P11998 (RISB_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
6,7-dimethyl-8-ribityllumazine synthase
Short name=DMRL synthase
Short name=LS
Short name=Lumazine synthase
EC=2.5.1.78

Alternative name(s):
Heavy riboflavin synthase beta subunit
Short name=HRS beta subunit

Gene names

Name:	ribH
Ordered Locus Names:	BSU23250

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	154 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Is able to use the non-natural R enantiomer of 3,4-dihydroxy-2-butanone 4-phosphate as a substrate, but with less efficiency than the natural S enantiomer. Cannot use unphosphorylated 3,4-dihydroxy-2-butanone, 3,4-dihydroxy-2-butanone 3-phosphate or diacetyl as substrates. Ref.4 Ref.8
Catalytic activity	1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate. Ref.4 Ref.8
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Ref.8
Subunit structure	Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Can interact with riboflavin synthase, forming a lumazine synthase/riboflavin synthase complex, also designated as 'heavy riboflavin synthase complex', which consists of a trimer of riboflavin synthase enclosed within the icosahedral structure composed of 60 subunits of 6,7-dimethyl-8-ribityllumazine synthase. Ref.7 Ref.9 Ref.10
Sequence similarities	Belongs to the DMRL synthase family.
Biophysicochemical properties	Kinetic parameters: kcat is 0.056 sec(-1) (Ref.4). KM=5 µM for 5-amino-6-(D-ribitylamino)uracil (Ref.8) Ref.4 Ref.8 KM=9 µM for 5-amino-6-(D-ribitylamino)uracil (Ref.4) KM=130 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate (Ref.8) KM=55 µM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate (Ref.4) Vmax=12000 nmol/h/mg enzyme (Ref.8) pH dependence: Optimum pH is 6.5-8.0.

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	riboflavin biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	riboflavin synthase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	6,7-dimethyl-8-ribityllumazine synthase activity Inferred from electronic annotation. Source: HAMAP transferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 154

154

6,7-dimethyl-8-ribityllumazine synthase HAMAP-Rule MF_00178

PRO_0000134715

Regions

Region

22 – 23

2

5-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178

Region

56 – 58

3

5-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178

Region

80 – 82

3

5-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178

Region

85 – 86

2

1-deoxy-L-glycero-tetrulose 4-phosphate binding Probable

Sites

Active site

88

1

Proton donor Potential

Binding site

113

1

5-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen

Binding site

127

1

1-deoxy-L-glycero-tetrulose 4-phosphate Probable

Experimental info

Mutagenesis

88

1

H → A: 10% of wild-type activity. 17-fold decrease in the affinity for the pyrimidine substrate, but no effect on that for 1-deoxy-L-glycero-tetrulose 4-phosphate. Ref.4

Mutagenesis

127

1

R → T: About 1% of wild-type activity. Ref.4

Sequence conflict

65

1

K → G AA sequence Ref.1

Secondary structure

1

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154

Helix Strand Turn

Details...

