Literature summary for 4.2.1.75 extracted from

Schubert, H.L.; Phillips, J.D.; Heroux, A.; Hill, C.P.
Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex (2008), Biochemistry, 47, 8648-8655.

Cloned(Commentary)

Cloned (Comment)	Organism
expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)	Thermus thermophilus

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme, three apoenzyme forms, U3S1, U3S2, U3S3, and one enzyme-product complex form, vapor diffusion in sitting drop method, mixing 0.002 ml of protein with 0.002 ml of precipitant solution and equilibration over 1 mL of precipitant solution of different compositions, for U3S1, 1.2 M NaH2PO4, 0.8 M K2H2PO4, for U3S2, 21-24% PEG 8000, 0.2 M Mg-acetate, 0.1 M MES-HCl, pH 6.5, 0.2 M NaCl, and for U3S3, 18-24% PEG 8000, 0.1 M Tris-HCl, pH 8.5, 0.2 mM MgCl2, 4°C, 1-7 days, X-ray diffraction structure determination and analysis at 1.6-2.0 A resolution	Thermus thermophilus

Crystallization (Comment)

Organism

purified recombinant enzyme, three apoenzyme forms, U3S1, U3S2, U3S3, and one enzyme-product complex form, vapor diffusion in sitting drop method, mixing 0.002 ml of protein with 0.002 ml of precipitant solution and equilibration over 1 mL of precipitant solution of different compositions, for U3S1, 1.2 M NaH2PO4, 0.8 M K2H2PO4, for U3S2, 21-24% PEG 8000, 0.2 M Mg-acetate, 0.1 M MES-HCl, pH 6.5, 0.2 M NaCl, and for U3S3, 18-24% PEG 8000, 0.1 M Tris-HCl, pH 8.5, 0.2 mM MgCl2, 4°C, 1-7 days, X-ray diffraction structure determination and analysis at 1.6-2.0 A resolution

Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
Hydroxymethylbilane	Thermus thermophilus	-	Uroporphyrinogen III	-	?
Hydroxymethylbilane	Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039	-	Uroporphyrinogen III	-	?

Organism

Organism	UniProt	Comment	Textmining
Thermus thermophilus	Q72KM1	-	-
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039	Q72KM1	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the tag is cleaved off by TEV, followed by gel filtration	Thermus thermophilus

Reaction

Reaction	Comment	Organism	Reaction ID
hydroxymethylbilane = uroporphyrinogen III + H2O	reaction mechanism via azafulvene and azofulvene intermediates, the product binds between the two domains and is held in place by a network of hydrogen bonds between the products side chain carboxylates and the proteins main chain amides. Interactions of the product A and B ring carboxylate side chains with both structural domains of U3S appear to dictate the relative orientation of the domains in the closed enzyme conformation and likely remain intact during catalysis. The product C and D rings are less constrained in the structure, consistent with the conformational changes required for the catalytic cyclization with inversion of D ring orientation. A conserved tyrosine residue is potentially positioned to facilitate loss of a hydroxyl from the substrate to initiate the catalytic reaction, overview	Thermus thermophilus	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
Hydroxymethylbilane	-	Thermus thermophilus	Uroporphyrinogen III	-	?
Hydroxymethylbilane	-	Thermus thermophilus	Uroporphyrinogen III	enzyme-product structure analysis, overview	?
Hydroxymethylbilane	-	Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039	Uroporphyrinogen III	-	?
Hydroxymethylbilane	-	Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039	Uroporphyrinogen III	enzyme-product structure analysis, overview	?

Synonyms

Synonyms	Comment	Organism
U3S	-	Thermus thermophilus
Uroporphyrinogen III synthase	-	Thermus thermophilus