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EC Tree
IUBMB Comments In the reverse direction, reduction on the 4-position of the hexose moiety takes place only while the substrate is bound to another enzyme that catalyses epimerization at C-3 and C-5; the complex has been referred to as dTDP-L-rhamnose synthase.
The enzyme appears in viruses and cellular organisms
Synonyms
4-ketoreductase, Agl14, bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase, dTDP-4-dehydrorhamnose reductase, dTDP-4-keto-L-rhamnose reductase, dTDP-4-keto-rhamnose reductase, dTDP-4-ketorhamnose reductase, dTDP-6-deoxy-L-lyxo-4-hexulose reductase, dTDP-6-deoxy-L-mannose dehydrogenase, dTDP-L-rhamnose synthetase,
more
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bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase
E3VXL5
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dTDP-4-dehydrorhamnose reductase
dTDP-4-keto-L-rhamnose reductase
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dTDP-4-keto-rhamnose reductase
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dTDP-4-ketorhamnose reductase
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dTDP-6-deoxy-L-lyxo-4-hexulose reductase
dTDP-6-deoxy-L-mannose dehydrogenase
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dTDP-L-rhamnose synthetase
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TDP-4-keto-rhamnose reductase
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TDP-4-ketorhamnose reductase
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thymidine diphosphate-4-dehydrorhamnose reductase
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thymidine diphosphate-6-deoxy-L-talose
thymidine diphospho-4-ketorhamnose reductase
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dTDP-4-dehydrorhamnose reductase
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dTDP-4-dehydrorhamnose reductase
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dTDP-4-dehydrorhamnose reductase
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dTDP-6-deoxy-L-lyxo-4-hexulose reductase
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dTDP-6-deoxy-L-lyxo-4-hexulose reductase
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dTDP-6-deoxy-L-lyxo-4-hexulose reductase
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dTDP-6-deoxy-L-lyxo-4-hexulose reductase
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RmlD
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thymidine diphosphate-6-deoxy-L-talose
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thymidine diphosphate-6-deoxy-L-talose
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dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
the complex has been referred to as dTDP-L-rhamnose synthase
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dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
in the reverse direction, reduction on the 4-position of the hexose moiety takes place only while the substrate is bound to another enzyme which catalyzes epimerization at C-3 and C-5
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dTDP-6-deoxy-beta-L-mannose:NADP+ 4-oxidoreductase
In the reverse direction, reduction on the 4-position of the hexose moiety takes place only while the substrate is bound to another enzyme that catalyses epimerization at C-3 and C-5; the complex has been referred to as dTDP-L-rhamnose synthase.
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dTDP-4-dehydro-6-deoxy-D-glucose + NADH + H+
dTDP-beta-L-rhamnose + NAD+
dTDP-4-dehydro-6-deoxy-D-glucose + NADPH
dTDP-beta-L-rhamnose + NADP+
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-
-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADPH + H+
dTDP-L-rhamnose + NADP+
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-
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NAD(P)H
dTDP-L-rhamnose + NAD(P)+
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-
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r
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
dTDP-alpha-D-glucose + NADP+
?
-
-
-
-
?
dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
UDP-4-dehydro-6-deoxy-D-glucose + NADPH
UDP-beta-L-rhamnose + NADP+
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?
UDP-4-keto-6-deoxy-D-glucose + NADPH + H+
UDP-L-rhamnose + NADP+
E3VXL5
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product identification by electrospray ionization-mass spectrometry and gas chromatography mass spectrometry
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?
additional information
?
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no substrate: GDP-4-keto-6-deoxy-mannose, UDP-glucose, dTDP-glucose, UDP-xylose, GDP-fucose
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-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADH + H+
dTDP-beta-L-rhamnose + NAD+
40% of the rate with NADPH
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-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADH + H+
dTDP-beta-L-rhamnose + NAD+
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-
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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-
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
-
synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
-
synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
Streptomyces mutans
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
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?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
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dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
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biosynthetic pathway, overview
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dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
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?
dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
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dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
Streptomyces mutans
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
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synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
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?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
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dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
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biosynthetic pathway, overview
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dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
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?
dTDP-beta-L-rhamnose + NADP+
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
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?
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NADH
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NADP+
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NADPH
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NADPH
Streptomyces mutans
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Mg2+
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situated at dimer interface
additional information
E3VXL5
divalent metal ions do not alter activity
additional information
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the enzyme does not require metal for its activity
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2,6,7-trihydroxy-9-(2-hydroxyphenyl)-3H-xanthen-3-one
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2,6,7-trihydroxy-9-methyl-3H-xanthen-3-one
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2,6,7-trihydroxy-9-phenyl-3H-xanthen-3-one
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5-ethenyl-1-methyl-9,10-dihydrophenanthrene-2,7-diol
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EDTA
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up to 0.3 mM, 70% loss of enzyme activity
additional information
not inhibitory: MgCl2, CaCl2, EDTA at 10mM
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additional information
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full activity restored with up to 0.3 mM MgCl2
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Tuberculosis
Ensemble-based high-throughput virtual screening of natural ligands using the Super Natural-II database against cell-wall protein dTDP-4-dehydrorhamnose reductase (RmlD) in Mycobacterium tuberculosis.
