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Information on EC 4.4.1.21 - S-ribosylhomocysteine lyase and Organism(s) Bacillus subtilis

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IUBMB Comments
Contains Fe2+. The 4,5-dihydroxypentan-2,3-dione formed spontaneously cyclizes and combines with borate to form an autoinducer (AI-2) in the bacterial quorum-sensing mechanism, which is used by many bacteria to control gene expression in response to cell density .
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This record set is specific for:
Bacillus subtilis
Word Map
The taxonomic range for the selected organisms is: Bacillus subtilis
The enzyme appears in selected viruses and cellular organisms
Synonyms
AI-2 synthase, autoinducer-2 synthase, BsLuxS, EcLuxS, lsrR, Lux S, LuxS, LuxS protein, S-ribosyl homocysteinase, S-ribosylhomocysteinase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
LuxS protein
-
-
S-ribosyl homocysteinase
-
-
S-ribosylhomocysteinase
S-ribosylhomocysteine lyase
-
S-ribosylhomocysteinelyase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C-S bond cleavage
-
-
additional information
Bacillus subtilis can use methionine as sole sulfur source, the BsluxS knockout mutant grows poorly in the presence of methionine compared to the wild-type strain, methionine utilization requires first its conversion to homocysteine
SYSTEMATIC NAME
IUBMB Comments
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine L-homocysteine-lyase [(4S)-4,5-dihydroxypentan-2,3-dione-forming]
Contains Fe2+. The 4,5-dihydroxypentan-2,3-dione formed spontaneously cyclizes and combines with borate to form an autoinducer (AI-2) in the bacterial quorum-sensing mechanism, which is used by many bacteria to control gene expression in response to cell density [2].
CAS REGISTRY NUMBER
COMMENTARY hide
37288-63-4
not distinguished from EC 3.2.1.148, formerly 3.3.1.3
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2R)-2-amino-4-[[(2S,4S)-2,4,5-trihydroxy-3-oxopentyl]sulfanyl]butanoic acid
L-homocysteine + ?
show the reaction diagram
-
-
-
-
?
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine
L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine
L-homocysteine + (S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
S-ribosylhomocysteine
L-homocysteine + (S)-4,5-dihydroxy-2,3-pentanedione
show the reaction diagram
-
assay at pH 7.0, 23C
-
-
?
S-ribosylhomocysteine
L-homocysteine + (S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
-
-
-
-
?
S-ribosylhomocysteine
L-homocysteine + 4,5-dihydroxy-2,3-pentanedione
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-(5-deoxy-D-ribos-5-yl)-L-homocysteine
L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
-
-
-
-
?
S-ribosylhomocysteine
L-homocysteine + 4,5-dihydroxy-2,3-pentanedione
show the reaction diagram
-
key step in biosynthesis pathway of type II autoinducer AI-2
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
; Co2+ substitution produces a highly stable enzyme
Zinc
-
zinc-dependent metalloenzyme, each active site contains a zinc ion coordinated by the conserved residues His54, His58 and Cys126, and includes residues from both subunits
additional information
-
to gain insight into the catalytic mechanism of the unusual reaction and the function of the metal cofactor, an efficient expression and purification system is developed to produce LuxS enriched in either Fe2+, Co2+ or Zn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2S)-2-amino-4-[(2R,3R)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
-
-
(2S)-2-amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
-
-
(2S)-2-amino-6-(N-formyl-N-hydroxyamino)hexanoic acid
-
-
D-erythronohydroxamic acid
-
-
D-ribosylornithine
-
-
methionine
-
-
S-(1-amino-1,4-anhydro-1,5-dideoxy-D-ribitol-5-yl)-L-homocysteine
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inhibition of Co(II)-substituted enzyme
S-(3,5-dideoxy-3-fluoro-1-O-methyl-D-xylofuranos-5-yl)-L-homocysteine
-
-
S-(3,5-dideoxy-3-fluoro-D-xylofuranos-5-yl)-L-homocysteine
-
-
S-(3,5-dideoxy-D-erythro-pentofuranos-5-yl)homocysteine
-
-
S-(4-amino-4,5-dideoxy-alpha/beta-D-ribofuranos-5-yl)-L-homocysteine
