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Protein

S-ribosylhomocysteine lyase

Gene

luxS

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentadione (DPD).

Catalytic activityi

S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione.

Cofactori

Fe cation1 PublicationNote: Binds 1 Fe cation per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi54 – 541Iron
Metal bindingi58 – 581Iron
Metal bindingi126 – 1261Iron

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Autoinducer synthesis, Quorum sensing

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU30670-MONOMER.
MetaCyc:MONOMER-14557.
BRENDAi4.4.1.21. 658.
SABIO-RKO34667.

Names & Taxonomyi

Protein namesi
Recommended name:
S-ribosylhomocysteine lyase (EC:4.4.1.21)
Alternative name(s):
AI-2 synthesis protein
Autoinducer-2 production protein LuxS
Gene namesi
Name:luxS
Synonyms:ytjB
Ordered Locus Names:BSU30670
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU30670. [Micado]

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi57 – 571E → A or Q: Complete loss of activity. 1 Publication
Mutagenesisi57 – 571E → D: 220-fold decrease in activity. 1 Publication
Mutagenesisi84 – 841C → A: Complete loss of activity. 1 Publication
Mutagenesisi84 – 841C → D or S: Almost complete loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 157157S-ribosylhomocysteine lyasePRO_0000172211Add
BLAST

Proteomic databases

PaxDbiO34667.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016691.

Structurei

Secondary structure

1
157
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 84Combined sources
Turni11 – 133Combined sources
Beta strandi16 – 2712Combined sources
Turni28 – 303Combined sources
Beta strandi31 – 399Combined sources
Turni43 – 453Combined sources
Helixi50 – 6819Combined sources
Beta strandi72 – 8110Combined sources
Beta strandi85 – 9410Combined sources
Helixi98 – 11215Combined sources
Turni123 – 1253Combined sources
Turni127 – 1304Combined sources
Helixi134 – 14512Combined sources
Helixi149 – 1524Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IE0X-ray1.60A1-157[»]
1J98X-ray1.20A1-157[»]
1JQWX-ray2.30A1-157[»]
1JVIX-ray2.20A1-157[»]
1YCLX-ray1.80A2-157[»]
2FQOX-ray1.87A1-157[»]
2FQTX-ray1.79A1-157[»]
ProteinModelPortaliO34667.
SMRiO34667. Positions 4-157.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO34667.

Family & Domainsi

Sequence similaritiesi

Belongs to the LuxS family.Curated

Phylogenomic databases

eggNOGiCOG1854.
HOGENOMiHOG000040372.
InParanoidiO34667.
KOiK07173.
OMAiLTKYDVR.
OrthoDBiEOG68WRBM.
PhylomeDBiO34667.

Family and domain databases

Gene3Di3.30.1360.80. 1 hit.
HAMAPiMF_00091. LuxS.
InterProiIPR011249. Metalloenz_LuxS/M16.
IPR003815. S-ribosylhomocysteinase.
[Graphical view]
PfamiPF02664. LuxS. 1 hit.
[Graphical view]
PIRSFiPIRSF006160. AI2. 1 hit.
PRINTSiPR01487. LUXSPROTEIN.
ProDomiPD013172. S-ribosylhomocysteinase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF63411. SSF63411. 1 hit.

Sequencei

Sequence statusi: Complete.

O34667-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSVESFELD HNAVVAPYVR HCGVHKVGTD GVVNKFDIRF CQPNKQAMKP
60 70 80 90 100
DTIHTLEHLL AFTIRSHAEK YDHFDIIDIS PMGCQTGYYL VVSGEPTSAE
110 120 130 140 150
IVDLLEDTMK EAVEITEIPA ANEKQCGQAK LHDLEGAKRL MRFWLSQDKE

ELLKVFG
Length:157
Mass (Da):17,714
Last modified:January 1, 1998 - v1
Checksum:iDD011A2A88BD2FFB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF008220 Genomic DNA. Translation: AAC00235.1.
AL009126 Genomic DNA. Translation: CAB15045.1.
PIRiA69994.
RefSeqiNP_390945.1. NC_000964.3.
WP_003219361.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB15045; CAB15045; BSU30670.
GeneIDi937106.
KEGGibsu:BSU30670.
PATRICi18978038. VBIBacSub10457_3207.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF008220 Genomic DNA. Translation: AAC00235.1.
AL009126 Genomic DNA. Translation: CAB15045.1.
PIRiA69994.
RefSeqiNP_390945.1. NC_000964.3.
WP_003219361.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IE0X-ray1.60A1-157[»]
1J98X-ray1.20A1-157[»]
1JQWX-ray2.30A1-157[»]
1JVIX-ray2.20A1-157[»]
1YCLX-ray1.80A2-157[»]
2FQOX-ray1.87A1-157[»]
2FQTX-ray1.79A1-157[»]
ProteinModelPortaliO34667.
SMRiO34667. Positions 4-157.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100016691.

Chemistry

BindingDBiO34667.
ChEMBLiCHEMBL5171.

Proteomic databases

PaxDbiO34667.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15045; CAB15045; BSU30670.
GeneIDi937106.
KEGGibsu:BSU30670.
PATRICi18978038. VBIBacSub10457_3207.

Organism-specific databases

GenoListiBSU30670. [Micado]

Phylogenomic databases

eggNOGiCOG1854.
HOGENOMiHOG000040372.
InParanoidiO34667.
KOiK07173.
OMAiLTKYDVR.
OrthoDBiEOG68WRBM.
PhylomeDBiO34667.

Enzyme and pathway databases

BioCyciBSUB:BSU30670-MONOMER.
MetaCyc:MONOMER-14557.
BRENDAi4.4.1.21. 658.
SABIO-RKO34667.

Miscellaneous databases

EvolutionaryTraceiO34667.
PROiO34667.

Family and domain databases

Gene3Di3.30.1360.80. 1 hit.
HAMAPiMF_00091. LuxS.
InterProiIPR011249. Metalloenz_LuxS/M16.
IPR003815. S-ribosylhomocysteinase.
[Graphical view]
PfamiPF02664. LuxS. 1 hit.
[Graphical view]
PIRSFiPIRSF006160. AI2. 1 hit.
PRINTSiPR01487. LUXSPROTEIN.
ProDomiPD013172. S-ribosylhomocysteinase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF63411. SSF63411. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
    Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
    Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "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.
  3. "S-ribosylhomocysteinase (LuxS) is a mononuclear iron protein."
    Zhu J., Dizin E., Hu X., Wavreille A.-S., Park J., Pei D.
    Biochemistry 42:4717-4726(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, CHARACTERIZATION, MUTAGENESIS OF GLU-57 AND CYS-84.
  4. Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS).
  5. "Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site."
    Hilgers M.T., Ludwig M.L.
    Proc. Natl. Acad. Sci. U.S.A. 98:11169-11174(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

Entry informationi

Entry nameiLUXS_BACSU
AccessioniPrimary (citable) accession number: O34667
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: June 24, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.