Tuberculosis
Novel inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) identified by virtual screening.
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0.0169
dTDP-4-keto-6-deoxy-D-glucose
pH 8.5, 30°C
0.37
dTDP-alpha-D-glucose
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at pH 7.5, temperature not specified in the publication
0.009
NADPH
pH 8.5, 30°C
1.83
UDP-4-keto-6-deoxy-D-glucose
E3VXL5
25°C, pH 7.5
0.106
NADH
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+/-0.018, pH 7.0
0.21
NADH
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+/-0.004, pH 7.0
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0.0021
2,6,7-trihydroxy-9-(2-hydroxyphenyl)-3H-xanthen-3-one
Mycobacterium tuberculosis
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pH and temperature not specified in the publication
0.0015
2,6,7-trihydroxy-9-methyl-3H-xanthen-3-one
Mycobacterium tuberculosis
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pH and temperature not specified in the publication
0.0009
2,6,7-trihydroxy-9-phenyl-3H-xanthen-3-one
Mycobacterium tuberculosis
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pH and temperature not specified in the publication
0.0025
5-ethenyl-1-methyl-9,10-dihydrophenanthrene-2,7-diol
Mycobacterium tuberculosis
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pH and temperature not specified in the publication
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0.0011
E3VXL5
25°C, pH 7.5
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10
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oxidation of dTDP-L-rhamnose
6.5
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reduction of dTDP-6-deoxy-L-lyxo-4-hexulose
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30
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45
about 35% of maximum activity
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gene L780
E3VXL5
UniProt
brenda
Y4, NCTC 9710
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brenda
bifunctional 3,5-epimerase/4-keto reductase
Swissprot
brenda
O45
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brenda
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UniProt
brenda
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brenda
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brenda
ATCC 7700
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brenda
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brenda
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brenda
Streptomyces mutans
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brenda
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brenda
K12
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brenda
O45
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brenda
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brenda
sedovar typhimurium
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brenda
serovar typhimurium LT2
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brenda
serovar typhimurium, LT2, gene rmlD
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brenda
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brenda
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brenda
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brenda
additional information
present in all tissues examined
brenda
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27500
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1 * 27500, SDS-PAGE
31900
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Y4 rmlD gene product, SDS-PAGE
32400
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NCTC 9710 rmlD gene product, SDS-PAGE
32540
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mass spectrometry, native protein
32560
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deduced from sequence
32600
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calculated from nucleotide sequence data
32730
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mass spectrometry, selenomethionine-enriched protein
33000
E3VXL5
x * 33000, UGER, SDS-PAGE
35000
x * 35500, deduced from gene sequence, x * 35000, SDS-PAGE
35500
x * 35500, deduced from gene sequence, x * 35000, SDS-PAGE
47000
E3VXL5
gel filtration
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?
x * 35500, deduced from gene sequence, x * 35000, SDS-PAGE
monomer or dimer
E3VXL5
x * 33000, UGER, SDS-PAGE
monomer
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1 * 27500, SDS-PAGE
monomer
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1 * 32000, calculated from amino acid sequence
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apo-enzyme, and in complex with NADH, NADPH or NADPH/dTDP-L-rhamnose
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sitting drop vapour-diffusion method, 6 d
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hanging drop vapor diffusion method, using 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MES/imidazole pH 6.5
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7
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37°C, 20 min, 75% activity loss
285846
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37
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pH 7.0, 75% activity loss
42
E3VXL5
stable for 30 min
50
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NADPH more than NADP+ prevents heat denaturation during 5 and 8 min
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NADPH and to a lesser degree NADP+ prevent denaturation at 50°C, NAD+ and NADH are less effective
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-20°C, purified protein, 50% glycerol
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-20°C, repeated freezing and thawing, loss of more than 60% of activity
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affinity and ion exchange chromatography
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ammonium sulfate precipitation, affinity chromatography, co-purification of enzyme I and II
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anion-exchange, hydrophobic chromatography
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HisTrap column chromatography and Superdex 75 gel filtration
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expressed in Escherichia coli BL21(DE3) cells
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expression in Escherichia coli
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gene L780, transcription profiling of UGER, phylogenetic analysis
E3VXL5
gene rmlD, expression in Escherichia coli strain BL21(DE3)
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native overexpressed in Escherichia coli BL21(DE3) and selenomethionine-enriched in B834(lambdaDE3)
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overexpressed in Escherichia coli BL21(lambdaDE3)
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overexpression in Escherichia coli DH5alpha, ER2566, BL21(DE3)
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synthesis
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development and evaluation of a modular system for large scale production of important dTDP-activated deoxyhexoses from dTMP and sucrose, overview
synthesis
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six enzymes, including the dTDP-4-keto-rhamnose reductase, are involved in the pathway and are prepared by recombinant expression in Escherichia coli for large scale production of O-antigen precursor sTDP-L-rhamnose in a one-pot reaction, overview
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Melo, A.; Glaser, L.
