RIB4_SCHPO
ID RIB4_SCHPO Reviewed; 159 AA.
AC Q9UUB1;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=6,7-dimethyl-8-ribityllumazine synthase;
DE Short=DMRL synthase;
DE Short=LS;
DE Short=Lumazine synthase;
DE EC=2.5.1.78;
DE AltName: Full=Riboflavin synthase beta chain;
GN Name=rib4; ORFNames=SPBC409.13;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS,
RP ACTIVITY REGULATION, SUBUNIT, MASS SPECTROMETRY, PATHWAY, CRYSTALLIZATION,
RP AND MUTAGENESIS OF TRP-27.
RC STRAIN=ATCC 16491;
RX PubMed=11856310; DOI=10.1046/j.0014-2956.2001.02674.x;
RA Fischer M., Haase I., Feicht R., Richter G., Gerhardt S., Changeux J.P.,
RA Huber R., Bacher A.;
RT "Biosynthesis of riboflavin: 6,7-dimethyl-8-ribityllumazine synthase of
RT Schizosaccharomyces pombe.";
RL Eur. J. Biochem. 269:519-526(2002).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF WILD-TYPE AND MUTANTS GLY-27;
RP TYR-63 AND PHE-119 IN COMPLEXES WITH SUBSTRATE AND PRODUCT ANALOG
RP INHIBITORS; RIBOFLAVIN AND PHOSPHATE, AND SUBUNIT.
RC STRAIN=ATCC 16491;
RX PubMed=12083520; DOI=10.1016/s0022-2836(02)00116-x;
RA Gerhardt S., Haase I., Steinbacher S., Kaiser J.T., Cushman M., Bacher A.,
RA Huber R., Fischer M.;
RT "The structural basis of riboflavin binding to Schizosaccharomyces pombe
RT 6,7-dimethyl-8-ribityllumazine synthase.";
RL J. Mol. Biol. 318:1317-1329(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF MUTANT TYR-27 IN COMPLEXES WITH
RP SUBSTRATE AND PRODUCT ANALOG INHIBITORS; RIBOFLAVIN AND PHOSPHATE, AND
RP SUBUNIT.
RC STRAIN=ATCC 16491;
RX PubMed=15265040; DOI=10.1111/j.1432-1033.2004.04253.x;
RA Koch M., Breithaupt C., Gerhardt S., Haase I., Weber S., Cushman M.,
RA Huber R., Bacher A., Fischer M.;
RT "Structural basis of charge transfer complex formation by riboflavin bound
RT to 6,7-dimethyl-8-ribityllumazine synthase.";
RL Eur. J. Biochem. 271:3208-3214(2004).
CC -!- FUNCTION: Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by
CC condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-
CC butanone 4-phosphate. This is the penultimate step in the biosynthesis
CC of riboflavin. Also binds riboflavin with an unexpected high affinity.
CC {ECO:0000269|PubMed:11856310}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-
CC ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2
CC H2O + phosphate; Xref=Rhea:RHEA:26152, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15934, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58201, ChEBI:CHEBI:58830; EC=2.5.1.78;
CC Evidence={ECO:0000269|PubMed:11856310};
CC -!- ACTIVITY REGULATION: Competitively inhibited by riboflavin (Ki of 17
CC uM). {ECO:0000269|PubMed:11856310}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5 uM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius
CC and pH 7.0) {ECO:0000269|PubMed:11856310};
CC KM=67 uM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees
CC Celsius and pH 7.0) {ECO:0000269|PubMed:11856310};
CC Vmax=13000 nmol/h/mg enzyme (at 37 degrees Celsius and pH 7.0)
CC {ECO:0000269|PubMed:11856310};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; riboflavin
CC from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-
CC ribitylamino)uracil: step 1/2. {ECO:0000269|PubMed:11856310}.
CC -!- SUBUNIT: Homopentamer. {ECO:0000269|PubMed:11856310,
CC ECO:0000269|PubMed:12083520, ECO:0000269|PubMed:15265040}.
CC -!- MASS SPECTROMETRY: Mass=17189; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:11856310};
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; CU329671; CAB52615.1; -; Genomic_DNA.
DR PIR; T40440; T40440.
DR RefSeq; NP_595463.1; NM_001021373.2.
DR PDB; 1KYV; X-ray; 2.40 A; A/B/C/D/E=1-159.
DR PDB; 1KYX; X-ray; 2.60 A; A/B/C/D/E=1-159.
DR PDB; 1KYY; X-ray; 2.40 A; A/B/C/D/E=1-159.
DR PDB; 1KZ1; X-ray; 2.00 A; A/B/C/D/E=1-159.
