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Literature summary extracted from

  • Ladenstein, R.; Fischer, M.; Bacher, A.
    The lumazine synthase/riboflavin synthase complex: shapes and functions of a highly variable enzyme system (2013), FEBS J., 280, 2537-2563.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.78 substrate binding site structure analysis of Aquifex aeolicus lumazine synthase in complex with the inhibitor 3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid Aquifex aeolicus

Protein Variants

EC Number Protein Variants Comment Organism
2.5.1.78 additional information homotopical sequence insertion into icosahedral lumazine synthase resulting in large particles. Mutations at the phosphate binding site Arg127 perturb enzymatic activity and also capsid assembly. The central channel of the pentameric building blocks appear significantly widened, indicating that the mode of interaction between the pentamer units and the topology of the subunit interfaces must have undergone significant changes, overview Aquifex aeolicus
2.5.1.78 R127H site-directed mutagenesis, the mutant shows 37% reduced activity compared to the wild-type enzyme Aquifex aeolicus
2.5.1.78 R127K site-directed mutagenesis, the mutant shows 91% reduced activity compared to the wild-type enzyme Aquifex aeolicus

General Stability

EC Number General Stability Organism
2.5.1.78 role of electrostatic interactions for the stability of beta60 enzyme particles, pentamers of beta subunits have maximal stability at a pH of approximately pH 8.0 and are more stable than dimers or trimers Aquifex aeolicus

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.5.1.78 3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid binding structure, overview Aquifex aeolicus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine Bacillus subtilis
-
 riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine Methanothermobacter thermautotrophicus
-
 riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine Methanocaldococcus jannaschii
-
 riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil Bacillus subtilis
-
 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil Saccharomyces cerevisiae
-
 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil Aquifex aeolicus
-
 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil Brucella abortus
-
 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.9 Bacillus subtilis
-
-
-
2.5.1.9 Methanocaldococcus jannaschii
-
-
-
2.5.1.9 Methanothermobacter thermautotrophicus
-
-
-
2.5.1.78 Aquifex aeolicus O66529 gene ribH
-
2.5.1.78 Bacillus subtilis P11998 gene ribH
-
2.5.1.78 Brucella abortus Q2YKV1 gene ribH2; gene ribH2
-
2.5.1.78 Brucella abortus Q2YNC6 gene ribH1; gene ribH1
-
2.5.1.78 Saccharomyces cerevisiae P50861 gene Rib4
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate critical involvement of the active-site residues Phe22, His88 and Arg127 in substrate binding and catalysis Bacillus subtilis
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine
-
 Bacillus subtilis riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine
-
 Methanothermobacter thermautotrophicus riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.9 6,7-dimethyl-8-(1-D-ribityl)lumazine
-
 Methanocaldococcus jannaschii riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
-
 Bacillus subtilis 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
-
 Saccharomyces cerevisiae 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
-
 Aquifex aeolicus 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
-
 Brucella abortus 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
 ?
2.5.1.78 additional information critical involvement of the active-site residues Phe22, His88 and Arg127 in substrate binding and catalysis Bacillus subtilis ?
-
 ?

Subunits

EC Number Subunits Comment Organism
2.5.1.9 homopentamer
-
 Methanocaldococcus jannaschii
2.5.1.9 homotrimer
-
 Bacillus subtilis
2.5.1.9 homotrimer
-
 Methanothermobacter thermautotrophicus
2.5.1.78 decamer the d5-symmetric protein is a dimer of pentamers Brucella abortus
2.5.1.78 More structure analysis and comparisons, overview Bacillus subtilis
2.5.1.78 More structure analysis and comparisons, overview Saccharomyces cerevisiae
2.5.1.78 More structure analysis and comparisons, overview Aquifex aeolicus
2.5.1.78 More structure analysis and comparisons, overview Brucella abortus
2.5.1.78 pentamer the lumazine protein folds into two closely similar domains Bacillus subtilis
2.5.1.78 pentamer the lumazine protein folds into two closely similar domains, the enzyme forms a dodecamer of pentamers, electrostatic model calculations Saccharomyces cerevisiae
2.5.1.78 pentamer the lumazine protein folds into two closely similar domains, the enzyme forms a dodecamer of pentamers, electrostatic model calculations Aquifex aeolicus

Synonyms

EC Number Synonyms Comment Organism
2.5.1.9 lumazine synthase/riboflavin synthase complex
-
 Bacillus subtilis
2.5.1.9 lumazine synthase/riboflavin synthase complex
-
 Methanothermobacter thermautotrophicus
2.5.1.9 lumazine synthase/riboflavin synthase complex
-
 Methanocaldococcus jannaschii
2.5.1.78 DMRL synthase
-
 Saccharomyces cerevisiae
2.5.1.78 lumazine synthase
-
 Bacillus subtilis
2.5.1.78 lumazine synthase
-
 Saccharomyces cerevisiae
2.5.1.78 lumazine synthase
-
 Aquifex aeolicus
2.5.1.78 lumazine synthase
-
 Brucella abortus
2.5.1.78 RIB4
-
 Saccharomyces cerevisiae

General Information

EC Number General Information Comment Organism
2.5.1.78 evolution in Bacillaceae, lumazine synthase and riboflavin synthase form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogues of lumazine synthase. The quaternary structure of the icosahedral beta subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids Bacillus subtilis
2.5.1.78 evolution in Bacillaceae, lumazine synthase and riboflavin synthase form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogues of lumazine synthase. The quaternary structure of the icosahedral beta subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids Aquifex aeolicus
2.5.1.78 evolution in Bacillaceae, lumazine synthase and riboflavin synthase form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogues of lumazine synthase. The quaternary structure of the icosahedral beta subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids Brucella abortus
2.5.1.78 metabolism the xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase as part of the riboflavin pathway, overview Bacillus subtilis
2.5.1.78 metabolism the xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase as part of the riboflavin pathway, overview Saccharomyces cerevisiae
2.5.1.78 metabolism the xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase as part of the riboflavin pathway, overview Aquifex aeolicus
2.5.1.78 metabolism the xylene ring of riboflavin (vitamin B2) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase as part of the riboflavin pathway, overview Brucella abortus
2.5.1.78 additional information modelling of the lumazine synthase/riboflavin synthase complex Bacillus subtilis
2.5.1.78 physiological function the enzyme is a strong Brucella antigen Brucella abortus