; Shellman, Y.; Chan, D.; Shabb, J.B.; Fitzpatrick, J.E.; Resing, K.A.; Sousa, M.C.; Ahn, N.G.
A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme
Mol. Cell. Proteomics
8
2308-2320
2009
Homo sapiens
brenda
Templeton, P.D.; Litman, E.S.; Metzner, S.I.; Ahn, N.G.; Sousa, M.C.
Structure of mediator of RhoA-dependent invasion (MRDI) explains its dual function as a metabolic enzyme and a mediator of cell invasion
Biochemistry
52
5675-5684
2013
Bacillus subtilis, Homo sapiens (Q9BV20), Homo sapiens
brenda
Mary, C.; Duek, P.; Salleron, L.; Tienz, P.; Bumann, D.; Bairoch, A.; Lane, L.
Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway
PLoS ONE
7
e52877
2012
Homo sapiens
brenda
Gogoi, P.; Srivastava, A.; Jayaprakash, P.; Jeyakanthan, J.; Kanaujia, S.P.
In silico analysis suggests that PH0702 and PH0208 encode for methylthioribose-1-phosphate isomerase and ribose-1,5-bisphosphate isomerase, respectively, rather than aIF2Bbeta and aIF2Bdelta
Gene
575
118-126
2016
Pyrococcus horikoshii (O58433), Pyrococcus horikoshii, Pyrococcus horikoshii DSM 12428 (O58433)
brenda
Ikeda, Y.; Isogai, A.; Moriyoshi, Y.; Kanda, R.; Iwashita, K.; Fujii, T.
Construction of sake yeast with low production of dimethyl trisulfide precursor by a self-cloning method
J. Biosci. Bioeng.
125
419-424
2018
Saccharomyces cerevisiae, Saccharomyces cerevisiae K901
brenda
Saito, Y.; Ashida, H.; Kojima, C.; Tamura, H.; Matsumura, H.; Kai, Y.; Yokota, A.
Enzymatic characterization of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis
Biosci. Biotechnol. Biochem.
71
2021-2028
2007
Bacillus subtilis (O31662), Bacillus subtilis, Bacillus subtilis 168 (O31662)
brenda
Gogoi, P.; Mordina, P.; Kanaujia, S.P.
Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase
J. Struct. Biol.
205
67-77
2019
Pyrococcus horikoshii (O58433)
brenda
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
Bacillus subtilis (O31662), Bacillus subtilis, Bacillus subtilis 168 (O31662)
brenda