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inhibition of Co(II)-substituted enzyme. The hemiaminal may undergo ring opening to form an aldehyde which may undergo the aldose-ketose isomerization reaction to form a 2-ketone, which presumably binds to the LuxS active site with higher affinity than the original ribose analogue
S-(4-amino-4,5-dideoxy-D-ribono-1,4-lactam-5-yl)-L-homocysteine
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inhibition of Co(II)-substituted enzyme
S-(5-deoxy-3-deoxy-3-bromo-D-xylofuranos-5-yl)-L-homocysteine
-
-
S-(5-deoxy-3-deoxy-3-fluoro-D-xylofuranos-5-yl)-L-homocysteine
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-
S-(5-deoxy-3-O-methyl-D-ribofuranos-5-yl)homocysteine
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-
S-(5-deoxy-3-O-methyl-D-xylofuranos-5-yl)homocysteine
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-
S-(5-deoxy-D-xylofuranos-5-yl)-L-homocysteine
-
-
S-[3-bromo-3,5-dideoxy-D-ribofuranos-5-yl]-L-homocysteine
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-
S-[3-fluoro-3,5-dideoxy-D-ribofuranos-5-yl]-L-homocysteine
-
-
additional information
-
5,6,7,8,9-pentadeoxy-6-fluoro-D-ribo-dec-5(Z)-enofuranuronate a S-ribosylhomocysteine analogue and 5,6-dideoxy-6-fluoro-D-ribo-hex-5-enofuranose a S-ribosylhomocysteine analogue have no inhibitory activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0036
(2R)-2-amino-4-[[(2S,4S)-2,4,5-trihydroxy-3-oxopentyl]sulfanyl]butanoic acid
-
wild type enzyme
0.0014 - 0.18
S-ribosylhomocysteine
additional information
additional information
-
KM-values of enzyme forms enriched in either Fe2+, Co2+ or Zn2+
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.038
(2R)-2-amino-4-[[(2S,4S)-2,4,5-trihydroxy-3-oxopentyl]sulfanyl]butanoic acid
-
wild type enzyme
0.03
S-ribosylhomocysteine
additional information
additional information
-
turnover numbers of enzyme forms enriched in either Fe2+, Co2+ or Zn2+
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00037 - 0.0106
(2S)-2-amino-4-[(2R,3R)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
0.00072 - 0.0196
(2S)-2-amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
0.147 - 2.4
D-erythronohydroxamic acid
0.068
D-ribosylornithine
-
Co2+ substituted enzyme
0.061
methionine
-
Co2+ substituted enzyme
0.048
S-(1-amino-1,4-anhydro-1,5-dideoxy-D-ribitol-5-yl)-L-homocysteine
-
pH 7.0, 22C
0.042
S-(3,5-dideoxy-3-fluoro-1-O-methyl-D-xylofuranos-5-yl)-L-homocysteine
-
pH 7.0, 23C
0.0077
S-(3,5-dideoxy-3-fluoro-D-xylofuranos-5-yl)-L-homocysteine
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pH 7.0, 23C
0.055
S-(3,5-dideoxy-D-erythro-pentofuranos-5-yl)homocysteine
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pH 7.0, 23C
0.0035
S-(4-amino-4,5-dideoxy-alpha/beta-D-ribofuranos-5-yl)-L-homocysteine
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pH 7.0, 22C
0.037
S-(4-amino-4,5-dideoxy-D-ribono-1,4-lactam-5-yl)-L-homocysteine
-
pH 7.0, 22C
0.0079
S-(5-deoxy-3-deoxy-3-bromo-D-xylofuranos-5-yl)-L-homocysteine
-
pH 7.0, 23C
0.0106
S-(5-deoxy-3-deoxy-3-fluoro-D-xylofuranos-5-yl)-L-homocysteine
-
pH 7.0, 23C
0.042
S-(5-deoxy-3-O-methyl-D-ribofuranos-5-yl)homocysteine
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pH 7.0, 23C
0.066
S-(5-deoxy-3-O-methyl-D-xylofuranos-5-yl)homocysteine
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pH 7.0, 23C
0.0042
S-(5-deoxy-D-xylofuranos-5-yl)-L-homocysteine
-
pH 7.0, 23C
0.0079
S-[3-bromo-3,5-dideoxy-D-ribofuranos-5-yl]-L-homocysteine
-
wild type enzyme
0.0106
S-[3-fluoro-3,5-dideoxy-D-ribofuranos-5-yl]-L-homocysteine
-
wild type enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
luxS expression is detectable only at the base of fruiting bodies
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
additional information
-
elucidation of the mechanism of the first stage of the enzyme catalytic process by docking and molecular dynamics simulations, overview. An active site water stably locates within the active site, it can facilitate ring-opening of either alpha-S-ribosylhomocysteine or beta-furanose, leading to formation of a common active-site-bound 2-keto-S-ribosylhomocysteine intermediate, without the need to pass through a linear aldose S-ribosylhomocysteine configuration. Catalytic importance of several active site residues including Ser6, His11, Arg39, Cys84, and Glu57
