Riboflavin synthase: Difference between revisions
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== '''Structure''' == |
== '''Structure''' == |
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Riboflavin synthase is a homotrimer with 23kDa subunits. Each monomer contains two β-barrels and one α-helix at the C-terminal (residues 186-206.) The monomer folds into pseudo two-fold symmetry, predicted by sequence similarity between the N-terminal barrels (residues 4-86) and the C-terminal barrel (residues 101-184). <ref>Liao |
Riboflavin synthase is a homotrimer with 23kDa subunits. Each monomer contains two β-barrels and one α-helix at the C-terminal (residues 186-206.) The monomer folds into pseudo two-fold symmetry, predicted by sequence similarity between the N-terminal barrels (residues 4-86) and the C-terminal barrel (residues 101-184). <ref name=Liao>{{cite journal | author=Liao D, Zdzislaw W, Calabrese J, Viltanen P, and Jordan D | title=Crystal Structure of Riboflavin Synthase | journal= Structure | volume=9 | pages=399-408 | year=2001 | doi:10.1016/S0969-2126(01)00600-1}}</ref> |
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== '''Active Site''' == |
== '''Active Site''' == |
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Two 6,7-dimethyl-8-ribityllumazine molecules are hydrogen bound to each monomer as the two domains are topologically similar.<ref>Fischer |
Two 6,7-dimethyl-8-ribityllumazine molecules are hydrogen bound to each monomer as the two domains are topologically similar.<ref name=Fischer>{{cite journal | author=Fischer M, Schott AK, Kemter K, Feicht, R, Richter G, Illarionov B, Eisenreich W, Gerhardt S, Cuhsman M, Steinbacher S, Huber R, and Bacher A | title=Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiment | journal= BMC Biochemistry | volume=4 | pages=399-408 | year=2001 | doi:10.1186/1471-2091-4-18}}</ref> The active sites are located in the interface of the substrates between monomer pairs and modeled structures of the active site dimer have been created. <ref name=Gerhardt>{{cite journal | author=Gerhardt S, Schott AK, Kairies N, Cushman M, Illarionov B, Eisenreich W, Bacher A, Huber R, Steinbacher S, and Fischer M | title=Studies on the Reaction Mechanism of Riboflavin Synthase: X-Ray Crystal Structure of a Complex with 6-Carboxyethyl-7-Oxo-8-Ribityllumazine | journal= Structure | volume=10 | pages=1371-1381 | year=2002 | doi:10.1016/S0969-2126(02)00864-X }}</ref> Only one of the active sites of the enzyme catalyze riboflavin formation at a time as the other two sites face outward and are exposed to solvent.<ref name=Liao/> The amino acid residues involved in hydrogen bonding to the ligand are pictured, participating residues may include Thr148, Met160, Ile162, Thr165, Val6, Tyr164, Ser146, and Gly96 at the C-terminal domain and Ser41, Thr50, Gly 62, Ala64, Ser64, Val103, Cys48, His102 at the N-terminal domain.<ref name=Fischer 2>{{cite journal | author=Fischer M, and Bacher A | title=Biosynthesis of vitamin B2: Structure and mechanism of riboflavin synthase | journal= Archives of Biochemistry and Biophysics | volume=474 | pages=252-265 | year=2008 | doi:10.1016/j.abb.2008.02.00}}</ref> |
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{{Protbox |
{{Protbox |
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Revision as of 22:22, 11 December 2008
Riboflavin synthase catalyzes the final reaction of riboflavin biosynthesis:
2 6,7-dimethyl-8-ribityllumazine → riboflavin + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
| Identifiers | |
| Symbol | RibE, RibH |
| PANTHER | PTHR21058 |
| INTERPRO | IPR002180 |
| PDB | 1PKV, 1i8d, 1KZL, 1i18 |
| EC Number | 2.5.1.9 |
Structure
Riboflavin synthase is a homotrimer with 23kDa subunits. Each monomer contains two β-barrels and one α-helix at the C-terminal (residues 186-206.) The monomer folds into pseudo two-fold symmetry, predicted by sequence similarity between the N-terminal barrels (residues 4-86) and the C-terminal barrel (residues 101-184). [1]
Active Site
Two 6,7-dimethyl-8-ribityllumazine molecules are hydrogen bound to each monomer as the two domains are topologically similar.[2] The active sites are located in the interface of the substrates between monomer pairs and modeled structures of the active site dimer have been created. [3] Only one of the active sites of the enzyme catalyze riboflavin formation at a time as the other two sites face outward and are exposed to solvent.[1] The amino acid residues involved in hydrogen bonding to the ligand are pictured, participating residues may include Thr148, Met160, Ile162, Thr165, Val6, Tyr164, Ser146, and Gly96 at the C-terminal domain and Ser41, Thr50, Gly 62, Ala64, Ser64, Val103, Cys48, His102 at the N-terminal domain.Cite error: The <ref> tag has too many names (see the help page).
