RISB_AQUAE
ID RISB_AQUAE Reviewed; 154 AA.
AC O66529;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 132.
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=ribH; OrderedLocusNames=aq_132;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND KINETIC PARAMETERS.
RC STRAIN=VF5;
RX PubMed=12603336; DOI=10.1046/j.1432-1033.2003.03478.x;
RA Haase I., Mortl S., Kohler P., Bacher A., Fischer M.;
RT "Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine
RT synthase of Methanococcus jannaschii.";
RL Eur. J. Biochem. 270:1025-1032(2003).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF APOENZYME, FUNCTION, CATALYTIC
RP ACTIVITY, TEMPERATURE DEPENDENCE, AND SUBUNIT.
RC STRAIN=VF5;
RX PubMed=11237620; DOI=10.1006/jmbi.2000.4435;
RA Zhang X., Meining W., Fischer M., Bacher A., Ladenstein R.;
RT "X-ray structure analysis and crystallographic refinement of lumazine
RT synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution:
RT determinants of thermostability revealed from structural comparisons.";
RL J. Mol. Biol. 306:1099-1114(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOG
RP OR REACTION INTERMEDIATE ANALOG INHIBITORS AND PHOSPHATE, PATHWAY, ACTIVE
RP SITE, AND REACTION MECHANISM.
RC STRAIN=VF5;
RX PubMed=12684006; DOI=10.1016/s0022-2836(03)00186-4;
RA Zhang X., Meining W., Cushman M., Haase I., Fischer M., Bacher A.,
RA Ladenstein R.;
RT "A structure-based model of the reaction catalyzed by lumazine synthase
RT from Aquifex aeolicus.";
RL J. Mol. Biol. 328:167-182(2003).
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:11237620,
CC ECO:0000269|PubMed:12603336}.
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:11237620, ECO:0000269|PubMed:12603336};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=10.0 uM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees
CC Celsius and pH 7.0) {ECO:0000269|PubMed:12603336};
CC KM=26 uM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees
CC Celsius and pH 7.0) {ECO:0000269|PubMed:12603336};
CC Vmax=31 nmol/min/mg enzyme (at 37 degrees Celsius and pH 7.0)
CC {ECO:0000269|PubMed:12603336};
CC Vmax=425 nmol/min/mg enzyme (at 70 degrees Celsius and pH 7.0)
CC {ECO:0000269|PubMed:12603336};
CC Temperature dependence:
CC Extremely thermostable. Has a melting temperature of 119.9 degrees
CC Celsius. {ECO:0000269|PubMed:11237620};
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:12684006}.
CC -!- SUBUNIT: Forms an icosahedral capsid composed of 60 subunits, arranged
CC as a dodecamer of pentamers. {ECO:0000269|PubMed:11237620}.
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; AE000657; AAC06489.1; -; Genomic_DNA.
DR PIR; F70312; F70312.
DR RefSeq; NP_213089.1; NC_000918.1.
DR RefSeq; WP_010880027.1; NC_000918.1.
DR PDB; 1HQK; X-ray; 1.60 A; A/B/C/D/E=1-154.
DR PDB; 1NQU; X-ray; 1.75 A; A/B/C/D/E=1-154.
DR PDB; 1NQV; X-ray; 2.05 A; A/B/C/D/E=1-154.
DR PDB; 1NQW; X-ray; 2.20 A; A/B/C/D/E=1-154.
DR PDB; 1NQX; X-ray; 1.82 A; A/B/C/D/E=1-154.
DR PDB; 5MPP; EM; 3.94 A; 0/1/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T=1-154.
DR PDB; 5MQ3; EM; 5.40 A; AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/BO=1-154.
DR PDB; 5MQ7; EM; 5.20 A; 0A/0B/0C/0D/0E/0X/1A/1B/1C/1D/1E/1X/2A/2B/2C/2D/2E/2X/3A/3B/3C/3D/3E/3X/4A/4B/4C/4D/4E/4X=1-154.
DR PDB; 7A4F; EM; 3.50 A; AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/CA/CB/CC/CD/CE/CF/CG/CH/CI/CJ=1-84.
DR PDB; 7A4G; EM; 4.20 A; AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/BO=1-84.
DR PDB; 7A4H; EM; 4.50 A; AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/BO=1-84.
DR PDB; 7A4I; EM; 7.04 A; 0A/0B/0C/0D/1A/1B/1C/1D/2A/2B/2C/2D/3A/3B/3C/3D/4A/4B/4C/4D/5A/5B/5C/5D/6A/6B/6C/6D/7A/7B=1-84.
DR PDB; 7A4J; EM; 3.04 A; 0A/0B/0C/0D/1A/1B/1C/1D/2A/2B/2C/2D/3A/3B/3C/3D/4A/4B/4C/4D/5A/5B/5C/5D/6A/6B/6C/6D/7A/7B=1-84.
DR PDBsum; 1HQK; -.
DR PDBsum; 1NQU; -.
DR PDBsum; 1NQV; -.
DR PDBsum; 1NQW; -.
DR PDBsum; 1NQX; -.
DR PDBsum; 5MPP; -.
DR PDBsum; 5MQ3; -.
DR PDBsum; 5MQ7; -.
DR PDBsum; 7A4F; -.
DR PDBsum; 7A4G; -.
DR PDBsum; 7A4H; -.
DR PDBsum; 7A4I; -.
DR PDBsum; 7A4J; -.
DR AlphaFoldDB; O66529; -.
DR SMR; O66529; -.
DR STRING; 224324.aq_132; -.
DR DrugBank; DB04262; 3-(7-hydroxy-8-ribityllumazine-6-yl) propionic acid.
DR DrugBank; DB04128; 5-Nitroso-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione.
DR DrugBank; DB02214; 6,7-dioxo-5H-8-ribitylaminolumazine.
DR EnsemblBacteria; AAC06489; AAC06489; aq_132.
DR KEGG; aae:aq_132; -.
DR PATRIC; fig|224324.8.peg.111; -.
DR eggNOG; COG0054; Bacteria.
DR HOGENOM; CLU_089358_1_1_0; -.
DR InParanoid; O66529; -.
DR OMA; CQGVTQG; -.
DR OrthoDB; 1680292at2; -.
DR BRENDA; 2.5.1.78; 396.
DR SABIO-RK; O66529; -.
DR UniPathway; UPA00275; UER00404.
DR EvolutionaryTrace; O66529; -.
DR Proteomes; UP000000798; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
DR GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IBA:GO_Central.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
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; Reference proteome; Riboflavin biosynthesis; Transferase.
FT CHAIN 1..154
FT /note="6,7-dimethyl-8-ribityllumazine synthase"
FT /id="PRO_0000134708"
FT ACT_SITE 88
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 22..23
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 56..58
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 80..82
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 85..86
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT BINDING 113
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 127
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT BINDING 135
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:1HQK"
FT STRAND 15..20
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 24..40
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1HQK"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:1HQK"
FT STRAND 74..82
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 88..107
FT /evidence="ECO:0007829|PDB:1HQK"
FT STRAND 111..120
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 121..127
FT /evidence="ECO:0007829|PDB:1HQK"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:1HQK"
FT HELIX 135..153
FT /evidence="ECO:0007829|PDB:1HQK"
SQ SEQUENCE 154 AA; 16705 MW; A189410A16454AB7 CRC64;
MQIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP
VAAGELARKE DIDAVIAIGV LIRGATPHFD YIASEVSKGL ANLSLELRKP ITFGVITADT
LEQAIERAGT KHGNKGWEAA LSAIEMANLF KSLR
