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Information on EC 2.5.1.78 - 6,7-dimethyl-8-ribityllumazine synthase and Organism(s) Aquifex aeolicus and UniProt Accession O66529
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2.5.1.78 6,7-dimethyl-8-ribityllumazine synthaseIUBMB Comments
Involved in riboflavin biosynthesis.
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Word Map
- 2.5.1.78
- brucella
-
capsid
-
icosahedral
-
aquifex
- aeolicus
- brucellosis
- 4-phosphate
-
pentamer
- abortus
- 3,4-dihydroxy-2-butanone
-
5-amino-6-ribitylamino-2,41h,3h-pyrimidinedione
- medicine
-
guest
-
decameric
-
supercharged
-
homopentamer
-
nanocompartments
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60-subunit
- biotechnology
- synthesis
- molecular biology
- analysis
- drug development
The taxonomic range for the selected organisms is: Aquifex aeolicus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
lumazine synthase, 6,7-dimethyl-8-ribityllumazine synthase, ribh2, ribh1, mj0303, ribh1 protein, dmrl synthase, 6,7-dimethyl-8-(d-ribityl)lumazine synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
5-amino-6-(D-ribitylamino)uracil butanedionetransferase
Involved in riboflavin biosynthesis.
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
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
?
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
penultimate step of riboflavin biosynthesis
-
-
?
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
?
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + L-3,4-dihydroxybutan-2-one 4-phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + 2 H2O + phosphate
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
-
-
-
-
?
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
-
the enzyme is involved in biosynthesis of riboflavin
-
-
?
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + L-3,4-dihydroxybutan-2-one 4-phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
-
?
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + L-3,4-dihydroxybutan-2-one 4-phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + 2 H2O + phosphate
-
an early optical transient absorbing around 330 nm is interpreted as a Schiff base intermediate obtained by reaction of the position 5 amino group of the heterocyclic substrate with the carbonyl group of 3,4-dihydroxy-2-butanone 4-phosphate. A second transient with an absorption maximum at 445 nm represents an intermediate resulting from the elimination of phosphate from the Schiff base. The rate-determining step is the subsequent formation of the 7-exomethylene type anion of 6,7-dimethyl-8-ribityllumazine
-
-
?
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
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
?
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
penultimate step of riboflavin biosynthesis
-
-
?
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil
6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
?
5-amino-6-(1-D-ribitylamino)pyrimidine-2,4(1H,3H)-dione + (S)-2-hydroxy-3-oxobutyl dihydrogen phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O
-
the enzyme is involved in biosynthesis of riboflavin
-
-
?
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione + L-3,4-dihydroxybutan-2-one 4-phosphate
6,7-dimethyl-8-(1-D-ribityl)lumazine + 2 H2O + phosphate
-
-
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid
binding structure, overview
5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid
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-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
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
physiological function
lumazine synthase forms cage complexes with the cognate riboflavin synthase when both proteins are coproduced in the cytosol of Escherichia coli. A 12-amino acid-long peptide at the C terminus of riboflavin synthase serves as a specific localization sequence responsible for targeting the guest to the protein compartment
metabolism
metabolism
-
enzyme AaLS catalyzes the penultimate step in riboflavin biosynthesis
metabolism
lumazine synthase forms specific inclusion complexes with riboflavin synthase when both proteins are co-expressed in a heterologous host. Encapsulation of specific enzymes in self-assembling protein cages is a hallmark of bacterial compartments that function as counterparts to eukaryotic organelles
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60-mer
sequence determinants responsible for the icosahedral quaternary structure
