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1080  structures 7218  species 1  interaction 8184  sequences 32  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

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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. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].

Literature references

  1. Zylberman V, Klinke S, Haase I, Bacher A, Fischer M, Goldbaum FA;, J Bacteriol. 2006;188:6135-6142.: Evolution of vitamin B2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of Brucella. PUBMED:16923880 EPMC:16923880

  2. Klinke S, Zylberman V, Bonomi HR, Haase I, Guimaraes BG, Braden BC, Bacher A, Fischer M, Goldbaum FA;, J Mol Biol. 2007;373:664-680.: Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. PUBMED:17854827 EPMC:17854827

  3. Bonomi HR, Marchesini MI, Klinke S, Ugalde JE, Zylberman V, Ugalde RA, Comerci DJ, Goldbaum FA;, PLoS One. 2010;5:e9435.: An atypical riboflavin pathway is essential for Brucella abortus virulence. PUBMED:20195542 EPMC:20195542


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002180

6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase, LS), catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate, the penultimate step in the biosynthesis of riboflavin.

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 (RS). 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 both lumazine synthase and riboflavin synthase. Both share sequence similarity, they appear to have diverged early in the evolution of archaea from a common ancestor.

Gene Ontology

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Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(710)
Full
(8184)
Representative proteomes UniProt
(22449)
NCBI
(21474)
Meta
(2158)
RP15
(1915)
RP35
(5040)
RP55
(7696)
RP75
(10821)
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PP/heatmap 1                

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  Seed
(710)
Full
(8184)
Representative proteomes UniProt
(22449)
NCBI
(21474)
Meta
(2158)
RP15
(1915)
RP35
(5040)
RP55
(7696)
RP75
(10821)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(710)
Full
(8184)
Representative proteomes UniProt
(22449)
NCBI
(21474)
Meta
(2158)
RP15
(1915)
RP35
(5040)
RP55
(7696)
RP75
(10821)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1503 (release 3.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 710
Number in full: 8184
Average length of the domain: 140.10 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 84.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 27.8 27.4
Noise cut-off 26.5 26.6
Model length: 141
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Interactions

There is 1 interaction for this family. More...

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 1080 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 sequence.

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