O34667 (LUXS_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
S-ribosylhomocysteine lyase
EC=4.4.1.21

Alternative name(s):
AI-2 synthesis protein
Autoinducer-2 production protein LuxS

Gene names

Name:	luxS
Synonyms:	ytjB
Ordered Locus Names:	BSU30670

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	157 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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). HAMAP MF_00091
Catalytic activity	S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione. HAMAP MF_00091
Cofactor	Binds 1 iron ion per subunit. Ref.3
Subunit structure	Homodimer.
Sequence similarities	Belongs to the LuxS family.

Ontologies

Keywords
Biological process	Autoinducer synthesis Quorum sensing
Ligand	Iron Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	quorum sensing Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	S-ribosylhomocysteine lyase activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 157

157

S-ribosylhomocysteine lyase HAMAP MF_00091

PRO_0000172211

Sites

Metal binding

54

1

Iron

Metal binding

58

1

Iron

Metal binding

126

1

Iron

Experimental info

Mutagenesis

57

1

E → A or Q: Complete loss of activity. Ref.3

Mutagenesis

57

1

E → D: 220-fold decrease in activity. Ref.3

Mutagenesis

84

1

C → A: Complete loss of activity. Ref.3

Mutagenesis

84

1

C → D or S: Almost complete loss of activity. Ref.3

Secondary structure

1

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157

Helix Strand Turn

Details...

Helix

5 – 8

4

Turn

11 – 13

3

Beta strand

16 – 27

12

Turn

28 – 30

3

Beta strand

31 – 39

9

Turn

43 – 45

3

Helix

50 – 68

19

Beta strand

72 – 81

10

Beta strand

85 – 94

10

Helix

98 – 112

15

Turn

123 – 125

3

Turn

127 – 130

4

Helix

134 – 145

12

Helix

149 – 152

4

Sequences

	Sequence		Length	Mass (Da)
	O34667 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: DD011A2A88BD2FFB	FASTA	157	17,714
	10 20 30 40 50 60 MPSVESFELD HNAVVAPYVR HCGVHKVGTD GVVNKFDIRF CQPNKQAMKP DTIHTLEHLL 70 80 90 100 110 120 AFTIRSHAEK YDHFDIIDIS PMGCQTGYYL VVSGEPTSAE IVDLLEDTMK EAVEITEIPA 130 140 150 ANEKQCGQAK LHDLEGAKRL MRFWLSQDKE ELLKVFG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 9387221] [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: 9384377] [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: 12705835] [Abstract] Cited for: COFACTOR, CHARACTERIZATION, MUTAGENESIS OF GLU-57 AND CYS-84.
[4]	"The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS." Ruzheinikov S.N., Das S.K., Sedelnikova S.E., Hartley A., Foster S.J., Horsburgh M.J., Cox A.G., McCleod C.W., Mekhalfia A., Blackburn G.M., Rice D.W., Baker P.J. J. Mol. Biol. 313:111-122(2001) [PubMed: 11601850] [Abstract] 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: 11553770] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF008220 Genomic DNA. Translation: AAC00235.1.
AL009126 Genomic DNA. Translation: CAB15045.1.

PIR

A69994.

RefSeq

NP_390945.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IE0	X-ray	1.60	A	1-157	[»]
1J98	X-ray	1.20	A	1-157	[»]
1JQW	X-ray	2.30	A	1-157	[»]
1JVI	X-ray	2.20	A	1-157	[»]
1YCL	X-ray	1.80	A	2-157	[»]
2FQO	X-ray	1.87	A	1-157	[»]
2FQT	X-ray	1.79	A	1-157	[»]

ProteinModelPortal

O34667.

SMR

O34667. Positions 4-157.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBBACT00000002568; EBBACP00000002568; EBBACG00000002563.

GeneID

937106.

GenomeReviews

Gene locus BSU30670 in contig AL009126_GR.

KEGG

bsu:BSU30670.

NMPDR

fig|224308.1.peg.3070.

PATRIC

18978038. VBIBacSub10457_3207.

Organism-specific databases

GenoList

BSU30670. [Micado]

Phylogenomic databases

GeneTree

EBGT00050000002559.

HOGENOM

HBG347473.

OMA

PHGDTIT.

PhylomeDB

O34667.

ProtClustDB

PRK02260.

Enzyme and pathway databases

BioCyc

BSUB:BSU30670-MONOMER.
MetaCyc:MONOMER-14557.

BRENDA

4.4.1.21. 700.

Family and domain databases

HAMAP

MF_00091. LuxS.
[Tree]

InterPro

IPR011249. Metalloenz_metal-bd.
IPR003815. S-ribosylhomocysteinase.
[Graphical view]

Gene3D

G3DSA:3.30.1360.80. S-ribosylhomocysteinase. 1 hit.

KO

K07173.

Pfam

PF02664. LuxS. 1 hit.
[Graphical view]

PIRSF

PIRSF006160. AI2. 1 hit.

PRINTS

PR01487. LUXSPROTEIN.

ProDom

PD013172. S-ribosylhomocysteinase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF63411. Metalloenz_metal-bd. 1 hit.

ProtoNet

Search...

Entry information

Entry name

LUXS_BACSU

Accession

Primary (citable) accession number: O34667

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 1, 1998
Last modified:	January 25, 2012
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program