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Conserved domains on  [gi|386271157|gb|AFJ02071|]
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6,7-dimethyl-8-ribityllumazine synthase [Methylophaga frappieri]

Protein Classification

6,7-dimethyl-8-ribityllumazine synthase( domain architecture ID 10000529)

6,7-dimethyl-8-ribityllumazine synthase catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone in riboflavin biosynthesis pathway

CATH:  3.40.50.960
EC:  2.5.1.78
Gene Ontology:  GO:0000906|GO:0009231|GO:0009349
PubMed:  11153262|16010344
SCOP:  4003586

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RibE COG0054
6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport ...
 6-157 4.61e-91

6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport and metabolism]; 6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


:

Pssm-ID: 439824  Cd Length: 152  Bit Score: 261.17  E-value: 4.61e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   6 TFSGDFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVI 85
Cdd:COG0054    1 TIEGDLPASGLRIAIVVARFNEDITDKLLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGRYDAVIALGCVI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386271157  86 RGGTPHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVLRQIG 157
Cdd:COG0054   81 RGETPHFDYVANEVTKGLMQVSLDTGVPVGFGVLTTDTIEQAIERAGGKAGNKGAEAALAALEMANLLRQLR 152
 
Name Accession Description Interval E-value
RibE COG0054
6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport ...
 6-157 4.61e-91

6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport and metabolism]; 6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 439824  Cd Length: 152  Bit Score: 261.17  E-value: 4.61e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   6 TFSGDFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVI 85
Cdd:COG0054    1 TIEGDLPASGLRIAIVVARFNEDITDKLLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGRYDAVIALGCVI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386271157  86 RGGTPHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVLRQIG 157
Cdd:COG0054   81 RGETPHFDYVANEVTKGLMQVSLDTGVPVGFGVLTTDTIEQAIERAGGKAGNKGAEAALAALEMANLLRQLR 152
ribH PRK00061
6,7-dimethyl-8-ribityllumazine synthase; Provisional
 4-157 2.23e-81

6,7-dimethyl-8-ribityllumazine synthase; Provisional


Pssm-ID: 234606  Cd Length: 154  Bit Score: 236.95  E-value: 2.23e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   4 INTFSGDFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGA 83
Cdd:PRK00061   1 MNIIEGNLVAKGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 386271157  84 VIRGGTPHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVLRQIG 157
Cdd:PRK00061  81 VIRGETPHFDYVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAIERAGTKAGNKGAEAALAALEMANLLKQLK 154
DMRL_synthase pfam00885
6,7-dimethyl-8-ribityllumazine synthase; This family includes the beta chain of 6, ...
 15-149 2.61e-76

6,7-dimethyl-8-ribityllumazine synthase; 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 Swiss: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. It has been established that lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganizms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric. 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.


Pssm-ID: 459980  Cd Length: 134  Bit Score: 223.44  E-value: 2.61e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   15 GMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEkDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDY 94
Cdd:pfam00885   1 GLRIGIVVARFNEDITDRLLEGALDALKRHGVAE-NIDVVRVPGAFELPLAAKKLAESGKYDAVIALGAVIRGETPHFDY 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 386271157   95 VAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEM 149
Cdd:pfam00885  80 VANEVAKGLMDVSLDTGVPVIFGVLTTDTEEQALERAGGKAGNKGREAAEAALEM 134
Lumazine_synthase-I cd09209
lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate ...
 18-150 6.76e-76

lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Type-I LS, also known as RibH1, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyse the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates to yield riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-I LSs form pentamers. The pathogen Brucella spp. encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be the functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS.


