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=Lumazine synthase
EC=2.5.1.9

Alternative name(s):
Riboflavin synthase beta chain

Gene names

Name:	ribH
Ordered Locus Names:	BSU23250

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

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

General annotation (Comments)

Function	Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2-butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate yielding 6,7-dimethyl-8-lumazine. HAMAP MF_00178
Catalytic activity	2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. HAMAP MF_00178
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 2/2. HAMAP MF_00178
Subunit structure	Oligomer consisting of 3 alpha subunits and 60 beta subunits. The beta subunits are arranged in twelve pentamers that give rise to a capsid. The capsid encloses the trimer of alpha subunits.
Sequence similarities	Belongs to the DMRL synthase family.

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: UniProtKB-KW
Cellular component	riboflavin synthase complex Inferred from electronic annotation. Source: InterPro
Molecular function	riboflavin synthase activity Inferred from electronic annotation. Source: EC
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 MF_00178

PRO_0000134715

Experimental info

Sequence conflict

65

1

K → G AA sequence Ref.1

Secondary structure

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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: 3100522] [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: 7934829] [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: 12581640] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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: 9384377] [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: 8755892] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-20. Strain: 168 / JH642.
[7]	"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: 3145341] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).
[8]	"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: 7473709] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
+	Additional computationally mapped references.

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...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBBACT00000001639; EBBACP00000001639; EBBACG00000001637.

GeneID

938949.

GenomeReviews

Gene locus BSU23250 in contig AL009126_GR.

KEGG

bsu:BSU23250.

NMPDR

fig|224308.1.peg.2329.

PATRIC

18976467. VBIBacSub10457_2424.

Organism-specific databases

GenoList

BSU23250. [Micado]

Phylogenomic databases

GeneTree

EBGT00050000002577.

HOGENOM

HBG311126.

OMA

DYVCNEA.

PhylomeDB

P11998.

ProtClustDB

PRK00061.

Enzyme and pathway databases

BioCyc

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

Family and domain databases

HAMAP

MF_00178. Lumazine_synth.
[Tree]

InterPro

IPR002180. DMRL_synthase.
[Graphical view]

Gene3D

G3DSA:3.40.50.960. DMRL_synthase. 1 hit.

KO

K00794.

PANTHER

PTHR21058. DMRL_synthase. 1 hit.

Pfam

PF00885. DMRL_synthase. 1 hit.
[Graphical view]

SUPFAM

SSF52121. DMRL_synthase. 1 hit.

TIGRFAMs

TIGR00114. Lumazine-synth. 1 hit.

ProtoNet

Search...

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:	January 25, 2012
This is version 104 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program