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
5.1.3.13
-
RECOMMENDED NAME
GeneOntology No.
dTDP-4-dehydrorhamnose 3,5-epimerase
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
-
-
-
-
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
dTDP-4-keto-L-rhamnose is formed as intermediate
-
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
dTDP-4-keto-L-rhamnose is formed as intermediate
Escherichia coli Y10
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
epimerization
-
-
-
-
epimerization
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
dTDP-beta-L-noviose biosynthesis
-
-
dTDP-L-rhamnose biosynthesis I
-
-
dTDPLrhamnose biosynthesis
-
-
Streptomycin biosynthesis
-
-
Polyketide sugar unit biosynthesis
-
-
Metabolic pathways
-
-
Biosynthesis of antibiotics
-
-
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.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
bifunctional UDP-4-keto-6-deoxy-D-glucose epimerase/reductase
-
deoxythymidine diphosphate-4-dehydrorhamnose 3,5-epimerase
-
-
deoxythymidine diphospho-4-keto-6-deoxyglucose 3,5-epimerase
-
deoxythymidine diphospho-4-keto-6-deoxyglucose 3,5-epimerase
-
-
dTDP-4-dehydrorhamnose 3,5-epimerase
-
-
dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase
Methanothermobacter thermautotrophicum
-
-
dTDP-4-keto-6-deoxyglucose 3,5-epimerase
-
-
-
-
dTDP-4-keto-6-deoxyglucose 3,5-epimerase
-
dTDP-4-keto-6-deoxyglucose 3,5-epimerase
-
-
dTDP-4-keto-L-rhamnose 3,5-epimerase
-
-
-
-
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
-
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
-
-
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
-
dTDP-L-rhamnose synthetase
-
-
-
-
Epimerase, thymidine diphospho-4-ketorhamnose 3,5-
-
-
-
-
NovW gene product
-
-
TDP-4-keto-6-deoxy-D-glucose 3,5-epimerase
-
TDP-4-keto-L-rhamnose-3,5-epimerase
-
-
-
-
TDP-4-ketorhamnose 3,5-epimerase
-
-
-
-
TDP-6-deoxy-D-xylo-4-hexopyranosid-4-ulose 3,5-epimerase
-
-
Thymidine diphospho-4-ketorhamnose 3,5-epimerase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37318-39-1
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain 045
-
-
Manually annotated by BRENDA team
strain Y10
-
-
Manually annotated by BRENDA team
Escherichia coli 45
strain 045
-
-
Manually annotated by BRENDA team
Escherichia coli Y10
strain Y10
-
-
Manually annotated by BRENDA team
mutant strain K3, isolated from Kombucha, Kombu Australia, Springwood, Queensland, Australia
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
-
-
-
Manually annotated by BRENDA team
serovar typhimurium
-
-
Manually annotated by BRENDA team
serovar typhimurium LT2
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
rhamnose and N-acetyl-galactosamine are not detected, and fucose is greatly diminished in the rmlC mutant (transposon pLOF/Sp inserted into rmlC (TDP-4-keto-6-deoxy-D-glucose 3,5-epimerase) compared with that in the wild-type strain)
malfunction
disruption of rmbC results in fragmented mycelia that quickly convert into gray pigmented spores
malfunction
-
disruption of rmbC results in fragmented mycelia that quickly convert into gray pigmented spores
-
metabolism
-
dTDP-4-dehydrorhamnose 3,5-epimerase is an enzyme which may be associated with the cellulose synthesis-reducing effect of the mutation in strain K3
metabolism
the enzyme is required for L-rhamnose synthesis
metabolism
the enzyme from the doxorubicin biosynthesis gene cluster is involved in the biosynthesis of dTDP-L-daunosamine, pathway overview. It does not compensate for the other dTDP-4-keto-6-deoxyglucose 3,5-epimerase encoded by gene rmbC. Although dnmU and rmbC encode for similar functional proteins, their native roles in their respective biosynthetic pathways in vivo are specific and independent of one other; the enzyme is involved in the biosynthesis of dTDP-L-rhamnose, a precursor of cell wall biosynthesis, pathway overview. It does not compensate for the other dTDP-4-keto-6-deoxyglucose 3,5-epimerase encoded by gene dnmU. Although dnmU and rmbC encode for similar functional proteins, their native roles in their respective biosynthetic pathways in vivo are specific and independent of one other
metabolism
-
the enzyme from the doxorubicin biosynthesis gene cluster is involved in the biosynthesis of dTDP-L-daunosamine, pathway overview. It does not compensate for the other dTDP-4-keto-6-deoxyglucose 3,5-epimerase encoded by gene rmbC. Although dnmU and rmbC encode for similar functional proteins, their native roles in their respective biosynthetic pathways in vivo are specific and independent of one other; the enzyme is involved in the biosynthesis of dTDP-L-rhamnose, a precursor of cell wall biosynthesis, pathway overview. It does not compensate for the other dTDP-4-keto-6-deoxyglucose 3,5-epimerase encoded by gene dnmU. Although dnmU and rmbC encode for similar functional proteins, their native roles in their respective biosynthetic pathways in vivo are specific and independent of one other
-
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)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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-alpha-D-glucose
dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
-
-
?
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-6-deoxy-L-mannose
show the reaction diagram
-
-
-
-
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-6-deoxy-L-mannose
show the reaction diagram
Escherichia coli Y10
-
-
-
-
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
-
-
-
dTDP-4-dehydro-6-deoxy-D-glucose
dTDP-4-dehydro-L-rhamnose
show the reaction diagram
-
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
-
?