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
A0A5D4NCX9_BACIU
157
0
17696
TrEMBL
A0A0F0AAE7_BACIU
157
0
17724
TrEMBL
A0A4R6HWE8_BACIU
157
0
17710
TrEMBL
A0A063XCC3_BACIU
157
0
17714
TrEMBL
A0A5Q2ZW32_BACIU
157
0
17715
TrEMBL
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Co2+-substituted BsLuxS is cocrystallized with inhibitors (2S)-2-amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid and (2S)-2-amino-4-[(2R,3R)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid by the hanging drop vapor diffusion method
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hanging drop vapor diffusion, inactive mutant C84A of Co2+-substituted LuxS is cocrystallized with the 2-ketone intermediate and the structure is determined to 1.8 A resolution
-
hanging-drop vapor diffusion method with ammonium sulfate as precipitant, structure at 1.6 A resolution
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hanging-drop vapour diffusion method with ammonium sulfate as the precipitant. The crystals belong to the enantiomorphic space groups P6(1)22 or P6(5)22 with approximate unit-cell parameters A = b = 63.6, c = 151.5 A. The crystals diffract X-rays to at least 1.55 A resolution on a synchrotron-radiation source
-
structure of LuxS is determined at 1.2 A resolution, together with the binary complexes of LuxS with S-ribosylhomocysteine and homocysteine to 2.2 A and 2.3 A resolution, hanging-drop vapour diffusion method
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C84S
-
more than 220fold reduced activity
C85A
-
catalytically inactive mutant
E57A
-
no detectable activity
E57D
-
220fold reduced activity
E57Q
-
no detectable activity
H11Q
-
by site directed mutagenesis
R39M
-
by site directed mutagenesis
S6A
-
by site directed mutagenesis
Y89F
-
by site directed mutagenesis
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
absorption and electron paramagnetic resonance spectroscopic studies reveals that the active form of LuxS contains a metal-bound water and a thiolate ion at Cys-83, an invariant Arg-39 in the active site is partially responsible for stabilizing the thiolate anion of Cys-83
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80C, when stored in the frozen form, the LuxS proteins are stable for at least 6 months
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Q-Sepharose Fast-Flow column chromatography and ultrafiltration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
-
expression in Escherichia coli BL21
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LuxS variants are overexpressed in Escherichia coli in their Fe2+, Zn2+- and Co2+-substituted forms; mutant LuxS variants are overexpressed in Escherichia coli in both Zn2+- and Co2+-substituted forms
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Das, S.K.; Sedelnikova, S.E.; Baker, P.J.; Ruzheinikov, S.N.; Foster, S.; Hartley, A.; Horsburgh, M.J.; Rice, D.W.
Cloning, purification, crystallization and preliminary crystallographic analysis of Bacillus subtilis LuxS
Acta Crystallogr. Sect. D
57
1324-1325
2001
Bacillus subtilis
Manually annotated by BRENDA team
Zhu, J.; Dizin, E.; Hu, X.; Wavreille, A.S.; Park, J.; Pei, D.
S-Ribosylhomocysteinase (LuxS) is a mononuclear iron protein
Biochemistry
42
4717-4726
2003
Bacillus subtilis
Manually annotated by BRENDA team
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.
The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS
J. Mol. Biol.
313
111-122
2001
Bacillus subtilis (O34667)
Manually annotated by BRENDA team
Hilgers, M.T.; Ludwig, M.L.
Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site
Proc. Natl. Acad. Sci. USA
98
11169-11174
2001
Bacillus subtilis (O34667)
Manually annotated by BRENDA team
Zhu, J.; Patel, R.; Pei, D.
Catalytic mechanism of S-ribosylhomocysteinase (LuxS): stereochemical course and kinetic isotope effect of proton transfer reactions
Biochemistry
43
10166-10172
2004
Bacillus subtilis, Vibrio harveyi
Manually annotated by BRENDA team
Rajan, R.; Zhu, J.; Hu, X.; Pei, D.; Bell, C.E.
Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate
Biochemistry
44
3745-3753
2005
Bacillus subtilis, Bacillus subtilis (O34667), Vibrio harveyi
Manually annotated by BRENDA team
Hullo, M.F.; Auger, S.; Soutourina, O.; Barzu, O.; Yvon, M.; Danchin, A.; Martin-Verstraete, I.
Conversion of methionine to cysteine in Bacillus subtilis and its regulation
J. Bacteriol.
189
187-197
2007
Bacillus subtilis 168 (O34667), Bacillus subtilis (O34667)
Manually annotated by BRENDA team
Zhu, J.; Knottenbelt, S.; Kirk, M.L.; Pei, D.
Catalytic mechanism of S-ribosylhomocysteinase: ionization state of active-site residues
Biochemistry
45
12195-12203
2006
Bacillus subtilis (O34667), Escherichia coli, Escherichia coli (P45578), Vibrio harveyi (Q9Z5X1)
Manually annotated by BRENDA team
Wnuk, S.F.; Lalama, J.; Robert, J.; Garmendia, C.A.
Novel S-ribosylhomocysteine analogues as potential inhibitors of LuxS enzyme
Nucleosides Nucleotides Nucleic Acids
26
1051-1055
2007
Bacillus subtilis (O34667)
Manually annotated by BRENDA team
Gopishetty, B.; Zhu, J.; Rajan, R.; Sobczak, A.J.; Wnuk, S.F.; Bell, C.E.; Pei, D.
Probing the catalytic mechanism of S-ribosylhomocysteinase (LuxS) with catalytic intermediates and substrate analogues
J. Am. Chem. Soc.
131
1243-1250
2009
Bacillus subtilis, Escherichia coli, Vibrio harveyi
Manually annotated by BRENDA team
Hardie, K.R.; Heurlier, K.
Establishing bacterial communities by word of mouth: LuxS and autoinducer 2 in biofilm development
Nat. Rev. Microbiol.
6
635-643
2008
Bacillus subtilis, Campylobacter jejuni, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Serratia plymuthica, Staphylococcus aureus, Vibrio harveyi
Manually annotated by BRENDA team
Wnuk, S.F.; Robert, J.; Sobczak, A.J.; Meyers, B.P.; Malladi, V.L.; Zhu, J.; Gopishetty, B.; Pei, D.
Inhibition of S-ribosylhomocysteinase (LuxS) by substrate analogues modified at the ribosyl C-3 position
Bioorg. Med. Chem.
17
6699-6706
2009
Bacillus subtilis (O34667)
Manually annotated by BRENDA team
Bhattacharyya, M.; Vishveshwara, S.
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks
BMC Struct. Biol.
9
8
2009
Bacillus anthracis (Q81KF3), Bacillus cereus (Q816N5), Bacillus clausii (Q5WDW1), Bacillus subtilis (O34667), Bifidobacterium longum (Q8G568), Campylobacter jejuni (Q9PN97), Clostridium perfringens (Q0SWJ6), Deinococcus geothermalis (Q1IW42), Deinococcus radiodurans (Q9RRU8), Escherichia coli (Q8X902), Haemophilus influenzae (P44007), Helicobacter pylori (Q9ZMW8), Lactobacillus acidophilus (Q5FK48), Lactobacillus johnsonii (Q74HV0), Lactobacillus reuteri (Q5QHW1), Psychromonas ingrahamii (A1SZZ2), Shigella flexneri (Q83JZ4), Staphylococcus aureus (Q6GEU1), Staphylococcus epidermidis (Q8CNI0), Streptococcus mutans (Q8DVK8), Streptococcus pyogenes (P0C0C7), Thermus thermophilus (Q72IE6), Vibrio cholerae (Q9KUG4)
Manually annotated by BRENDA team
Malladi, V.L.; Sobczak, A.J.; Meyer, T.M.; Pei, D.; Wnuk, S.F.
Inhibition of LuxS by S-ribosylhomocysteine analogues containing a [4-aza]ribose ring
Bioorg. Med. Chem.
19
5507-5519
2011
Bacillus subtilis
Manually annotated by BRENDA team
Huang, W.; Gherib, R.; Gauld, J.W.
An active site water broadens substrate specificity in S-ribosylhomocysteinase (LuxS): a docking, MD, and QM/MM study
J. Phys. Chem. B
116
8916-8929
2012
Bacillus subtilis
Manually annotated by BRENDA team
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