Literature summary for 5.1.3.13 extracted from

Shornikov, A.; Tran, H.; Macias, J.; Halavaty, A.S.; Minasov, G.; Anderson, W.F.; Kuhn, M.L.
Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC) (2017), Acta Crystallogr. Sect. F, 73, 664-671 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant His-tagged enzyme expression in Escherichia coli strain BL21(DE3) Magic	Bacillus anthracis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified mixture containing all four dTDP-L-rhamnose biosynthetic enzymes, RfbA, RfbB, RfbC and RfbD, sitting drop vapor diffusion method, mixing of 0.001 ml of protein solution, containing 10mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM 2-mercaptoethanol, 1 mM dTTP, 1 mM Glc1P, 1 mM NAD+, 1 mM NADP+, and 1mM MgCl2, with 0.001 ml of reservoir solution containing 0.2 M diammonium citrate, pH 5.0, 20% w/v, and PEG 3350, at room temperature, X-ray diffraction structure determination and analysis at 1.63 A resolution, molecular replacement using one monomer from PDB ID 1dzr as the search model	Bacillus anthracis

Crystallization (Comment)

Organism

purified mixture containing all four dTDP-L-rhamnose biosynthetic enzymes, RfbA, RfbB, RfbC and RfbD, sitting drop vapor diffusion method, mixing of 0.001 ml of protein solution, containing 10mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM 2-mercaptoethanol, 1 mM dTTP, 1 mM Glc1P, 1 mM NAD+, 1 mM NADP+, and 1mM MgCl2, with 0.001 ml of reservoir solution containing 0.2 M diammonium citrate, pH 5.0, 20% w/v, and PEG 3350, at room temperature, X-ray diffraction structure determination and analysis at 1.63 A resolution, molecular replacement using one monomer from PDB ID 1dzr as the search model

Bacillus anthracis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
dTDP-4-dehydro-6-deoxy-alpha-D-glucose	Bacillus anthracis	-	dTDP-4-dehydro-beta-L-rhamnose	-	r
dTDP-4-dehydro-6-deoxy-alpha-D-glucose	Bacillus anthracis Ames	-	dTDP-4-dehydro-beta-L-rhamnose	-	r

Organism

Organism	UniProt	Comment	Textmining
Bacillus anthracis	Q81TP1	-	-
Bacillus anthracis Ames	Q81TP1	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) Magic by nickel affinity chromatography and tag removal	Bacillus anthracis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
dTDP-4-dehydro-6-deoxy-alpha-D-glucose	-	Bacillus anthracis	dTDP-4-dehydro-beta-L-rhamnose	-	r
dTDP-4-dehydro-6-deoxy-alpha-D-glucose	-	Bacillus anthracis Ames	dTDP-4-dehydro-beta-L-rhamnose	-	r

Subunits

Subunits	Comment	Organism
dimer	crystal structure determination	Bacillus anthracis

Synonyms

Synonyms	Comment	Organism
dTDP-4-dehydrorhamnose 3,5-epimerase	-	Bacillus anthracis
RfbC	-	Bacillus anthracis
RmlC	-	Bacillus anthracis

General Information

General Information	Comment	Organism
evolution	structural comparison of the enzyme structure with RfbC homologues shows that the key active-site residues are conserved across kingdoms. RmlC-like epimerases belongs to the diverse cupin superfamily	Bacillus anthracis
metabolism	the biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes, RfbA, RfbB, RfbC and RfbD. RfbC catalyzes the third reaction, a double epimerization producing dTDP-6-deoxy-L-lyxo-4-hexulose (dTDP-4-dehydro-L-rhamnose)	Bacillus anthracis
additional information	two different ligands are bound in the protein structure: diphosphate in the active site of one monomer and dTDP in the other monomer, active site structure, overview	Bacillus anthracis
physiological function	the exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes, RfbA, RfbB, RfbC and RfbD. The dTDP-4-dehydrorhamnose 3,5-epimerase, RfbC, epimerizes dTDP-4-dehydro-6-deoxy-alpha-D-glucose into dTDP-4-dehydro-beta-L-rhamnose	Bacillus anthracis