RISB2_RHILO
ID RISB2_RHILO Reviewed; 157 AA.
AC Q986N2;
DT 23-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=6,7-dimethyl-8-ribityllumazine synthase 2;
DE Short=DMRL synthase 2;
DE Short=LS 2;
DE Short=Lumazine synthase 2;
DE EC=2.5.1.78;
DE AltName: Full=Type II lumazine synthase;
GN Name=ribH2; OrderedLocusNames=mll7281;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [2]
RP GENE NAME.
RX PubMed=16923880; DOI=10.1128/jb.00207-06;
RA Zylberman V., Klinke S., Haase I., Bacher A., Fischer M., Goldbaum F.A.;
RT "Evolution of vitamin B2 biosynthesis: 6,7-dimethyl-8-ribityllumazine
RT synthases of Brucella.";
RL J. Bacteriol. 188:6135-6142(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG
RP INHIBITOR AND PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS,
RP AND SUBUNIT.
RX PubMed=17854827; DOI=10.1016/j.jmb.2007.08.021;
RA Klinke S., Zylberman V., Bonomi H.R., Haase I., Guimaraes B.G.,
RA Braden B.C., Bacher A., Fischer M., Goldbaum F.A.;
RT "Structural and kinetic properties of lumazine synthase isoenzymes in the
RT order Rhizobiales.";
RL J. Mol. Biol. 373:664-680(2007).
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:17854827}.
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:17854827};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=20 uM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius
CC and pH 7.0) {ECO:0000269|PubMed:17854827};
CC KM=450 uM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees
CC Celsius and pH 7.0) {ECO:0000269|PubMed:17854827};
CC Note=kcat is inferior to 0.0003 sec(-1) (at 37 degrees Celsius and pH
CC 7.0).;
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.
CC -!- SUBUNIT: Homodecamer, arranged as a dimer of pentamers.
CC {ECO:0000269|PubMed:17854827}.
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; BA000012; BAB53421.1; -; Genomic_DNA.
DR RefSeq; WP_010914728.1; NC_002678.2.
DR PDB; 2OBX; X-ray; 2.53 A; A/B/C/D/E/F/G/H/I/J=1-157.
DR PDBsum; 2OBX; -.
DR AlphaFoldDB; Q986N2; -.
DR SMR; Q986N2; -.
DR STRING; 266835.14026825; -.
DR EnsemblBacteria; BAB53421; BAB53421; BAB53421.
DR KEGG; mlo:mll7281; -.
DR PATRIC; fig|266835.9.peg.5816; -.
DR eggNOG; COG0054; Bacteria.
DR HOGENOM; CLU_089358_0_0_5; -.
DR OMA; PHHFHEH; -.
DR OrthoDB; 1680292at2; -.
DR BRENDA; 2.5.1.78; 3243.
DR UniPathway; UPA00275; UER00404.
DR EvolutionaryTrace; Q986N2; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
DR GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
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.
PE 1: Evidence at protein level;
KW 3D-structure; Riboflavin biosynthesis; Transferase.
FT CHAIN 1..157
FT /note="6,7-dimethyl-8-ribityllumazine synthase 2"
FT /id="PRO_0000134792"
FT ACT_SITE 87
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 21
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 55..57
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 79..81
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 112
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 126
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000250"
FT STRAND 12..19
FT /evidence="ECO:0007829|PDB:2OBX"
FT HELIX 23..41
FT /evidence="ECO:0007829|PDB:2OBX"
FT STRAND 44..54
FT /evidence="ECO:0007829|PDB:2OBX"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:2OBX"
FT HELIX 58..68
FT /evidence="ECO:0007829|PDB:2OBX"
FT STRAND 72..79
FT /evidence="ECO:0007829|PDB:2OBX"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:2OBX"
FT HELIX 89..106
FT /evidence="ECO:0007829|PDB:2OBX"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:2OBX"
FT HELIX 124..154
FT /evidence="ECO:0007829|PDB:2OBX"
SQ SEQUENCE 157 AA; 17281 MW; 26277728CDB09D7B CRC64;
MNQHSHKDYE TVRIAVVRAR WHADIVDQCV SAFEAEMADI GGDRFAVDVF DVPGAYEIPL
HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVIDGMM NVQLSTGVPV LSAVLTPHNY
HDSAEHHRFF FEHFTVKGKE AARACVEILA AREKIAA