DR PDB; 1KZ4; X-ray; 3.10 A; A/B/C/D/E=1-159.
DR PDB; 1KZ6; X-ray; 2.70 A; A/B/C/D/E=1-159.
DR PDB; 1KZ9; X-ray; 3.10 A; A/B/C/D/E=1-159.
DR PDB; 2A57; X-ray; 2.75 A; A/B/C/D/E=1-159.
DR PDB; 2A58; X-ray; 2.80 A; A/B/C/D/E=1-159.
DR PDB; 2A59; X-ray; 2.70 A; A/B/C/D/E=1-159.
DR PDBsum; 1KYV; -.
DR PDBsum; 1KYX; -.
DR PDBsum; 1KYY; -.
DR PDBsum; 1KZ1; -.
DR PDBsum; 1KZ4; -.
DR PDBsum; 1KZ6; -.
DR PDBsum; 1KZ9; -.
DR PDBsum; 2A57; -.
DR PDBsum; 2A58; -.
DR PDBsum; 2A59; -.
DR AlphaFoldDB; Q9UUB1; -.
DR SMR; Q9UUB1; -.
DR BioGRID; 277640; 4.
DR STRING; 4896.SPBC409.13.1; -.
DR MaxQB; Q9UUB1; -.
DR PaxDb; Q9UUB1; -.
DR EnsemblFungi; SPBC409.13.1; SPBC409.13.1:pep; SPBC409.13.
DR GeneID; 2541125; -.
DR KEGG; spo:SPBC409.13; -.
DR PomBase; SPBC409.13; rib4.
DR VEuPathDB; FungiDB:SPBC409.13; -.
DR eggNOG; KOG3243; Eukaryota.
DR HOGENOM; CLU_089358_2_0_1; -.
DR InParanoid; Q9UUB1; -.
DR OMA; CQGVTQG; -.
DR PhylomeDB; Q9UUB1; -.
DR BRENDA; 2.5.1.78; 5613.
DR SABIO-RK; Q9UUB1; -.
DR UniPathway; UPA00275; UER00404.
DR EvolutionaryTrace; Q9UUB1; -.
DR PRO; PR:Q9UUB1; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0005737; C:cytoplasm; HDA:PomBase.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
DR GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IDA:PomBase.
DR GO; GO:1902444; F:riboflavin binding; IDA:PomBase.
DR GO; GO:0009231; P:riboflavin biosynthetic process; EXP:PomBase.
DR CDD; cd09209; Lumazine_synthase-I; 1.
DR Gene3D; 3.40.50.960; -; 1.
DR HAMAP; MF_00178; Lumazine_synth; 1.
DR InterPro; IPR034964; LS.
DR InterPro; IPR002180; LS/RS.
DR InterPro; IPR036467; LS/RS_sf.
DR PANTHER; PTHR21058; PTHR21058; 1.
DR Pfam; PF00885; DMRL_synthase; 1.
DR SUPFAM; SSF52121; SSF52121; 1.
DR TIGRFAMs; TIGR00114; lumazine-synth; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Riboflavin biosynthesis; Transferase.
FT CHAIN 1..159
FT /note="6,7-dimethyl-8-ribityllumazine synthase"
FT /id="PRO_0000134856"
FT ACT_SITE 94
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 27
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 62..64
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 86..88
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 91..92
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT BINDING 119
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 133
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT MUTAGEN 27
FT /note="W->F,Y: Minor effects on the kinetic properties."
FT /evidence="ECO:0000269|PubMed:11856310"
FT MUTAGEN 27
FT /note="W->G,H,I,S: Reduced affinity for riboflavin and for
FT the substrate 5-amino-6-(D-ribitylamino)uracil."
FT /evidence="ECO:0000269|PubMed:11856310"
FT STRAND 20..24
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 29..47
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:1KZ1"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 65..75
FT /evidence="ECO:0007829|PDB:1KZ1"
FT STRAND 79..88
FT /evidence="ECO:0007829|PDB:1KZ1"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 94..113
FT /evidence="ECO:0007829|PDB:1KZ1"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 127..133
FT /evidence="ECO:0007829|PDB:1KZ1"
FT HELIX 142..156
FT /evidence="ECO:0007829|PDB:1KZ1"
SQ SEQUENCE 159 AA; 17188 MW; ADB5F20D5BA74601 CRC64;
MFSGIKGPNP SDLKGPELRI LIVHARWNLQ AIEPLVKGAV ETMIEKHDVK LENIDIESVP
GSWELPQGIR ASIARNTYDA VIGIGVLIKG STMHFEYISE AVVHGLMRVG LDSGVPVILG
LLTVLNEEQA LYRAGLNGGH NHGNDWGSAA VEMGLKALY
