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6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (EC 2.5.1.78)

 RISB_MYCTU              Reviewed;         160 AA.
P9WHE9; L0T874; P66034; P71685;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
12-SEP-2018, entry version 26.
RecName: Full=6,7-dimethyl-8-ribityllumazine synthase;
Short=DMRL synthase;
Short=LS;
Short=Lumazine synthase;
EC=2.5.1.78;
Name=ribH; OrderedLocusNames=Rv1416; ORFNames=MTCY21B4.34;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
ACTIVITY REGULATION.
PubMed=14750781; DOI=10.1021/jo030278k;
Cushman M., Sambaiah T., Jin G., Illarionov B., Fischer M., Bacher A.;
"Design, synthesis, and evaluation of 9-D-ribitylamino-1,3,7,9-
tetrahydro-2,6,8-purinetriones bearing alkyl phosphate and
alpha,alpha-difluorophosphonate substituents as inhibitors of
riboflavin synthase and lumazine synthase.";
J. Org. Chem. 69:601-612(2004).
[3]
IDENTIFICATION BY MASS SPECTROMETRY, AND DETERMINATION OF
TRANSLATIONAL START SITE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=17259624; DOI=10.1099/mic.0.2006/001537-0;
Rison S.C., Mattow J., Jungblut P.R., Stoker N.G.;
"Experimental determination of translational starts using peptide mass
mapping and tandem mass spectrometry within the proteome of
Mycobacterium tuberculosis.";
Microbiology 153:521-528(2007).
[4]
IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
PubMed=19099550; DOI=10.1186/1752-0509-2-109;
Raman K., Yeturu K., Chandra N.;
"targetTB: a target identification pipeline for Mycobacterium
tuberculosis through an interactome, reactome and genome-scale
structural analysis.";
BMC Syst. Biol. 2:109-109(2008).
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[6]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH PURINETRIONE
INHIBITORS, FUNCTION, AND SUBUNIT.
PubMed=15723519; DOI=10.1021/bi047848a;
Morgunova E., Meining W., Illarionov B., Haase I., Jin G., Bacher A.,
Cushman M., Fischer M., Ladenstein R.;
"Crystal structure of lumazine synthase from Mycobacterium
tuberculosis as a target for rational drug design: binding mode of a
new class of purinetrione inhibitors.";
Biochemistry 44:2746-2758(2005).
[7]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEXES WITH PURINETRIONE
AND CHLOROPYRIMIDINE INHIBITORS.
PubMed=16984393; DOI=10.1111/j.1742-4658.2006.05481.x;
Morgunova E., Illarionov B., Sambaiah T., Haase I., Bacher A.,
Cushman M., Fischer M., Ladenstein R.;
"Structural and thermodynamic insights into the binding mode of five
novel inhibitors of lumazine synthase from Mycobacterium
tuberculosis.";
FEBS J. 273:4790-4804(2006).
[8]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH A REACTION
INTERMEDIATE ANALOG INHIBITOR AND PHOSPHATE, AND REACTION MECHANISM.
PubMed=18331058; DOI=10.1021/jo702631a;
Zhang Y., Illarionov B., Morgunova E., Jin G., Bacher A., Fischer M.,
Ladenstein R., Cushman M.;
"A new series of N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-
tetrahydropyrimidin-5-yl]oxalamic acid derivatives as inhibitors of
lumazine synthase and riboflavin synthase: design, synthesis,
biochemical evaluation, crystallography, and mechanistic
implications.";
J. Org. Chem. 73:2715-2724(2008).
-!- FUNCTION: Catalyzes the formation of 6,7-dimethyl-8-
ribityllumazine by condensation of 5-amino-6-(D-
ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate.
This is the penultimate step in the biosynthesis of riboflavin.
{ECO:0000269|PubMed:15723519}.
-!- CATALYTIC ACTIVITY: 1-deoxy-L-glycero-tetrulose 4-phosphate + 5-
amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-
ribityl)lumazine + 2 H(2)O + phosphate.
-!- ACTIVITY REGULATION: Activity is competitively inhibited by
substituted ribitylpurinetrione compounds such as 3-(1,3,7,9-
tetrahydro-9-D-ribityl-2,6,8-trioxopurin-7-yl)propane 1-phosphate,
with inhibition constants in the 4-5 nM range.
{ECO:0000269|PubMed:14750781}.
-!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis;
riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-
ribitylamino)uracil: step 1/2.
-!- SUBUNIT: Homopentamer. {ECO:0000269|PubMed:15723519,
ECO:0000269|PubMed:18331058}.