The mechanism of 6-deoxyhexose synthesis. II. Conversion of deoxythymidine diphosphate 4-keto-6-deoxy-D-glucose to deoxythymidine diphosphate L-rhamnose
J. Biol. Chem.
243
1475-1478
1968
Pseudomonas aeruginosa
brenda
Giraud, M.F.; McMiken, H.J.; Leonard, G.A.; Messner, P.; Whitfield, C.; Naismith, J.H.
Overexpression, purification, crystallization and preliminary structural study of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD), the fourth enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar typhimurium
Acta Crystallogr. Sect. D
55
2043-2046
1999
Escherichia coli, Salmonella enterica, Shigella flexneri, Streptomyces mutans, Xanthomonas campestris
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brenda
Nakano, Y.; Suzuki, N.; Yoshida, Y.; Nezu, T.; Yamashita, Y.; Koga, T.
Thymidine diphosphate-6-deoxy-L-lyxo-4-hexulose reductase synthesizing dTDP-6-deoxy-L-talose from Actinobacillus actinomycetemcomitans
J. Biol. Chem.
275
6806-6812
2000
Aggregatibacter actinomycetemcomitans, Escherichia coli, Escherichia coli O45
brenda
Graninger, M.; Nidetzky, B.; Heinrichs, D.E.; Whitfield, C.; Messner, P.
Characterization of dTDP-4-dehydrorhamnose 3,5-epimerase and dTDP-4-dehydrorhamnose reductase, required for dTDP-L-rhamnose biosynthesis in Salmonella enterica serovar typhimurium LT2
J. Biol. Chem.
274
25069-25077
1999
Salmonella enterica
brenda
Watt, G.; Leoff, C.; Harper, A.D.; Bar-Peled, M.
A bifunctional 3,5-epimerase/4-keto reductase for nucleotide-rhamnose synthesis in Arabidopsis
Plant Physiol.
134
1337-1346
2004
Arabidopsis thaliana (Q9LQ04)
brenda
Blankenfeldt, W.; Kerr, I.D.; Giraud, M.F.; McMiken, H.J.; Leonard, G.; Whitfield, C.; Messner, P.; Graninger, M.; Naismith, J.H.
Variation on a theme of SDR: dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode
Structure
10
773-786
2002
Salmonella enterica
brenda
Elling, L.; Rupprath, C.; Gunther, N.; Romer, U.; Verseck, S.; Weingarten, P.; Drager, G.; Kirschning, A.; Piepersberg, W.
An enzyme module system for the synthesis of dTDP-activated deoxysugars from dTMP and sucrose
ChemBioChem
6
1423-1430
2005
Salmonella enterica
brenda
Kang, Y.; Yang, Y.; Lee, K.; Lee, S.; Sohng, J.K.; Lee, H.C.; Liou, K.; Kim, B.
Preparative synthesis of dTDP-L-rhamnose through combined enzymatic pathways
Biotechnol. Bioeng.
93
21-27
2005
Mesorhizobium loti
brenda
Parakkottil Chothi, M.; Duncan, G.; Armirotti, A.; Abergel, C.; Gurnon, J.; Van Etten, J.; Bernardi, C.; Damonte, G.; Tonetti, M.
Identification of an L-rhamnose synthetic pathway in two nucleocytoplasmic large DNA viruses
J. Virol.
84
8829-8838
2010
Acanthamoeba polyphaga Mimivirus (E3VXL5)
brenda
Wang, Y.; Hess, T.N.; Jones, V.; Zhou, J.Z.; McNeil, M.R.; Andrew McCammon, J.
Novel inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) identified by virtual screening
Bioorg. Med. Chem. Lett.
21
7064-7067
2011
Mycobacterium tuberculosis
brenda
van der Beek, S.L.; Le Breton, Y.; Ferenbach, A.T.; Chapman, R.N.; van Aalten, D.M.; Navratilova, I.; Boons, G.J.; McIver, K.S.; van Sorge, N.M.; Dorfmueller, H.C.
GacA is essential for group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD)
Mol. Microbiol.
98
946-962
2015
Streptococcus sp.
brenda
Kaminski, L.; Eichler, J.
Haloferax volcanii N-glycosylation: delineating the pathway of dTDP-rhamnose biosynthesis
PLoS ONE
9
e97441
2014
Haloferax volcanii (D4GU71), Haloferax volcanii
brenda
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