Information on EC 5.1.3.13 - dTDP-4-dehydrorhamnose 3,5-epimerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.1.3.13
-
RECOMMENDED NAME
GeneOntology No.
dTDP-4-dehydrorhamnose 3,5-epimerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
epimerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
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dTDP-4-O-demethyl-beta-L-noviose biosynthesis
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dTDP-L-rhamnose biosynthesis I
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dTDPLrhamnose biosynthesis
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Metabolic pathways
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Polyketide sugar unit biosynthesis
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Streptomycin biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
dTDP-4-dehydro-6-deoxy-D-glucose 3,5-epimerase
The enzyme occurs in a complex with EC 1.1.1.133 dTDP-4-dehydrorhamnose reductase.
CAS REGISTRY NUMBER
COMMENTARY hide
37318-39-1
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain 045
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Manually annotated by BRENDA team
strain Y10
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Manually annotated by BRENDA team
mutant strain K3, isolated from Kombucha, Kombu Australia, Springwood, Queensland, Australia
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Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
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-
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Manually annotated by BRENDA team
strain H37Rv
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
the rmlC mutant strain colonizes the rabbit mitral valves approximately 3fold less effectively than the wild type strain
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
dTDP-4-dehydro-6-deoxy-D-glucose
?
show the reaction diagram
-
enzyme in biosynthesis of dTDP-L-dihydrostreptose from dTDP-6-deoxy-D-xylo-4-hexosulose
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-
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dTDP-4-dehydro-6-deoxy-D-glucose
dTDP-4-dehydro-6-deoxy-L-mannose
show the reaction diagram
dTDP-4-dehydro-6-deoxy-D-glucose
dTDP-4-dehydro-L-rhamnose
show the reaction diagram
dTDP-6-deoxy-D-xylo-4-hexulose
dTDP-6-deoxy-L-lyxo-4-hexulose
show the reaction diagram
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
TDP-6-deoxy-D-xylo-4-hexosulose
TDP-6-deoxy-L-lyxo-4-hexosulose
show the reaction diagram
TDP-6-deoxy-D-xylo-hexopyranosid-4-ulose
TDP-L-rhamnose
show the reaction diagram
conversion of TDP-6-deoxy-D-xylo-hexopyranosid-4-ulose to TDP-L-rhamnose, catalyzed by the two enzymes TDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase, RmlC, and TDP-deoxy-L-lyxo-4-hexulose reductase, RmlD, overview
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-
?
UDP-4-dehydro-6-deoxy-D-glucose
UDP-4-dehydro-6-deoxy-L-mannose
show the reaction diagram
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i.e. UDP-4-dehydro-L-rhamnose, product identification by electrospray ionization-mass spectrometry and gas chromatography mass spectrometry
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
dTDP-4-dehydro-6-deoxy-D-glucose
?
show the reaction diagram
-
enzyme in biosynthesis of dTDP-L-dihydrostreptose from dTDP-6-deoxy-D-xylo-4-hexosulose
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dTDP-4-dehydro-6-deoxy-D-glucose
dTDP-4-dehydro-L-rhamnose
show the reaction diagram
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the enzyme is involved in the dTDP-rhamnose synthesis pathway which consists of three steps: (i) the synthesis of dTDP-4-keto-6-deoxy-D-glucose from glucose 1-phosphate and dTDP, (ii) the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-4-keto-L-rhamnose by dTDP-4-dehydrorhamnose 3,5-epimerase and (iii) the reduction of dTDP-4-keto-L-rhamnose to dTDP-L-rhamnose. The mutant K3 strain, with a spontaneous mutation that results in lower cellulose production, shows deoxythymidine diphosphate-4-dehydrorhamnose 3,5-epimerase activity, while the wild-type does not, determined by 2D-gel electrophoresis. It is possible that in the wild-type, transcription of the gene responsible for the expression of dTDP-4-dehydrorhamnose 3,5-epimerase is repressed by a transcription factor, and that a mutation in the gene encoding the transcription factor has rendered it non-functional
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-
?