Pssm-ID: 187742  Cd Length: 133  Bit Score: 222.32  E-value: 6.76e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  18 VGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVAG 97
Cdd:cd09209    1 IAIVVSRFNEEITDALLEGALDALKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDAIIALGCVIRGETPHFDYVCN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 386271157  98 ECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMV 150
Cdd:cd09209   81 EVTRGLMRLSLETGVPVIFGVLTTDNEEQALERAGGKAGNKGAEAALAALEMA 133
lumazine-synth TIGR00114
6,7-dimethyl-8-ribityllumazine synthase; This enzyme catalyzes the cyclo-ligation of 3, ...
 17-153 2.12e-61

6,7-dimethyl-8-ribityllumazine synthase; This enzyme catalyzes the cyclo-ligation of 3,4-dihydroxy-2-butanone-4-P and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 6,7-dimethyl-8-ribityllumazine, the immediate precursor of riboflavin. Sometimes referred to as riboflavin synthase, beta subunit, this should not be confused with the alpha subunit which carries out the subsequent reaction. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD]


Pssm-ID: 211550  Cd Length: 138  Bit Score: 186.03  E-value: 2.12e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   17 RVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVA 96
Cdd:TIGR00114   2 RVGIVIARFNRFITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAESGKYDAVIALGTVIRGGTPHFEYVA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 386271157   97 GECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVL 153
Cdd:TIGR00114  82 DEAAKGIADLALDYGKPVIFGILTTETIEQAIERAGTKAGNKGVEAAVKALEMANLL 138
 
Name Accession Description Interval E-value
RibE COG0054
6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport ...
 6-157 4.61e-91

6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport and metabolism]; 6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 439824  Cd Length: 152  Bit Score: 261.17  E-value: 4.61e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   6 TFSGDFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVI 85
Cdd:COG0054    1 TIEGDLPASGLRIAIVVARFNEDITDKLLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGRYDAVIALGCVI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386271157  86 RGGTPHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVLRQIG 157
Cdd:COG0054   81 RGETPHFDYVANEVTKGLMQVSLDTGVPVGFGVLTTDTIEQAIERAGGKAGNKGAEAALAALEMANLLRQLR 152
ribH PRK00061
6,7-dimethyl-8-ribityllumazine synthase; Provisional
 4-157 2.23e-81

6,7-dimethyl-8-ribityllumazine synthase; Provisional


Pssm-ID: 234606  Cd Length: 154  Bit Score: 236.95  E-value: 2.23e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   4 INTFSGDFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGA 83
Cdd:PRK00061   1 MNIIEGNLVAKGLRIGIVVARFNDFITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIALGA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 386271157  84 VIRGGTPHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVLRQIG 157
Cdd:PRK00061  81 VIRGETPHFDYVANEVAKGLADVSLETGVPVGFGVLTTDTIEQAIERAGTKAGNKGAEAALAALEMANLLKQLK 154
DMRL_synthase pfam00885
6,7-dimethyl-8-ribityllumazine synthase; This family includes the beta chain of 6, ...
 15-149 2.61e-76

6,7-dimethyl-8-ribityllumazine synthase; 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 Swiss: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. It has been established that lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganizms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric. 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.


Pssm-ID: 459980  Cd Length: 134  Bit Score: 223.44  E-value: 2.61e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   15 GMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEkDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDY 94
Cdd:pfam00885   1 GLRIGIVVARFNEDITDRLLEGALDALKRHGVAE-NIDVVRVPGAFELPLAAKKLAESGKYDAVIALGAVIRGETPHFDY 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 386271157   95 VAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEM 149
Cdd:pfam00885  80 VANEVAKGLMDVSLDTGVPVIFGVLTTDTEEQALERAGGKAGNKGREAAEAALEM 134
Lumazine_synthase-I cd09209
lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate ...
 18-150 6.76e-76

lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Type-I LS, also known as RibH1, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyse the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates to yield riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-I LSs form pentamers. The pathogen Brucella spp. encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be the functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS.


Pssm-ID: 187742  Cd Length: 133  Bit Score: 222.32  E-value: 6.76e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  18 VGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVAG 97
Cdd:cd09209    1 IAIVVSRFNEEITDALLEGALDALKRHGVKEENIDVVRVPGAFEIPLAAKRLARSGKYDAIIALGCVIRGETPHFDYVCN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 386271157  98 ECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMV 150
Cdd:cd09209   81 EVTRGLMRLSLETGVPVIFGVLTTDNEEQALERAGGKAGNKGAEAALAALEMA 133
lumazine-synth TIGR00114
6,7-dimethyl-8-ribityllumazine synthase; This enzyme catalyzes the cyclo-ligation of 3, ...
 17-153 2.12e-61

