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Information on EC 1.1.1.133 - dTDP-4-dehydrorhamnose reductase
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1.1.1.133 dTDP-4-dehydrorhamnose reductaseIUBMB 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.
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Word Map
- 1.1.1.133
- dtdp-l-rhamnose
- dttp
- actinomycetemcomitans
-
actinobacillus
- glucose-1-phosphate
-
3,5-epimerase
- synthesis
- oleandomycin
-
c-specific
-
s-layer
-
deoxysugars
- dtdp-glucose-4,6-dehydratase
- dtdp-d-glucose
-
thymidylyltransferase
-
o-antigen
- dtdp-4-keto-6-deoxy-d-glucose
-
4,6-dehydratase
- alpha-d-glucose-1-phosphate
The enzyme appears in viruses and cellular organisms
Synonyms
4-ketoreductase, dtdp-6-deoxy-l-lyxo-4-hexulose reductase, agl14, dtdp-4-dehydrorhamnose reductase, dtdp-4-keto-rhamnose reductase, thymidine diphosphate-4-dehydrorhamnose reductase, dtdp-4-keto-l-rhamnose reductase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase
E3VXL5
-
dTDP-4-dehydrorhamnose reductase
dTDP-6-deoxy-L-lyxo-4-hexulose reductase
RmlD
thymidine diphosphate-6-deoxy-L-talose
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH + H+
the complex has been referred to as dTDP-L-rhamnose synthase
-
-
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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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
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SYSTEMATIC NAME
IUBMB Comments
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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CAS REGISTRY NUMBER
COMMENTARY
37250-64-9
-
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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
dTDP-4-dehydro-6-deoxy-D-glucose + NADPH
dTDP-beta-L-rhamnose + NADP+
-
-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADPH + H+
dTDP-L-rhamnose + NADP+
-
-
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NAD(P)H
dTDP-L-rhamnose + NAD(P)+
-
-
-
r
UDP-4-dehydro-6-deoxy-D-glucose + NADPH
UDP-beta-L-rhamnose + NADP+
-
-
?
UDP-4-keto-6-deoxy-D-glucose + NADPH + H+
UDP-L-rhamnose + NADP+
E3VXL5
-
product identification by electrospray ionization-mass spectrometry and gas chromatography mass spectrometry
?
additional information
?
-
no substrate: GDP-4-keto-6-deoxy-mannose, UDP-glucose, dTDP-glucose, UDP-xylose, GDP-fucose
-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADH + H+
dTDP-beta-L-rhamnose + NAD+
40% of the rate with NADPH
-
?
dTDP-4-dehydro-6-deoxy-D-glucose + NADH + H+
dTDP-beta-L-rhamnose + NAD+
-
-
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
-
-
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
-
-
-
?
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
-
?
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
-
?
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
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
Streptomyces mutans
-
synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
-
?
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
-
?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
-
-
-
?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
-
-
-
?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
-
biosynthetic pathway, overview
-
?
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+
-
-
-
?
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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
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
-
?
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
-
?
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
-
?
dTDP-6-deoxy-L-lyxo-4-hexulose + NADPH
dTDP-L-rhamnose + NADP+
Streptomyces mutans
-
synthesis of L-rhamnose precurser dTDP-L-rhamnose, essential cell wall component of pathogenic bacteria
-
?
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
-
?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
-
-
-
-
?
dTDP-6-deoxy-L-mannose + NADP+
dTDP-4-dehydro-6-deoxy-L-mannose + NADPH
-
biosynthetic pathway, overview
-
-
?
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+
-
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
E3VXL5
divalent metal ions do not alter activity
additional information
-
the enzyme does not require metal for its activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
not inhibitory: MgCl2, CaCl2, EDTA at 10mM
-
additional information
-
full activity restored with up to 0.3 mM MgCl2
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.37
dTDP-alpha-D-glucose
-
at pH 7.5, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0021
2,6,7-trihydroxy-9-(2-hydroxyphenyl)-3H-xanthen-3-one
Mycobacterium tuberculosis
-
pH and temperature not specified in the publication
0.0015
2,6,7-trihydroxy-9-methyl-3H-xanthen-3-one
Mycobacterium tuberculosis
-
pH and temperature not specified in the publication
0.0009
2,6,7-trihydroxy-9-phenyl-3H-xanthen-3-one
Mycobacterium tuberculosis
-
pH and temperature not specified in the publication
0.0025
5-ethenyl-1-methyl-9,10-dihydrophenanthrene-2,7-diol
Mycobacterium tuberculosis
-
pH and temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
Show AA Sequence and Transmembrane Helices (34242 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
-
NADPH more than NADP+ prevents heat denaturation during 5 and 8 min
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
NADPH and to a lesser degree NADP+ prevent denaturation at 50°C, NAD+ and NADH are less effective
-
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, repeated freezing and thawing, loss of more than 60% of activity
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, affinity chromatography, co-purification of enzyme I and II
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene L780, transcription profiling of UGER, phylogenetic analysis
E3VXL5
native overexpressed in Escherichia coli BL21(DE3) and selenomethionine-enriched in B834(lambdaDE3)
-
overexpression in Escherichia coli DH5alpha, ER2566, BL21(DE3)
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
synthesis
-
development and evaluation of a modular system for large scale production of important dTDP-activated deoxyhexoses from dTMP and sucrose, overview
synthesis
-
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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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
-
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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