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Information on EC 5.3.1.23 - S-methyl-5-thioribose-1-phosphate isomerase and Organism(s) Bacillus subtilis and UniProt Accession O31662
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5.3.1.23 S-methyl-5-thioribose-1-phosphate isomeraseSpecify your search results
Word Map
- 5.3.1.23
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salvage
- phosphorylase
- mta
- dehydratase
- s-adenosylmethionine
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ribose-1,5-bisphosphate
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mill
- 5'-deoxy-5'-methylthioadenosine
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aci-reductone
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universally
- avocado
- persea
- nucleosidase
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auxotrophic
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klebsiella
- transaminase
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pyrococcus
- horikoshii
- americana
- polyamine
- brewing
The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
mtr-1-p, ph0702, ypr118w, methylthioribose-1-phosphate isomerase, 5'-methylthioribose-1-phosphate isomerase, 5-methylthioribose-1-phosphate isomerase, 5-methylthioribose 1-phosphate isomerase, meu1p, bs-m1pi, 1-pmtr isomerase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
1-PMTR isomerase
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5-methylthio-5-deoxy-D-ribose-1-phosphate ketol-isomerase
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5-methylthioribose-1-phosphate isomerase
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Isomerase, methylthioribose 1-phosphate
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
isomerization
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intramolecular oxidoreduction
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PATHWAY SOURCE
PATHWAYS
BRENDA
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-, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
S-methyl-5-thio-alpha-D-ribose-1-phosphate aldose-ketose-isomerase
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CAS REGISTRY NUMBER
COMMENTARY
91608-95-6
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5-Methylthio-5-deoxy-D-ribose 1-phosphate
5-Methylthio-5-deoxy-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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r
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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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
M1Pi does not require any metals to exhibit catalytic activity
additional information
-
M1Pi does not require any metals to exhibit catalytic activity
additional information
enzyme M1Pi does not require any metals to exhibit its catalytic activity
additional information
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enzyme M1Pi does not require any metals to exhibit its catalytic activity
additional information
the activity is not at all influenced by EDTA treatment, indicating that the Bacillus subtilis MTR-1-P isomerase does not require a metal ion for its catalysis
additional information
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the activity is not at all influenced by EDTA treatment, indicating that the Bacillus subtilis MTR-1-P isomerase does not require a metal ion for its catalysis
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten kinetics
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additional information
additional information
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Michaelis-Menten kinetics
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
additional information
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)
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
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
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the tag is cleaved off by thrombin, followed by gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene mtnA, sequence comparisons and phylogenetic tree, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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
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
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)
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)
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