6,7-dimethyl-8-ribityllumazine synthase; This enzyme catalyzes the cyclo-ligation of 3,4-dihydroxy-2-butanone-4-P and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 6,7-dimethyl-8-ribityllumazine, the immediate precursor of riboflavin. Sometimes referred to as riboflavin synthase, beta subunit, this should not be confused with the alpha subunit which carries out the subsequent reaction. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD]


Pssm-ID: 211550  Cd Length: 138  Bit Score: 186.03  E-value: 2.12e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157   17 RVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVA 96
Cdd:TIGR00114   2 RVGIVIARFNRFITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAESGKYDAVIALGTVIRGGTPHFEYVA 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 386271157   97 GECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEMVNVL 153
Cdd:TIGR00114  82 DEAAKGIADLALDYGKPVIFGILTTETIEQAIERAGTKAGNKGVEAAVKALEMANLL 138
PLN02404 PLN02404
6,7-dimethyl-8-ribityllumazine synthase
 10-149 5.16e-51

6,7-dimethyl-8-ribityllumazine synthase


Pssm-ID: 178026  Cd Length: 141  Bit Score: 159.52  E-value: 5.16e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  10 DFSAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGT 89
Cdd:PLN02404   2 LLDGEGLRFGVVVARFNEIITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILCIGAVIRGDT 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  90 PHFDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIEQAIERSGTKAGNKGAEAAMGTIEM 149
Cdd:PLN02404  82 THYDAVANSAASGVLSAGLNSGVPCIFGVLTCDDMEQALNRAGGKAGNKGAEAALTAVEM 141
Lumazine_synthase-like cd08371
lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) ...
 18-148 5.56e-35

lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway; This superfamily contains lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) and riboflavin synthase (RS). Both enzymes play important roles in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. In the final steps of the riboflavin biosynthetic pathway, LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and RS catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. In bacteria and eukaryotes, there are two types of LS: type-I LS forms homo-pentamers or icosahedrally arranged dodecamers of pentamers, type-II LS forms decamers (dimers of pentamers). In archaea LSs and RSs appear to have diverged early in the evolution of archaea from a common ancestor.


Pssm-ID: 187740  Cd Length: 129  Bit Score: 118.67  E-value: 5.56e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  18 VGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKdIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVAG 97
Cdd:cd08371    1 VGIVDARFNRDIVDALVKGAIAELAELGGNIK-IIVVTVPGAYEIPLAAKKLLEKEDYDAVVAIGVVIKGETYHFEIVAH 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 386271157  98 ECSKGLGQLNLELDMPVSFGVLTVDSI-EQAIERSGTkaGNKGAEAAMGTIE 148
Cdd:cd08371   80 EVSRGLMNLQLETDKPVIFGVLTPDNAeEQADERAKR--GNKGEEAARAAVE 129
PRK12419 PRK12419
6,7-dimethyl-8-ribityllumazine synthase;
12-159 2.19e-18

6,7-dimethyl-8-ribityllumazine synthase;


Pssm-ID: 237096  Cd Length: 158  Bit Score: 76.99  E-value: 2.19e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  12 SAKGMRVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPH 91
Cdd:PRK12419   7 FATPQRIAFIQARWHADIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVAAALVVDGGIYR 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386271157  92 FDYVAGECSKGLGQLNLELDMPVSFGVLTVDSIE-----QAIERSGTKAgnKGAEAAMGTIEMVNVLRQIGAA 159
Cdd:PRK12419  87 HEFVAQAVIDGLMRVQLDTEVPVFSVVLTPHHFHeseehHDFFRAHFVV--KGAEAAHACADTLLSRERLRAQ 157
Lumazine_synthase_archaeal cd09211
lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes the penultimate ...
 18-153 1.51e-16

lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); Archaeal LS is an important enzyme in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. In the final steps of the riboflavin biosynthetic pathway LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and riboflavin synthase (RS) catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. LS from Methanococcus jannaschii forms capsids with icosahedral 532 symmetry consisting of 60 subunits. Archaeal LSs share sequence similarity with archaeal RSs, both appear to have diverged early in the evolution of archaea from a common ancestor.