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
TDP-6-deoxy-L-lyxo-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-4-hexosulose
?
show the reaction diagram
-
enzyme in biosynthesis of the cell wall component 6-deoxy-L-talose
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
-
enzyme in biosynthesis of dTDP-L-rhamnose from dTDP-D-glucose
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
-
enzyme is required for biosynthesis of the daunorubicin precursor thymidine diphospho-L-daunosamine
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
Escherichia coli 45
-
enzyme in biosynthesis of the cell wall component 6-deoxy-L-talose
-
-
-
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
-
?
UDP-4-dehydro-6-deoxy-D-glucose
UDP-4-dehydro-6-deoxy-L-mannose
show the reaction diagram
-
i.e. UDP-4-dehydro-L-rhamnose, product identification by electrospray ionization-mass spectrometry and gas chromatography mass spectrometry
?
dTDP-6-deoxy-D-xylo-4-hexulose
dTDP-6-deoxy-L-lyxo-4-hexulose
show the reaction diagram
-
third enzyme of the rhamnose pathway
-
?
additional information
?
-
Methanothermobacter thermautotrophicum
-
the enzyme is involved in the biosynthesis of dTDP-L-rhamnose, which is an essential component of the bacterial cell wall
-
-
?
additional information
?
-
-
the enzyme is required for dTDP-L-rhamnose biosynthesis
-
-
?
additional information
?
-
-
third enzyme of dTDP-L-rhamnose pathway
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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
C5J048, O33707
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
dTDP-4-dehydro-beta-L-rhamnose
show the reaction diagram
C5J048, O33707
-
-
?
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
-
-
-
dTDP-4-dehydro-6-deoxy-D-glucose
dTDP-4-dehydro-L-rhamnose
show the reaction diagram
-
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
-
?
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
-
enzyme in biosynthesis of the cell wall component 6-deoxy-L-talose
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
-
enzyme in biosynthesis of dTDP-L-rhamnose from dTDP-D-glucose
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
-
enzyme is required for biosynthesis of the daunorubicin precursor thymidine diphospho-L-daunosamine
-
-
-
TDP-6-deoxy-D-xylo-4-hexosulose
?
show the reaction diagram
Escherichia coli 45
-
enzyme in biosynthesis of the cell wall component 6-deoxy-L-talose
-
-
-
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
-
?
dTDP-6-deoxy-D-xylo-4-hexulose
dTDP-6-deoxy-L-lyxo-4-hexulose
show the reaction diagram
-
third enzyme of the rhamnose pathway
-
?
additional information
?
-
-
the enzyme is required for dTDP-L-rhamnose biosynthesis
-
-
?
additional information
?
-
-
third enzyme of dTDP-L-rhamnose pathway
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
no cofactors are required
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
divalent metal ions do not alter activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
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
-
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
-
1-(3-(5-ethyl-5H-[1,2,4]triazino[5,6-b]indol-3-ylsulfonyl)-propyl)-1H-benzo[d]imidazol-2(3H)-one
-
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
-
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
modeling of triazinoindol-benzimidazolones into the active site of RmlC, overview
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.025
dTDP-4-dehydro-6-deoxy-D-glucose
-
-
0.35
dTDP-6-deoxy-D-xylo-4-hexulose
-
RmlC K73A
0.48
dTDP-6-deoxy-D-xylo-4-hexulose
-
RmlC Y133F
0.71
dTDP-6-deoxy-D-xylo-4-hexulose
-
pH 7.0, 25C
0.71
dTDP-6-deoxy-D-xylo-4-hexulose
-
native
additional information
additional information
-
-
-
additional information
additional information
Michaelis-Menten kinetics
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.016
dTDP-6-deoxy-D-xylo-4-hexulose
Salmonella enterica
-
RmlC Y133F
0.095
dTDP-6-deoxy-D-xylo-4-hexulose
Salmonella enterica
-
RmlC K73A
39
dTDP-6-deoxy-D-xylo-4-hexulose
Salmonella enterica
-
pH 7.0, 25C
39
dTDP-6-deoxy-D-xylo-4-hexulose
Salmonella enterica
-
native
additional information
additional information
Streptococcus suis
-
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
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
-
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
-
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
LITERATURE
7.5
assay at; assay at
7.5 - 8.5
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
assay at; assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
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
LITERATURE
40600
-
gel filtration
285846
47000
gel filtration
716065
67000
-
gel filtration
2252
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
-
each monomer is formed mainly from two beta-sheets arranged in a beta-sandwich. The structure of a dTDP-phenol-enzyme complex shows the substrate-binding site to be located between the two beta-sheets, this site is formed from residues of both monomers
monomer
-
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
-
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
LITERATURE
42
stable for 30 min
716065
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
-
Methanothermobacter thermautotrophicum
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recombinant
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene L780, transcription profiling of UGER, phylogenetic analysis
cloned into pET23b using the Ligation Independent Clone system
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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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expression in Escherichia coli
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expression in Escherichia coli
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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
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
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
generation of rmbC-defective mutant
additional information
-
generation of rmbC-defective mutant
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
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validated anti-bacterial drug target
medicine
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validated anti-bacterial drug target
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medicine
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validated anti-bacterial drug target
synthesis
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the enzyme is part of an enzyme module system for the synthesis of dTDP-activated deoxysugars from dTMP and sucrose
synthesis
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potential application in altering the enzyme behavior for use in synthesis of bioactive carbohydrates