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Information on EC 2.5.1.9 - riboflavin synthase and Organism(s) Schizosaccharomyces pombe and UniProt Accession Q9Y7P0
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2.5.1.9 riboflavin synthaseIUBMB Comments
A flavoprotein (riboflavin).
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Word Map
- 2.5.1.9
- 6,7-dimethyl-8-ribityllumazine
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cyclohydrolase
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5-amino-6-ribitylamino-2,41h,3h-pyrimidinedione
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dismutation
- guilliermondii
- 3,4-dihydroxy-2-butanone
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icosahedral
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bartonellae
- photobacterium
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flavinogenic
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flavinogenesis
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ashbyii
- eremothecium
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ribitylated
- leiognathi
- henselae
- famata
- drug development
- pharmacology
- medicine
The taxonomic range for the selected organisms is: Schizosaccharomyces pombe
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
riboflavin synthase, riboflavin synthetase, heavy riboflavin synthase, light riboflavin synthase, lumazine synthase/riboflavin synthase complex, riboflavine synthetase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
light riboflavin synthase
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riboflavin synthetase
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riboflavine synthase
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riboflavine synthetase
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synthase, riboflavin
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
catalytic mechanism, stereochemistry
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2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
reaction mechanism
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
substrate binding site
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
detailed catalytic mechanism, Cys48 is involved
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dismutation
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PATHWAY SOURCE
PATHWAYS
BRENDA
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-, -, -
SYSTEMATIC NAME
IUBMB Comments
6,7-dimethyl-8-(1-D-ribityl)lumazine:6,7-dimethyl-8-(1-D-ribityl)lumazine 2,3-butanediyltransferase
A flavoprotein (riboflavin).
CAS REGISTRY NUMBER
COMMENTARY
9075-82-5
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
6,7-dimethyl-8-ribityllumazine + 6,7-dimethyl-8-ribityllumazine
riboflavin + 4-(1'-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
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-
-
?
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
ultimate step in the biosynthesis of riboflavin, pathway overview
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r
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
mechanistically complex dismutation
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r
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
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final step of biosynthesis of vitamin B2, i.e. riboflavin, the universal precursor of flavocoenzymes, overview
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?
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
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dismutation, exchange of a C4 fragment, regio- and stereospecific reaction
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?
additional information
?
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structure-function relationship
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?
additional information
?
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substrate binding structure and catalytic mechanism by NMR analysis and protein perturbation studies using fluoro-substituted reaction intermediate analogues, i.e. 2 epimers of 6,7-bis(trifluoromethyl)-8-ribityllumazine hydrate, 6-trifluoromethyl-7-oxo-8-ribityllumazine, 6-carboxyethyl-7-oxo-8-ribityllumazine, and 5-nitro-6-ribitylamino-2,4-pyrimidinedione, overview
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?
additional information
?
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substrate binding structure and catalytic mechanism by NMR analysis and protein perturbation studies using fluoro-substituted reaction intermediate analogues, i.e. 2 epimers of 6,7-bis(trifluoromethyl)-8-ribityllumazine hydrate, 6-trifluoromethyl-7-oxo-8-ribityllumazine, 6-carboxyethyl-7-oxo-8-ribityllumazine, and 5-nitro-6-ribitylamino-2,4-pyrimidinedione, overview
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
ultimate step in the biosynthesis of riboflavin, pathway overview
-
-
r
6,7-dimethyl-8-ribityllumazine + 6,7-dimethyl-8-ribityllumazine
riboflavin + 4-(1'-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
-
-
-
?
6,7-dimethyl-8-(1-D-ribityl)lumazine
riboflavin + 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
-
final step of biosynthesis of vitamin B2, i.e. riboflavin, the universal precursor of flavocoenzymes, overview
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-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0057
6,7-dimethyl-8-(1-D-ribityl)lumazine
pH 7.2, 37°C, recombinant enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
trimer
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folding topology, each subunit binds one substrate molecule
additional information
additional information
structure model, biological implication
additional information
2 similar folding domains per subunit
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of enzyme complexed with 6-carboxyethyl-7-oxo-8-ribityllumazine, sitting drop vapour diffusion method against equal amounts of reservoir solution containing 0.1 M bicine, pH 9.0, 65% v/v 2-mehyl-2,4-pentanediol, enzyme solution: 9 mg/ml, 20 mM TrisHCl, pH 7.0, 0.1 M KCl, 10 molar excess of solid 8, X-ray structure determination and analysis, structure model building and refinement, overview
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C48S
site-directed mutagenesis, highly decreased activity compared to the wild-type enzyme
S146A
site-directed mutagenesis, slightly increased activity compared to the wild-type enzyme
S146C
site-directed mutagenesis, slightly increased activity compared to the wild-type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli by ion exchange chromatography, ultrafiltration, gel filtration, and hydrophobic interaction chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, subcloning and expression in Escherichia coli strains M15 and XL1-Blue, wild-type and mutant enzymes
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pharmacology
the enzyme is a target for development of antiinfective drugs
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gerhardt, S.; Schott, A.K.; Kairies, N.; Cushman, M.; Illarionov, B.; Eisenreich, W.; Bacher, A.; Huber, R.; Steinbacher, S.; Fischer, M.
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
2002
Schizosaccharomyces pombe (Q9Y7P0), Schizosaccharomyces pombe
Fischer, M.; Romisch, W.; Illarionov, B.; Eisenreich, W.; Bacher, A.
Structures and reaction mechanisms of riboflavin synthases of eubacterial and archaeal origin
Biochem. Soc. Trans.
33
780-784
2005
Arabidopsis thaliana, Escherichia coli, Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, Schizosaccharomyces pombe
Fischer, M.; Schott, A.K.; Kemter, K.; Feicht, R.; Richter, G.; Illarionov, B.; Eisenreich, W.; Gerhardt, S.; Cushman, M.; Steinbacher, S.; Huber, R.; Bacher, A.
Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiments
BMC Biochem.
4
18
2003
Schizosaccharomyces pombe (Q9Y7P0), Schizosaccharomyces pombe
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