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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, dtdp-4-dehydrorhamnose reductase, dtdp-6-deoxy-l-lyxo-4-hexulose reductase, dtdp-4-keto-l-rhamnose reductase, dtdp-4-keto-rhamnose reductase, thymidine diphosphate-4-dehydrorhamnose reductase,
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-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-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-beta-L-rhamnose + NADP+
dTDP-6-deoxy-L-lyxo-4-hexulose + NAD(P)H
dTDP-L-rhamnose + NAD(P)+
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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+
?
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?
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-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-beta-L-rhamnose + NADP+
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?
dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-beta-L-rhamnose + NADP+
enzyme in the dTDP-beta-L-rhamnose-biosynthetic pathway
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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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?
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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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-4-dehydro-beta-L-rhamnose + NADPH + H+
dTDP-beta-L-rhamnose + NADP+
enzyme in the dTDP-beta-L-rhamnose-biosynthetic pathway
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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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NADH
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NADP+
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NADPH
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NADPH
Streptomyces mutans
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NADPH
based on our structural comparison of the enzyme (RfbD) with its homologs, it is found that RfbD is likely to utilize either NAD(H) or NADP(H) as a coenzyme
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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
does not require Mg2+ for activity
additional information
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does not require Mg2+ for 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
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
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UniProt
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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drug target
the dTDP-beta-L-rhamnose-biosynthetic pathway is absent in humans, which make them ideal targets for therapeutic development to combat pathogens (e.g. Bacillus anthracis, the causative agent of the deadly disease Anthrax)
metabolism
enzyme in the dTDP-beta-L-rhamnose-biosynthetic pathway
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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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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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vapor diffusion sitting drop method, the 2.65 A resolution crystal structure of the enzyme in complex with NADP+
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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expression in Escherichia coli BL21(DE3)
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, cry