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Literature summary 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

Application

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

Cloned(Commentary)

EC Number Cloned (Comment) Organism
5.1.3.13 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
5.1.3.13 cloned into pET23b using the Ligation Independent Clone system Mycobacterium tuberculosis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
5.1.3.13 enzymatically Mycobacterium tuberculosis
5.1.3.13 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

EC Number Protein Variants Comment Organism
5.1.3.13 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
5.1.3.13 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
5.1.3.13 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
5.1.3.13 0.35
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC K73A Salmonella enterica
5.1.3.13 0.48
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC Y133F Salmonella enterica
5.1.3.13 0.71
-
 dTDP-6-deoxy-D-xylo-4-hexulose native Salmonella enterica

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
5.1.3.13 22000
-
-
 Pseudomonas aeruginosa
5.1.3.13 22000
-
-
 Mycobacterium tuberculosis
5.1.3.13 22000
-
-
 Salmonella enterica

Natural Substrates/ Products (Substrates)

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

Organism

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

Substrates and Products (Substrate)

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

Synonyms

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

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
5.1.3.13 additional information
-
 additional information no activity with dTDP-6-deoxy-D-xylo-4-hexulose (RmlC H63A) Salmonella enterica
5.1.3.13 0.016
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC Y133F Salmonella enterica
5.1.3.13 0.095
-
 dTDP-6-deoxy-D-xylo-4-hexulose RmlC K73A Salmonella enterica
5.1.3.13 39
-
 dTDP-6-deoxy-D-xylo-4-hexulose native Salmonella enterica

Cofactor

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