pentamer
the lumazine protein folds into two closely similar domains, the enzyme forms a dodecamer of pentamers, electrostatic model calculations
60-mer
-
the spherical protein consists of 60 identical subunits with strict icosahedral 532 symmetry
additional information
additional information
lumazine synthase is found in different species in two different quaternary structures, pentameric and icosahedral, built from practically the same structural monomeric unit. The icosahedral structure is best described as a capsid of twelve pentamers. Despite this noticeable difference, the active sites are virtually identical in all structurally studied members. The main regions involved in the catalysis are located at the interface between adjacent subunits in the pentamer. Combined analysis that includes sequence-structure and evolutionary studies to find the sequence determinants of the different quaternary assemblies of this enzyme. The positions involved in icosahedral contacts suffer a larger increase in constraints than the rest. Eight sequence sites that would be the most important icosahedral sequence determinants are identified
additional information
-
enzyme AaLS consists of 60 identical subunits that form an icosahedral capsid architecture with 15.4 nm exterior and 9 nm interior diameters
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
substrate binding site structure analysis of Aquifex aeolicus lumazine synthase in complex with the inhibitor 3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid
crystallized at room temperature by sitting-drop vapor-diffusion method, the protein is crystallized in the cubic space group I23 with the cell dimensions a = b = c = 180.8 A, diffraction data are collected to 1.6 A resolution
-
sitting-drop vapor diffusion method, crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures are refined at resolutions of 1.72 A (enzyme-7-dioxo-5H-8-ribitylaminolumazine complex), 1.85 A (enzyme-3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid complex), 2.05 A (enzyme-5-nitroso-6-ribityl-amino-2,4(1H,3H)pyrimidinedione complex) and 2.2 A (enzyme-5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid complex), respectively. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single site mutants of lumazine synthase from Bacillus subtilis show that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, phosphate elimination, formation of the Schiff base and cyclization is proposed
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R108C
site-directed mutagenesis, substitution of the arginine residue at position 108 with cysteine, which is exposed on the exterior surface of the enzyme and can be used as a site for the attachment of small molecules. Construction of an in vivo applicable magnetic resonance positive contrast agent by conjugating Gd(III)-chelating agent complexes to lumazine synthase AaLS isolated from Aquifex aeolicus, measurement of T1 relaxation times of the Gd(III)-DOTA-AaLS, overview
R127H
site-directed mutagenesis, the mutant shows 37% reduced activity compared to the wild-type enzyme
R127K
site-directed mutagenesis, the mutant shows 91% reduced activity compared to the wild-type enzyme
additional information
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
additional information
-
a 12-amino acid-long peptide at the C terminus of riboflavin synthase serves as a specific localization sequence responsible for targeting the guest to the protein compartment. Covalent fusion of this peptide tag to heterologous guest molecules leads to their internalization into lumazine synthase assemblies both in vivo and in vitro
additional information
a 12-amino acid-long peptide at the C terminus of riboflavin synthase serves as a specific localization sequence responsible for targeting the guest to the protein compartment. Covalent fusion of this peptide tag to heterologous guest molecules leads to their internalization into lumazine synthase assemblies both in vivo and in vitro
additional information
a circularly permuted variant of lumazine synthase affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Permutated lumazine synthase proteins integrate into wild-type and other engineered lumazine synthase assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments
additional information
-
a circularly permuted variant of lumazine synthase affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Permutated lumazine synthase proteins integrate into wild-type and other engineered lumazine synthase assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments
