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Literature summary for 5.1.3.13 extracted from

  • Dong, C.; Major, L.L.; Srikannathasan, V.; Errey, J.C.; Giraud, M.F.; Lam, J.S.; Graninger, M.; Messner, P.; McNeil, M.R.; Field, R.A.; Whitfield, C.; Naismith, J.H.
    RmlC, a C3 and C5 carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation (2007), J. Mol. Biol., 365, 146-159.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 5.1.3.13

Application

Application Comment Organism
medicine validated anti-bacterial drug target Pseudomonas aeruginosa
medicine validated anti-bacterial drug target Mycobacterium tuberculosis
medicine validated anti-bacterial drug target Salmonella enterica

Cloned(Commentary)

Cloned (Comment) Organism
cloned into pET23a(+) with an N-terminal 6× His tag and a linker consisting of Gly-Ser-Met-Ala, overexpression in Escherichia coli Pseudomonas aeruginosa
cloned into pET23b using the Ligation Independent Clone system Mycobacterium tuberculosis

Crystallization (Commentary)

Crystallization (Comment) Organism
enzymatically Mycobacterium tuberculosis
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) Pseudomonas aeruginosa

Protein Variants

Protein Variants Comment Organism
H63A 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'. Salmonella enterica
K73A 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'. Salmonella enterica
Y133F 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'. Salmonella enterica

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.35
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC K73A Salmonella enterica
0.48
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC Y133F Salmonella enterica
0.71
-
 dTDP-6-deoxy-D-xylo-4-hexulose native Salmonella enterica

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
22000
-
-
 Pseudomonas aeruginosa
22000
-
-
 Mycobacterium tuberculosis
22000
-
-
 Salmonella enterica

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
dTDP-6-deoxy-D-xylo-4-hexulose Pseudomonas aeruginosa third enzyme of the rhamnose pathway dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose Mycobacterium tuberculosis third enzyme of the rhamnose pathway dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose Salmonella enterica third enzyme of the rhamnose pathway dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose Mycobacterium tuberculosis H37Rv third enzyme of the rhamnose pathway dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?

Organism

Organism UniProt Comment Textmining
Mycobacterium tuberculosis
-
-
-
Mycobacterium tuberculosis H37Rv
-
-
-
Pseudomonas aeruginosa
-
-
-
Salmonella enterica
-
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
dTDP-6-deoxy-D-xylo-4-hexulose third enzyme of the rhamnose pathway Pseudomonas aeruginosa dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose third enzyme of the rhamnose pathway Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose third enzyme of the rhamnose pathway Salmonella enterica dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?
dTDP-6-deoxy-D-xylo-4-hexulose third enzyme of the rhamnose pathway Mycobacterium tuberculosis H37Rv dTDP-6-deoxy-L-lyxo-4-hexulose
-
 ?

Synonyms

Synonyms Comment Organism
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
 Pseudomonas aeruginosa
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
 Mycobacterium tuberculosis
dTDP-6-deoxy-D-xylo-4-hexulose 3',5'-epimerase
-
 Salmonella enterica
RmlC
-
 Salmonella enterica

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
 additional information no activity with dTDP-6-deoxy-D-xylo-4-hexulose (RmlC H63A) Salmonella enterica
0.016
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC Y133F Salmonella enterica
0.095
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC K73A Salmonella enterica
39
-
 dTDP-6-deoxy-D-xylo-4-hexulose native Salmonella enterica

Cofactor

Cofactor Comment Organism Structure
additional information no cofactors are required Pseudomonas aeruginosa
additional information no cofactors are required Mycobacterium tuberculosis
additional information no cofactors are required Salmonella enterica