Pssm-ID: 187744  Cd Length: 131  Bit Score: 71.20  E-value: 1.51e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  18 VGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKdiEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVAG 97
Cdd:cd09211    1 LGIVVAEFNYDITYMMEEKALEHAKFLGAEVK--YVLRVPGVFDMPLAVKKLLEKDDIDAVVTLGAVIKGETKHDELIAN 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 386271157  98 ECSKGLGQLNLELDMPVSFGVLTVD-SIEQAIERSGtKAGNKGAEAAmgtIEMVNVL 153
Cdd:cd09211   79 QAARKILDLSLEYGKPVTLGISGPGmSRLQALERIE-YYAKRAVEAA---VKMVKRL 131
Lumazine_synthase-II cd09208
lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate ...
 17-120 4.04e-16

lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-II; Type-II LS also known as RibH2, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyses the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates yielding riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-II LSs form decamers (dimers of pentamers). The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS and may be regulated by a riboswitch that senses FMN, suggesting that the type-II LSs may have evolved into very poor catalysts or, that they may harbor a new, as-yet-unknown function.


Pssm-ID: 187741  Cd Length: 137  Bit Score: 70.52  E-value: 4.04e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  17 RVGIVAGRFNEFVVSSLIDGAVDTLLRHGASEKDIEIARVPGAVEIPLAVKRMGQTKKYDAIIALGAVIRGGTPHFDYVA 96
Cdd:cd09208    2 RIAFIQARWHADIVDQARKGFEAEMAAKGGASDEVDIFDVPGAFEIPLHAKRLARTGRYAAIVGAALVVDGGIYRHEFVA 81

                         90       100
                 ....*....|....*....|....
gi 386271157  97 GECSKGLGQLNLELDMPVSFGVLT 120
Cdd:cd09208   82 QAVIDGLMRVQLETEVPVFSVVLT 105
PRK06455 PRK06455
riboflavin synthase; Provisional
 15-109 6.16e-05

riboflavin synthase; Provisional


Pssm-ID: 235804  Cd Length: 155  Bit Score: 40.70  E-value: 6.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  15 GMRVGIVAGRFNEFVVSSLidgAVDTLLRHGAsekDIEIAR--VPGAVEIPLAVKRMGQTKKYDAIIALGAVirGGTPHF 92
Cdd:PRK06455   1 MMKIGIADTTFARVDMGSA---AIDELRKLDP---SAKIIRytVPGIKDLPVAAKKLIEEEGCDIVMALGMP--GPTEKD 72

                         90
                 ....*....|....*..
gi 386271157  93 DYVAGECSKGLGQLNLE 109
Cdd:PRK06455  73 KYCAHEASIGLIMAQLM 89
Riboflavin_synthase_archaeal cd09210
archaeal riboflavin synthase (RS); involved in the biosynthesis pathway of riboflavin (vitamin ...
 18-110 1.64e-03

archaeal riboflavin synthase (RS); involved in the biosynthesis pathway of riboflavin (vitamin B2); Archaeal RSs are homopentamers catalyzing the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine in riboflavin biosynthesis. Divalent metal ions, preferably manganese or magnesium, are needed for maximum activity. Riboflavin serves as the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), essential cofactors for several oxidoreductases that are indispensable in most living cells. In the final steps of the riboflavin biosynthetic pathway, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), followed by RS which catalyzes a dismutation of DMRL yielding riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. Archaeal RSs share sequence similarity with LSs, both appear to have diverged early in the evolution of archaea from a common ancestor.


Pssm-ID: 187743  Cd Length: 143  Bit Score: 36.60  E-value: 1.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271157  18 VGIVAGRFNEFVVSSLidgAVDTLLRHGAsekDIEIAR--VPGAVEIPLAVKRMGQTKKYDAIIALGAVirGGTPHFDYV 95
Cdd:cd09210    1 IGIVDTTFARVDMGSV---AIDELKKLLP---GIKIVRytVPGIKDLPVAAKKLIEEEGCDIVMALGWV--GPTEKDKVS 72

                         90
                 ....*....|....*
gi 386271157  96 AGECSKGLGQLNLEL 110
Cdd:cd09210   73 YHEASLGLILVQLMT 87
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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