additional information
-
development of lumazine synthase, isolated from hyperthermophile Aquifex aeolicus, as a modular delivery nanoplatform for the targeted delivery of diagnostic and/or therapeutic molecules depending on target cancer cells, method evaluation, overview. The enzyme is engineered for its binding and transport/ligand presentation function by mutation of rg108 to Cys, and insertion the RGD4C peptide with extra linker sequences (GGGCDCRGDCFCASGGG) to the position between residues 70 and 71, where the exterior loop is formed, allowing RGD4C peptides to adopt an active cyclic form through intramolecular disulfide bonds. In parallel, the SP94 peptide (SFSIIHTPILPL) is introduced at the C-terminal end of AaLS because the C-termini are on the exterior surface based on atomic resolution structural information and the linear form of SP94 peptide being the most active, ESI-TOF MS, UV/Vis spectrophotometric, and size-exclusion chromatographic analysis, overview. The construct binds selectively to their target cells, KB or HepG2 cells. Conjugation of bifunctional N-(3,4-dihydroxyphenethyl)-3-maleimido-propanamide to SP94-AaLS via a thiolmaleimide Michael-type addition and introduction of anti-cancer drug bortezomib (BTZ). The cytoxicity of HepG2 cells treated with BTZ-Catechol-SP94-AaLS also increases in a dose-dependent manner, similar to that of free BTZ, while SP94-AaLS without BTZ has almost no cytotoxicity on the cells
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
lumazine synthase forms cage complexes with the cognate riboflavin synthase from Aquifex aeolicus when both proteins are co-produced in the cytosol of Escherichia coli. A 12-amino acid-long peptide at the C terminus of riboflavin synthase serves as a specific localization sequence responsible for targeting the guest to the protein compartment
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
development and characterization of an in vivo applicable magnetic resonance positive contrast agent by conjugating Gd(III)-chelating agent complexes to lumazine synthase isolated from Aquifex aeolicus (AaLS). The r1 relaxivity of Gd(III)-DOTA-AaLS-R108C is 16.49 mM/s and its r1/r2 ratio is 0.52 at the magnetic field strength of 7 T. The results of 3D MR angiography demonstrate the feasibility of vasculature imaging within 2 h of intravenous injection of the agent and a significant reduction in T1 values observed in the tumor region 7 h post-injection in the SCC-7 flank tumor model. Gd(III)-DOTA-AaLS-R108C can serve as a potential theranostic nanoplatform at high magnetic field strength
biotechnology
a circularly permuted variant of lumazine synthase affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Permutated lumazine synthase proteins integrate into wild-type and other engineered lumazine synthase assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments
molecular biology
-
outside of the cell, the hollow spherical architecture of the enzyme capsid is used as a template for the encapsulation of cargo proteins, such as green fluorescent proteins, and HIV proteases, and fabrication of uniform layer-by-layer assemblies using non-covalent interactions between surface-displayed His6 and Ni-NTA of enzyme AaLS. The enzyme shows encapsulation capability and surface presentation of ligands, which represent the great potential of AaLS as a versatile delivery vehicle
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Haase, I.; Mrtl, S.; Khler, P.; Bacher, A.; Fischer, M.
Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii
Eur. J. Biochem.
270
1025-1032
2003
Aquifex aeolicus, Methanocaldococcus jannaschii (Q57751), Methanocaldococcus jannaschii
Haase, I.; Fischer, M.; Bacher, A.; Schramek, N.
Temperature-dependent presteady state kinetics of lumazine synthase from the hyperthermophilic eubacterium Aquifex aeolicus
J. Biol. Chem.
278
37909-37915
2003
Aquifex aeolicus
Zhang, X.; Meining, W.; Fischer, M.; Bacher, A.; Ladenstein, R.
X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons
J. Mol. Biol.
306
1099-1114
2001
Aquifex aeolicus
Zhang, X.; Meining, W.; Cushman, M.; Haase, I.; Fischer, M.; Bacher, A.; Ladenstein, R.
A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus
J. Mol. Biol.
328
167-182
2003
Aquifex aeolicus
Fornasari, M.S.; Laplagne, D.A.; Frankel, N.; Cauerhff, A.A.; Goldbaum, F.A.; Echave, J.
Sequence determinants of quaternary structure in lumazine synthase
Mol. Biol. Evol.