dTDP-6-deoxy-D-xylo-4-hexulose
dTDP-6-deoxy-L-lyxo-4-hexulose
show the reaction diagram
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
TDP-6-deoxy-D-xylo-hexopyranosid-4-ulose
TDP-L-rhamnose
show the reaction diagram
P9WH11
conversion of TDP-6-deoxy-D-xylo-hexopyranosid-4-ulose to TDP-L-rhamnose, catalyzed by the two enzymes TDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase, RmlC, and TDP-deoxy-L-lyxo-4-hexulose reductase, RmlD, overview
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-
?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
divalent metal ions do not alter activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-(3-(5-allyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfonyl)-propyl)-1H-benzo[d]imidazol-2(3H)-one
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1-(3-(5-allyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. 77074, a SID 7975595 analogue
1-(3-(5-allyl-8-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
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1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfonyl)-propyl)-1H-benzo[d]imidazol-2(3H)-one
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1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. SID 7975595, a competitive, fast-on rate, fully reversible inhibitor of RmlC. Increases the Km for TDP-6-deoxy-D-xylo-hexopyranosid-4-ulose. Cytotoxic SID 7975595 has an IC50 of approximately 0.075 mM in HAE cells
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1-(3-(5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. 77072, a SID 7975595 analogue
1-(3-(5-methylphenyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. 77070, a SID 7975595 analogue
1-(3-(5-propyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. 77071, a SID 7975595 analogue
1-(3-(5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
i.e. 77073, a SID 7975595 analogue
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.025
dTDP-4-dehydro-6-deoxy-D-glucose
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0.35 - 0.71
dTDP-6-deoxy-D-xylo-4-hexulose
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016 - 39
dTDP-6-deoxy-D-xylo-4-hexulose
additional information
additional information
Streptococcus suis
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0004
1-(3-(5-allyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfonyl)-propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
0.00012
1-(3-(5-allyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
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0.02
1-(3-(5-allyl-8-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
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0.0008
1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfonyl)-propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
0.0002
1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
-
0.0005
1-(3-(5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
0.0029
1-(3-(5-methylphenyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
0.00125
1-(3-(5-propyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
0.0033
1-(3-(5H-[1,2,4]triazino[5,6-b]indol-3-ylthio)propyl)-1H-benzo[d]imidazol-2(3H)-one
Mycobacterium tuberculosis
P9WH11
pH 7.4, 25C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
7.5
assay at; assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
assay at; assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40600
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gel filtration
67000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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1 * 40000, SDS-PAGE
monomer or dimer
x * 33000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, crystal structure in presence and absence of dTDP
Methanothermobacter thermautotrophicum
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incubating RmlC with 20 mM dTDP-6-deoxy-D-xylo-4-hexulose, for 2 h at room temperature, prior to setting up crystal plates with 25% PEG 8000, 0.2 M sodium tartrate, 0.1 M Mes (pH 6.2)
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the structure is determined by multiwavelength anomalous diffraction to a resolution of 2.17 A
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sitting drop method, crystals of native and selenomethionine protein, crystals in complex with dTDP-D-glucose and dTDP-D-xylose
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloned into pET23a(+) with an N-terminal 6 His tag and a linker consisting of Gly-Ser-Met-Ala, overexpression in Escherichia coli
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cloned into pET23b using the Ligation Independent Clone system
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expression in Escherichia coli
gene dnmU, DNA and amino acid sequence determination, analysis, and comparison, genetic organization, overview. Recombinant expression in Escherichia coli; gene rmbC, DNA and amino acid sequence determination, analysis, and comparison, genetic organization, overview. Recombinant expression in Escherichia coli
gene L780, transcription profiling of UGER, phylogenetic analysis
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H63A
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The mutants were examined by circular dichroism, which confirmed no detectable structural changes that would influence the native fold. H63A is catalytically inactive and shows no deuterium incorporation above background at either C3'or C5'.
K73A
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The mutants were examined by circular dichroism, which confirmed no detectable structural changes that would influence the native fold. K73A is reduced in activity by over 100-fold and a small amount of enzyme catalyzed deuterium incorporation was observed at C5', while only background levels were seen at C3'. This suggests that for the K73A mutant, C5' exchange is more rapid than at C3'.
Y133F
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The mutants were examined by circular dichroism, which confirmed no detectable structural changes that would influence the native fold. The catalytic activity of the Y133F mutant is reduced 1000-fold but shows some deuterium incorporation at C3' but none at C5' (above background). This indicates that RmlC can catalyze exchange of the proton at C3' without Tyr133 but not at C5'.
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
synthesis
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