RIB4_YEAST
ID RIB4_YEAST Reviewed; 169 AA.
AC P50861; D6W1S6; Q08286;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 179.
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;
GN Name=RIB4; OrderedLocusNames=YOL143C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION, FUNCTION, ROLE IN
RP RIBOFLAVIN BIOSYNTHESIS, SUBUNIT, INDUCTION, AND PATHWAY.
RX PubMed=7559556; DOI=10.1074/jbc.270.40.23801;
RA Garcia-Ramirez J.J., Santos M.A., Revuelta J.L.;
RT "The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-
RT ribityllumazine synthase involved in riboflavin biosynthesis. Molecular
RT characterization of the gene and purification of the encoded protein.";
RL J. Biol. Chem. 270:23801-23807(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBUNIT, AND PATHWAY.
RX PubMed=8969176; DOI=10.1074/jbc.271.52.33201;
RA Moertl S., Fischer M., Richter G., Tack J., Weinkauf S., Bacher A.;
RT "Biosynthesis of riboflavin. Lumazine synthase of Escherichia coli.";
RL J. Biol. Chem. 271:33201-33207(1996).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=22984289; DOI=10.1074/mcp.m112.021105;
RA Voegtle F.N., Burkhart J.M., Rao S., Gerbeth C., Hinrichs J.,
RA Martinou J.C., Chacinska A., Sickmann A., Zahedi R.P., Meisinger C.;
RT "Intermembrane space proteome of yeast mitochondria.";
RL Mol. Cell. Proteomics 11:1840-1852(2012).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH A REACTION
RP INTERMEDIATE ANALOG, SUBUNIT, AND REACTION MECHANISM.
RX PubMed=10860731; DOI=10.1006/jmbi.2000.3742;
RA Meining W., Moertl S., Fischer M., Cushman M., Bacher A., Ladenstein R.;
RT "The atomic structure of pentameric lumazine synthase from Saccharomyces
RT cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate
RT intermediate analogue.";
RL J. Mol. Biol. 299:181-197(2000).
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. {ECO:0000269|PubMed:7559556,
CC ECO:0000269|PubMed:8969176}.
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:8969176};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.0 uM for 5-amino-6-(D-ribitylamino)uracil
CC {ECO:0000269|PubMed:8969176};
CC KM=90 uM for 3,4-dihydroxy-2-butanone 4-phosphate
CC {ECO:0000269|PubMed:8969176};
CC Vmax=15400 nmol/h/mg enzyme {ECO:0000269|PubMed:8969176};
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:7559556,
CC ECO:0000269|PubMed:8969176}.
CC -!- SUBUNIT: Homopentamer. {ECO:0000269|PubMed:10860731,
CC ECO:0000269|PubMed:7559556, ECO:0000269|PubMed:8969176}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion intermembrane space
CC {ECO:0000269|PubMed:22984289}.
CC -!- INDUCTION: Is constitutively expressed at moderate levels.
CC {ECO:0000269|PubMed:7559556}.
CC -!- MISCELLANEOUS: Present with 3260 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; Z21620; CAA79744.1; -; Genomic_DNA.
DR EMBL; Z74885; CAA99164.1; -; Genomic_DNA.
DR EMBL; AY558430; AAS56756.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10642.1; -; Genomic_DNA.
DR PIR; S61871; S61871.
DR RefSeq; NP_014498.1; NM_001183397.1.
DR PDB; 1EJB; X-ray; 1.85 A; A/B/C/D/E=2-169.
DR PDBsum; 1EJB; -.
DR AlphaFoldDB; P50861; -.
DR SMR; P50861; -.
DR BioGRID; 34274; 30.
DR DIP; DIP-1931N; -.
DR IntAct; P50861; 9.
DR MINT; P50861; -.
DR STRING; 4932.YOL143C; -.
DR MaxQB; P50861; -.
DR PaxDb; P50861; -.
DR PRIDE; P50861; -.
DR TopDownProteomics; P50861; -.
DR EnsemblFungi; YOL143C_mRNA; YOL143C; YOL143C.
DR GeneID; 854022; -.
DR KEGG; sce:YOL143C; -.
DR SGD; S000005503; RIB4.
DR VEuPathDB; FungiDB:YOL143C; -.
DR eggNOG; KOG3243; Eukaryota.
DR HOGENOM; CLU_089358_2_2_1; -.
DR InParanoid; P50861; -.
DR OMA; CQGVTQG; -.
DR BioCyc; MetaCyc:YOL143C-MON; -.
DR BioCyc; YEAST:YOL143C-MON; -.
DR BRENDA; 2.5.1.78; 984.
DR SABIO-RK; P50861; -.
DR UniPathway; UPA00275; UER00404.
DR EvolutionaryTrace; P50861; -.
DR PRO; PR:P50861; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; P50861; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
DR GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IDA:SGD.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:SGD.
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; Mitochondrion; Reference proteome; Riboflavin biosynthesis;
KW Transferase.
FT CHAIN 1..169
FT /note="6,7-dimethyl-8-ribityllumazine synthase"
FT /id="PRO_0000134857"
FT ACT_SITE 98
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 61..63
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 90..92
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 95..96
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT BINDING 123
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 137
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT CONFLICT 44
FT /note="A -> V (in Ref. 1; CAA79744)"
FT /evidence="ECO:0000305"
FT CONFLICT 51
FT /note="N -> K (in Ref. 1; CAA79744)"
FT /evidence="ECO:0000305"
FT STRAND 20..24
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 29..45
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1EJB"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 64..77
FT /evidence="ECO:0007829|PDB:1EJB"
FT STRAND 83..92
FT /evidence="ECO:0007829|PDB:1EJB"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 98..117
FT /evidence="ECO:0007829|PDB:1EJB"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 131..137
FT /evidence="ECO:0007829|PDB:1EJB"
FT HELIX 149..164
FT /evidence="ECO:0007829|PDB:1EJB"
SQ SEQUENCE 169 AA; 18556 MW; 574E847FA6F2860E CRC64;
MAVKGLGKPD QVYDGSKIRV GIIHARWNRV IIDALVKGAI ERMASLGVEE NNIIIETVPG
SYELPWGTKR FVDRQAKLGK PLDVVIPIGV LIKGSTMHFE YISDSTTHAL MNLQEKVDMP
VIFGLLTCMT EEQALARAGI DEAHSMHNHG EDWGAAAVEM AVKFGKNAF