21
97-107
2003
Spinacia oleracea, Corynebacterium ammoniagenes (O24753), Helicobacter pylori (O24854), Methanothermobacter thermautotrophicus (O27443), Archaeoglobus fulgidus (O28152), Aquifex aeolicus (O66529), Sulfurospirillum multivorans (O68250), Arabidopsis thaliana (O80575), Chlamydia trachomatis (O84737), Bacillus subtilis (P11998), Haemophilus influenzae (P45149), Actinobacillus pleuropneumoniae (P50856), Saccharomyces cerevisiae (P50861), Photobacterium phosphoreum (P51963), Pasteurella multocida (P57869), Brucella abortus (P61711), Synechocystis sp. (P73527), Photobacterium leiognathi (Q01994), Photobacterium leiognathi (Q93E92), Bacillus amyloliquefaciens (Q44681), Rhodococcus erythropolis (Q53107), Methanocaldococcus jannaschii (Q57751), Buchnera aphidicola (Q8K9A6), Buchnera aphidicola (Q9ZNM0), Chlorobaculum tepidum (Q8KAW4), Corynebacterium glutamicum (Q8NQ53), Xanthomonas campestris (Q8PCM7), Xanthomonas citri (Q8PPD6), Methanosarcina mazei (Q8Q093), Fusobacterium nucleatum (Q8RIR4), Methanosarcina acetivorans (Q8TPT7), Methanopyrus kandleri (Q8TYL5), Agrobacterium tumefaciens (Q8UG70), Clostridium perfringens (Q8XMW9), Ralstonia solanacearum (Q8Y1H8), Anabaena sp. (Q8YQ43), Yersinia pestis (Q8ZC41), Pyrobaculum aerophilum (Q8ZTE3), Sinorhizobium meliloti (Q92NI1), Sinorhizobium meliloti (Q92QU0), Sulfurisphaera tokodaii (Q975M5), Clostridium acetobutylicum (Q97LG8), Mesorhizobium loti (Q983B0), Mesorhizobium loti (Q986N2), Caulobacter vibrioides (Q9A8J4), Caulobacter vibrioides (Q9A9S4), Mycobacterium leprae (Q9CCP3), Lactococcus lactis subsp. lactis (Q9CGU6), Streptomyces coelicolor (Q9EWJ9), Halobacterium salinarum (Q9HRM5), Pseudomonas aeruginosa (Q9HWX5), Halalkalibacterium halodurans (Q9KCL4), Vibrio cholerae (Q9KPU4), Xylella fastidiosa (Q9PES4), Campylobacter jejuni (Q9PIB9), Chlamydia muridarum (Q9PLJ4), Bartonella henselae (Q9REF4), Deinococcus radiodurans (Q9RXZ8), Schizosaccharomyces pombe (Q9UUB1), Pyricularia grisea (Q9UVT8), Thermotoga maritima (Q9X2E5), Nicotiana tabacum (Q9XH13), Chlamydia pneumoniae (Q9Z733), Helicobacter pylori J99 (Q9ZN56), Agrobacterium tumefaciens C58 / ATCC 33970 (Q8UG70)
Ladenstein, R.; Fischer, M.; Bacher, A.
The lumazine synthase/riboflavin synthase complex: shapes and functions of a highly variable enzyme system
FEBS J.
280
2537-2563
2013
Aquifex aeolicus (O66529), Bacillus subtilis (P11998), Saccharomyces cerevisiae (P50861), Brucella abortus (Q2YKV1), Brucella abortus (Q2YNC6)
Min, J.; Kim, S.; Lee, J.; Kang, S.
Lumazine synthase protein cage nanoparticles as modular delivery platforms for targeted drug delivery
RSC Adv.
4
48596-48600
2014
Aquifex aeolicus
-
Song, Y.; Kang, Y.J.; Jung, H.; Kim, H.; Kang, S.; Cho, H.
Lumazine synthase protein nanoparticle-Gd(III)-DOTA conjugate as a T1 contrast agent for high-field MRI
Sci. Rep.
5
15656
2015
Aquifex aeolicus (O66529), Aquifex aeolicus
Azuma, Y.; Herger, M.; Hilvert, D.
Diversification of protein cage structure using circularly permuted subunits
J. Am. Chem. Soc.
140
558-561
2018
Aquifex aeolicus (O66529), Aquifex aeolicus
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