Beta strand

2 – 4

3

Beta strand

15 – 21

7

Helix

24 – 40

17

Helix

45 – 47

3

Beta strand

48 – 55

8

Helix

56 – 58

3

Helix

59 – 68

10

Beta strand

73 – 82

10

Beta strand

85 – 87

3

Helix

88 – 107

20

Beta strand

111 – 120

10

Helix

121 – 126

6

Beta strand

128 – 130

3

Helix

135 – 152

18

Sequences

	Sequence		Length	Mass (Da)
	P11998 [UniParc]. Last modified February 1, 1994. Version 2. Checksum: 76CB336DF6A4BFEB	FASTA	154	16,287
	10 20 30 40 50 60 MNIIQGNLVG TGLKIGIVVG RFNDFITSKL LSGAEDALLR HGVDTNDIDV AWVPGAFEIP 70 80 90 100 110 120 FAAKKMAETK KYDAIITLGT VIRGATTHYD YVCNEAAKGI AQAANTTGVP VIFGIVTTEN 130 140 150 IEQAIERAGT KAGNKGVDCA VSAIEMANLN RSFE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Heavy riboflavin synthase of Bacillus subtilis. Primary structure of the beta subunit." Ludwig H.C., Lottspeich F., Henschen A., Ladenstein R., Bacher A. J. Biol. Chem. 262:1016-1021(1987) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE.
[2]	"The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data." Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P. Mol. Microbiol. 10:385-395(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
[3]	Mironov V.N. Thesis (1989), USSR Academy of Sciences, Russia Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / SHGW.
[4]	"Enzyme catalysis via control of activation entropy: site-directed mutagenesis of 6,7-dimethyl-8-ribityllumazine synthase." Fischer M., Haase I., Kis K., Meining W., Ladenstein R., Cushman M., Schramek N., Huber R., Bacher A. J. Mol. Biol. 326:783-793(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, MUTAGENESIS OF HIS-88 AND ARG-127, MUTAGENESIS OF OTHER RESIDUES.
[5]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[6]	"Cold shock stress-induced proteins in Bacillus subtilis." Graumann P., Schroeder K., Schmid R., Marahiel M.A. J. Bacteriol. 178:4611-4619(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-20. Strain: 168 / JH642.
[7]	"Heavy riboflavin synthase from Bacillus subtilis. Quaternary structure and reaggregation." Bacher A., Ludwig H.C., Schnepple H., Ben-Shaul Y. J. Mol. Biol. 187:75-86(1986) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[8]	"Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase." Kis K., Volk R., Bacher A. Biochemistry 34:2883-2892(1995) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, STEREOSPECIFICITY, REACTION MECHANISM, PATHWAY.
[9]	"Heavy riboflavin synthase from Bacillus subtilis. Crystal structure analysis of the icosahedral beta 60 capsid at 3.3-A resolution." Ladenstein R., Schneider M., Huber R., Bartunik H.-D., Wilson K., Schott K., Bacher A. J. Mol. Biol. 203:1045-1070(1988) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), SUBUNIT.
[10]	"Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor at 2.4-A resolution." Ritseert K., Huber R., Turk D., Ladenstein R., Schmidt-Baese K., Bacher A. J. Mol. Biol. 253:151-167(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG INHIBITOR AND PHOSPHATE, SUBUNIT, ACTIVE SITE, REACTION MECHANISM.
[11]	"Crystal structure of recombinant lumazine synthase (hexagonal form)." Lopez-Jaramillo F.J. Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG INHIBITOR AND PHOSPHATE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L09228 Genomic DNA. Translation: AAA67484.1.
X51510 Genomic DNA. Translation: CAA35881.1.
AF516949 Genomic DNA. Translation: AAN01132.1.
AL009126 Genomic DNA. Translation: CAB14257.1.

PIR

A26708. S45546.

RefSeq

NP_390206.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RVV	X-ray	2.40	1/2/3/4/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z	1-154	[»]
1ZIS	X-ray	2.90	A/B/C/D/E/F/G/H/I/J	1-154	[»]

ProteinModelPortal

P11998.

SMR

P11998. Positions 1-154.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU23250.

Proteomic databases

PaxDb

P11998.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB14257; CAB14257; BSU23250.

GeneID

938949.

KEGG

bsu:BSU23250.

PATRIC

18976467. VBIBacSub10457_2424.

Organism-specific databases

GenoList

BSU23250. [Micado]

Phylogenomic databases

eggNOG

COG0054.

HOGENOM

HOG000229249.

KO

K00794.

OMA

GRFNSFI.

ProtClustDB

PRK00061.

Enzyme and pathway databases

BioCyc

BSUB:BSU23250-MONOMER.
MetaCyc:MONOMER-14609.

SABIO-RK

P11998.

UniPathway

UPA00275; UER00404.

Family and domain databases

Gene3D

3.40.50.960. 1 hit.

HAMAP

MF_00178. Lumazine_synth.

InterPro

IPR002180. DMRL_synthase.
[Graphical view]

PANTHER

PTHR21058. PTHR21058. 1 hit.

Pfam

PF00885. DMRL_synthase. 1 hit.
[Graphical view]

SUPFAM

SSF52121. DMRL_synthase. 1 hit.

TIGRFAMs

TIGR00114. lumazine-synth. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P11998.

Entry information

Entry name

RISB_BACSU

Accession

Primary (citable) accession number: P11998
Secondary accession number(s): P17621

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	February 1, 1994
Last modified:	May 1, 2013
This is version 114 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program