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450  structures 3970  species 1  interaction 4443  sequences 14  architectures

Family: DMRL_synthase (PF00885)

Summary: 6,7-dimethyl-8-ribityllumazine synthase

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This is the Wikipedia entry entitled "Riboflavin synthase". More...

Riboflavin synthase Edit Wikipedia article

Riboflavin synthase
Crystal structure.jpg
Crystallographic structure of E. coli
riboflavin synthase.[1]
Identifiers
EC number 2.5.1.9
CAS number 9075-82-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
6,7-dimethyl-8-ribityllumazine synthase
Monomer With Ligands.jpg
Riboflavin synthase from S. pombe bound to carboxyethyllumazine.[2]
Identifiers
Symbol DMRL_synthase
Pfam PF00885
InterPro IPR002180
SCOP 1rvv
SUPERFAMILY 1rvv

Riboflavin synthase is an enzyme that catalyzes the final reaction of riboflavin biosynthesis:

(2) 6,7-dimethyl-8-ribityllumazineriboflavin + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione

Structure[edit]

The Riboflavin synthase monomer is 23kDa. Each monomer contains two beta-barrels and one α-helix at the C-terminus (residues 186-206.) The monomer folds into pseudo two-fold symmetry, predicted by sequence similarity between the N-terminus barrels (residues 4-86) and the C-terminus barrel (residues 101-184).[1] The enzyme from different species adopts different quaternary structures, from monomeric to 60 subunits[3]

Active site[edit]

Two 6,7-dimethyl-8-ribityllumazine (Lumazine synthase) molecules are hydrogen bound to each monomer as the two domains are topologically similar.[4] The active site is located in the interface of the substrates between monomer pairs and modeled structures of the active site dimer have been created.[2] 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.[5]

Mechanism[edit]

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.[6]

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.[6] 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.[7] 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.[1] 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.[7]

Mech 1.jpg Mech 2.jpg Mech 3.jpg Mech 4.jpg

Drug Production[edit]

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.[5][8] 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.[8]

See also[edit]

References[edit]

  1. ^ a b c d PDB 1i8d; Liao DI, Wawrzak Z, Calabrese JC, Viitanen PV, Jordan DB (May 2001). "Crystal structure of riboflavin synthase". Structure 9 (5): 399–408. doi:10.1016/S0969-2126(01)00600-1. PMID 11377200. 
  2. ^ a b c d PDB 1kzl; Gerhardt S, Schott AK, Kairies N, Cushman M, Illarionov B, Eisenreich W, Bacher A, Huber R, Steinbacher S, Fischer M (October 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 (10): 1371–81. doi:10.1016/S0969-2126(02)00864-X. PMID 12377123. 
  3. ^ http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/enzyme/?ec=2.5.1.9&tab=assemblies
  4. ^ Fischer M, Schott AK, Kemter K, Feicht R, Richter G, Illarionov B, Eisenreich W, Gerhardt S, Cushman M, Steinbacher S, Huber R, Bacher A (December 2003). "Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiments". BMC Biochem. 4: 18. doi:10.1186/1471-2091-4-18. PMC 337094. PMID 14690539. 
  5. ^ a b Fischer M, Bacher A (June 2008). "Biosynthesis of vitamin B2: Structure and mechanism of riboflavin synthase". Arch. Biochem. Biophys. 474 (2): 252–65. doi:10.1016/j.abb.2008.02.008. PMID 18298940. 
  6. ^ a b Bacher A, Eberhardt S, Fischer M, Kis K, Richter G (2000). "Biosynthesis of vitamin b2 (riboflavin)". Annu. Rev. Nutr. 20: 153–67. doi:10.1146/annurev.nutr.20.1.153. PMID 10940330. 
  7. ^ a b Zheng YJ, Jordan DB, Liao DI (August 2003). "Examination of a reaction intermediate in the active site of riboflavin synthase". Bioorg. Chem. 31 (4): 278–87. doi:10.1016/S0045-2068(03)00029-4. PMID 12877878. 
  8. ^ a b Cushman M, Yang D, Kis K, Bacher A (December 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): 8320–7. doi:10.1021/jo010706r. PMID 11735509. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

6,7-dimethyl-8-ribityllumazine synthase Provide feedback

This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002180

6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.

The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase [PUBMED:18298940]. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase [PUBMED:18331058].

This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example SWISSPROT.

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Seed source: Pfam-B_1503 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 104
Number in full: 4443
Average length of the domain: 140.60 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 89.31 %

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Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 21.7 21.2
Noise cut-off 20.3 19.2
Model length: 144
Family (HMM) version: 14
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DMRL_synthase

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DMRL_synthase domain has been found. There are 450 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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