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Information on EC 5.3.2.5 - 2,3-diketo-5-methylthiopentyl-1-phosphate enolase and Organism(s) Geobacillus kaustophilus and UniProt Accession Q5L1E2

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EC Tree
IUBMB Comments
The enzyme participates in the methionine salvage pathway in Bacillus subtilis .In some species a single bifunctional enzyme, EC 3.1.3.77, acireductone synthase, catalyses both this reaction and EC 3.1.3.87, 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase .
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Geobacillus kaustophilus
UNIPROT: Q5L1E2
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The taxonomic range for the selected organisms is: Geobacillus kaustophilus
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
dk-mtp-1-p enolase, 2,3-diketo-5-methylthiopentyl-1-phosphate enolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2,3-diketo-5-methylthiopentane 1-phosphate enolase
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DK-MTP 1-P enolase
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2,3-diketo-5-methylthiopentane 1-phosphate enolase
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DK-MTP 1-P enolase
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DK-MTP-1-P enolase
MtnW
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RuBisCO-like protein
YkrW
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
5-(methylsulfanyl)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate
show the reaction diagram
structure-function relationship and reaction mechanism, overview
5-(methylsulfanyl)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate
show the reaction diagram
reaction mechanism, overview
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2,3-diketo-5-methylthiopentyl-1-phosphate keto-enol-isomerase
The enzyme participates in the methionine salvage pathway in Bacillus subtilis [2].In some species a single bifunctional enzyme, EC 3.1.3.77, acireductone synthase, catalyses both this reaction and EC 3.1.3.87, 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase [1].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-(methylthio)-2,3-dioxopentyl phosphate
2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate
show the reaction diagram
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?
5-(methylthio)-2,3-dioxopentyl phosphate
2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate
show the reaction diagram
additional information
?
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the enzyme catalyzes the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate in the methionine salvage pathway in which 5-methylthio-D-ribose derived from 5'-methylthioadenosine is converted to methionine. The reaction is accomplished by abstraction of the 1-proS proton from C1 of the DK-MTP 1-P substrate to form the tautomerized product, a conjugated enol. Stabilization of an enolate anion intermediate by coordination to an active site Mg2+. Structure-function relationships, overview. The enolase from Geobacillus kaustophilus catalyzes stereospecific abstraction of the 1-proS proton of the DK-MTP 1-P substrate
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
5-(methylthio)-2,3-dioxopentyl phosphate
2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate
show the reaction diagram
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-
?
5-(methylthio)-2,3-dioxopentyl phosphate
2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate
show the reaction diagram
additional information
?
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the enzyme catalyzes the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate in the methionine salvage pathway in which 5-methylthio-D-ribose derived from 5'-methylthioadenosine is converted to methionine. The reaction is accomplished by abstraction of the 1-proS proton from C1 of the DK-MTP 1-P substrate to form the tautomerized product, a conjugated enol. Stabilization of an enolate anion intermediate by coordination to an active site Mg2+. Structure-function relationships, overview. The enolase from Geobacillus kaustophilus catalyzes stereospecific abstraction of the 1-proS proton of the DK-MTP 1-P substrate
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
active site Mg2+, required
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme belongs to the RuBisCO superfamily. The functionally divergent Geobacillus kaustophilus member of the RuBisCO superfamily uses the same structural strategy as RuBisCO for stabilizing the enolate anion intermediate, i.e., coordination to an essential Mg2+, but the proton abstraction is catalyzed by a different general base
metabolism
the enzyme is involved in the methionine salvage pathway. It is a heterofunctional homologue of RuBisCO catalyzing the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate in the methionine salvage pathway in which 5-methylthio-D-ribose derived from 5'-methylthioadenosine is converted to methionine
evolution
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the Geobacillus kaustophilis enzyme belongs to the RLPalpha-1 enzyme group, functional and evolutionary relationships between Bacillus subtilis RLP of the methionine salvage pathway, other RLPs, and photosynthetic RuBisCO, overview
metabolism
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Geobacillus kaustophilis RLP is involved in the methionine salvage pathway, overview
additional information
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
structure modeling, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
activated wild-type enolase, carboxylated on Lys173, with Mg2+ alone, or Mg2+, and HCO3-, or Mg2+ and substrate 2,3-diketohexane 1-phosphate, and of the selenomethionine-substituted enzyme variant, hanging drop method, 10-15 mg/ml protein in 20 mM Tris-HCl, pH 7.9, 100 mM NaCl, and 5-10 mM MgCl2, 100 mM NaCl, and 1-5 mM NaHCO3, mixed with 24% PEG 3350, 0.1 M Tris-HCl, pH 8.5, and 0.2 M ammonium acetate as precipitant for the crystals of wild-type enzyme with Mg2+, or 25% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.2 M ammonium acetate as precipitant for the other crystal variants, room temperature, 6 days, X-ray diffraction structure determination and analysis at 1.7 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K147A
site-directed mutagenesis, the mutant requires a 10fold greater concentration of protein for enolization of the natural substrate, reduced activity compared to the wild-type enzyme
K173A
site-directed mutagenesis, the mutant is able to catalyze enolization at approximately the same rate as the wild-type enzyme
K98A
site-directed mutagenesis, the mutant is unable to catalyze the enolase reaction
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by two different steps of anion exchange chromatography and ultrafiltration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Geobacillus kaustophilis RLPalpha-1 sequence determination and analysis, and phylogenetic analysis
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Imker, H.J.; Fedorov, A.A.; Fedorov, E.V.; Almo, S.C.; Gerlt, J.A.
Mechanistic diversity in the RuBisCO superfamily: the enolase in the methionine salvage pathway in Geobacillus kaustophilus
Biochemistry
46
4077-4089
2007
Bacillus subtilis, Bacillus subtilis 168, Geobacillus kaustophilus (Q5L1E2)
Manually annotated by BRENDA team
Ashida, H.; Saito, Y.; Nakano, T.; Tandeau de Marsac, N.; Sekowska, A.; Danchin, A.; Yokota, A.
RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO
J. Exp. Bot.
59
1543-1554
2008
Bacillus subtilis, Geobacillus kaustophilus, Microcystis aeruginosa, Rhodopseudomonas palustris, Rhodospirillum rubrum
Manually annotated by BRENDA team
Warlick, B.P.; Imker, H.J.; Sriram, J.; Tabita, F.R.; Gerlt, J.A.
Mechanistic diversity in the RuBisCO superfamily: RuBisCO from Rhodospirillum rubrum is not promiscuous for reactions catalyzed by RuBisCO-like proteins
Biochemistry
51
9470-9479
2012
Geobacillus kaustophilus, no activity in Rhodospirillum rubrum
Manually annotated by BRENDA team