-!- MISCELLANEOUS: Was identified as a high-confidence drug target.
-!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP44175.1; -; Genomic_DNA.
PIR; E70902; E70902.
RefSeq; NP_215932.2; NC_000962.3.
RefSeq; WP_003898872.1; NZ_KK339370.1.
PDB; 1W19; X-ray; 2.00 A; A/B/C/D/E=1-160.
PDB; 1W29; X-ray; 2.30 A; A/B/C/D/E=1-160.
PDB; 2C92; X-ray; 1.60 A; A/B/C/D/E=1-160.
PDB; 2C94; X-ray; 1.90 A; A/B/C/D/E=1-160.
PDB; 2C97; X-ray; 2.00 A; A/B/C/D/E=1-160.
PDB; 2C9B; X-ray; 2.75 A; A/B/C/D/E/F/G/H/I/J=1-160.
PDB; 2C9D; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J=1-160.
PDB; 2VI5; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J=1-160.
PDBsum; 1W19; -.
PDBsum; 1W29; -.
PDBsum; 2C92; -.
PDBsum; 2C94; -.
PDBsum; 2C97; -.
PDBsum; 2C9B; -.
PDBsum; 2C9D; -.
PDBsum; 2VI5; -.
ProteinModelPortal; P9WHE9; -.
SMR; P9WHE9; -.
STRING; 83332.Rv1416; -.
BindingDB; P9WHE9; -.
ChEMBL; CHEMBL1075177; -.
PaxDb; P9WHE9; -.
EnsemblBacteria; CCP44175; CCP44175; Rv1416.
GeneID; 886681; -.
KEGG; mtu:Rv1416; -.
TubercuList; Rv1416; -.
eggNOG; ENOG4108UTT; Bacteria.
eggNOG; COG0054; LUCA.
KO; K00794; -.
OMA; HGNKGTE; -.
UniPathway; UPA00275; UER00404.
Proteomes; UP000001584; Chromosome.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IBA:GO_Central.
GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
CDD; cd09209; Lumazine_synthase-I; 1.
Gene3D; 3.40.50.960; -; 1.
HAMAP; MF_00178; Lumazine_synth; 1.
InterPro; IPR034964; LS.
InterPro; IPR002180; LS/RS.
InterPro; IPR036467; LS/RS_sf.
PANTHER; PTHR21058; PTHR21058; 1.
Pfam; PF00885; DMRL_synthase; 1.
SUPFAM; SSF52121; SSF52121; 1.
TIGRFAMs; TIGR00114; lumazine-synth; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Reference proteome;
Riboflavin biosynthesis; Transferase.
CHAIN 1 160 6,7-dimethyl-8-ribityllumazine synthase.
/FTId=PRO_0000134772.
REGION 59 61 5-amino-6-(D-ribitylamino)uracil binding.
REGION 81 83 5-amino-6-(D-ribitylamino)uracil binding.
REGION 86 87 1-deoxy-L-glycero-tetrulose 4-phosphate
binding. {ECO:0000305}.
ACT_SITE 89 89 Proton donor. {ECO:0000255}.
BINDING 27 27 5-amino-6-(D-ribitylamino)uracil.
BINDING 114 114 5-amino-6-(D-ribitylamino)uracil; via
amide nitrogen and carbonyl oxygen.
BINDING 128 128 1-deoxy-L-glycero-tetrulose 4-phosphate.
{ECO:0000305}.
STRAND 20 25 {ECO:0000244|PDB:2C92}.
HELIX 29 45 {ECO:0000244|PDB:2C92}.
STRAND 52 58 {ECO:0000244|PDB:2C92}.
HELIX 59 61 {ECO:0000244|PDB:2C92}.
HELIX 62 70 {ECO:0000244|PDB:2C92}.
STRAND 74 83 {ECO:0000244|PDB:2C92}.
HELIX 89 108 {ECO:0000244|PDB:2C92}.
STRAND 112 121 {ECO:0000244|PDB:2C92}.
HELIX 122 126 {ECO:0000244|PDB:2C92}.
HELIX 138 156 {ECO:0000244|PDB:2C92}.
SEQUENCE 160 AA; 16371 MW; 20E837C273312E83 CRC64;
MKGGAGVPDL PSLDASGVRL AIVASSWHGK ICDALLDGAR KVAAGCGLDD PTVVRVLGAI
EIPVVAQELA RNHDAVVALG VVIRGQTPHF DYVCDAVTQG LTRVSLDSST PIANGVLTTN
TEEQALDRAG LPTSAEDKGA QATVAALATA LTLRELRAHS


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