-
Hydrogen bonding between substrate and enzyme at the C-terminal domain -
Hydrogen bonding between substrate and enzyme at the N-terminal domain
Mechanism
No cofactors are needed for catalysis. Additionally, the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine can occur in boiling aqueous solution in the absence riboflavin synthase.[4]
At the interface of the substrate between monomer pairs, the enzyme holds the two 6,7-dimethyl-8-ribityllumazine molecules in position via hydrogen bonding to catalyze the dismutation reaction. [5] Additionally, acid/base catalysis by the amino acid residues has been suggested. Specific residues may include the His102/Thr148 dyad as a base for deprotonation of the C7a methyl group. Of the dyad, His102 is from the N-barrel and Thr148 is from the C-barrel, highlighting the importance of the proximity of the two subunits of the enzyme in the early stages of the reaction. [6] It has also been suggested that the identity of the nucleophile is one of the following conserved residues: Ser146, Ser41, Cys48, or Thr148, or water in the uncatalyzed reaction.[7] In studies on the role of Cys48 as a possible nucleophile, it has not been determined if nucleophilic displacement occurs via an SN1 or SN2 reaction. [8]
Drug Production
Scientists have hypothesized that enzymes involved in the riboflavin biosynthesis pathway, including riboflavin synthase, can be used to develop antibacterial drugs in order to treat infections caused by Gram-negative bacteria and yeasts. This hypothesis is based on the inability of Gram-negative bacteria, such as E. coli and S. typhimurium, to uptake riboflavin from the external environment. [9][10] As Gram-negative bacteria need to produce their own riboflavin, inhibiting riboflavin synthase or other enzymes involved in the pathway may be useful tools in developing antibacterial drugs.
The most potent riboflavin synthase inhibitor is 9-D-ribityl-1,3,7-trihydropurine-2,6,8-trione, with Ki value of 0.61 μM. 9-D-ribityl-1,3,7-trihydropurine-2,6,8-trione is thought to work through competitive inhibition with 6,7-dimethyl-8-ribityllumazine.[11]
References
- ^ a b Liao D, Zdzislaw W, Calabrese J, Viltanen P, and Jordan D (2001). "Crystal Structure of Riboflavin Synthase". Structure. 9: 399–408.
{{cite journal}}: Text "doi:10.1016/S0969-2126(01)00600-1" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Fischer M, Schott AK, Kemter K, Feicht, R, Richter G, Illarionov B, Eisenreich W, Gerhardt S, Cuhsman M, Steinbacher S, Huber R, and Bacher A (2001). "Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiment". BMC Biochemistry. 4: 399–408.
{{cite journal}}: Text "doi:10.1186/1471-2091-4-18" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Gerhardt S, Schott AK, Kairies N, Cushman M, Illarionov B, Eisenreich W, Bacher A, Huber R, Steinbacher S, and Fischer M (2002). "Studies on the Reaction Mechanism of Riboflavin Synthase: X-Ray Crystal Structure of a Complex with 6-Carboxyethyl-7-Oxo-8-Ribityllumazine". Structure. 10: 1371–1381.
{{cite journal}}: Text "doi:10.1016/S0969-2126(02)00864-X" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Bacher, A., Eberhardt, S., Fischer, M., Kis, K., and Richter, G. (2000). “Biosynthesis of Vitamin B2 (Riboflavin).” Annu. Rev. Nutr. 20:153-67.
- ^ Bacher, A., Eberhardt, S., Fischer, M., Kis, K., and Richter, G. (2000). “Biosynthesis of Vitamin B2 (Riboflavin).” Annu. Rev. Nutr. 20:153-67.
- ^ Zheng, V.J, Jordan, D., and Liao, D. (2003). "Examination of a reaction intermediate in the active site of riboflavin synthase. Bioorganic Chemistry. 31(4):278-287 doi:10.1016/S0045-2068(03)00029-4
- ^ Liao, D., Zdzislaw W., Calabrese, J., Viltanen, P., and Jordan, D. (2001). “Crystal Structure of Riboflavin Synthase.” Structure. 9 (5): 399-408. doi:10.1016/S0969-2126(01)00600-1
- ^ Zheng, V.J, Jordan, D., and Liao, D. (2003). "Examination of a reaction intermediate in the active site of riboflavin synthase. Bioorganic Chemistry. 31(4):278-287 doi:10.1016/S0045-2068(03)00029-4
- ^ Fischer, M. & Bacher, A. (2008) Biosynthesis of vitamin B2: Structure and mechanism of riboflavin synthase. Archives of Biochemistry and Biophysics. 474 (2), 252-265. doi:10.1016/j.abb.2008.02.008
- ^ Cushman, M., Yang, D., Kis, K. & Bacher, A. (2001) Design, Synthesis, and Evaluation of 9-D-Ribityl-1,3,7-trihydro-2,6,8-purinetrione, a Potent Inhibitor of Riboflavin Synthase and Lumazine Synthase. J. Org. Chem. 66 (25), 8320–8327 doi 10.1021/jo010706r
- ^ Cushman, M., Yang, D., Kis, K. & Bacher, A. (2001) Design, Synthesis, and Evaluation of 9-D-Ribityl-1,3,7-trihydro-2,6,8-purinetrione, a Potent Inhibitor of Riboflavin Synthase and Lumazine Synthase. J. Org. Chem. 66 (25), 8320– 8327 doi 10.1021/jo010706r
See also
External links
- Riboflavin+synthase at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
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