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Information on EC 4.4.1.21 - S-ribosylhomocysteine lyase and Organism(s) Escherichia coli

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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:
Escherichia coli
Word Map
The taxonomic range for the selected organisms is: Escherichia coli
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
S-ribosylhomocysteinase
S-ribosylhomocysteine lyase
S-ribosylhomocysteinelyase
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C-S bond cleavage
-
-
additional information
-
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
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 + (S)-4,5-dihydroxypentan-2,3-dione
show the reaction diagram
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
additional information
?
-
-
LuxS is required for normal biofilm development
-
-
-
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-ribosylhomocysteine
L-homocysteine + 4,5-dihydroxy-2,3-pentanedione
show the reaction diagram
additional information
?
-
-
LuxS is required for normal biofilm development
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
-
Zn2+ substitution produces an enzyme with 10-fold lower activity
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
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-
D-erythronohydroxamic acid
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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
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-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.027
(2R)-2-amino-4-[[(2S,4S)-2,4,5-trihydroxy-3-oxopentyl]sulfanyl]butanoic acid
-
wild type enzyme
0.016 - 0.037
S-ribosylhomocysteine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
(2R)-2-amino-4-[[(2S,4S)-2,4,5-trihydroxy-3-oxopentyl]sulfanyl]butanoic acid
-
wild type enzyme
0.4
S-ribosylhomocysteine
-
wild type enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0127
(2S)-2-amino-4-[(2R,3R)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
-
Co2+ substituted enzyme
0.0032
(2S)-2-amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoylpropylmercapto] butyric acid
-
Co2+ substituted enzyme
0.72
D-erythronohydroxamic acid
-
Co2+ substituted enzyme
0.047
S-[3-bromo-3,5-dideoxy-D-ribofuranos-5-yl]-L-homocysteine
-
wild type enzyme
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
mutation affects motility/flagella formation/metabolism
physiological function
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mutation of luxS leads to profound differences in activated methyl cycle metabolite concentrations. Unable to metabolize these substrates, the concentration of S-ribosylhomocysteine continues to accrue throughout their growth. By the stationary phase, the concentration of ribosylhomocysteine in the DELTAluxS mutant is approximately 460fold higher when compared with that in the wild-type strain. Homocysteine is significantly lower in the mutant when compared with the wild-type
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
A0A1Y2YCU9_ECOLX
171
0
19460
TrEMBL
A0A4T4NWB2_ECOLX
171
0
19402
TrEMBL
A0A376D3C4_ECOLX
108
0
12352
TrEMBL
A0A3K0UC65_ECOLX
171
0
19430
TrEMBL
A0A5E9ZYL6_ECOLX
171
0
19433
TrEMBL
A0A0K6DC98_ECOLX
171
0
19401
TrEMBL
A0A0K4SB60_ECOLX
171
0
19357
TrEMBL
A0A377FJ40_ECOLX
171
0
19442
TrEMBL
J7QGW0_ECOLX
171
0
19430
TrEMBL
C3SY42_ECOLX
171
0
19444
TrEMBL
A0A4U9U5C7_ECOLX
156
0
17514
TrEMBL
A0A4V6LXZ6_ECOLX
171
0
19454
TrEMBL
A0A3Z3EQV8_ECOLX
171
0
19415
TrEMBL
A0A5B9ARD5_ECOLX
171
0
19386
TrEMBL
A0A066RNM3_ECOLX
171
0
19417
TrEMBL
F2XHH9_ECOLX
171
0
19416
TrEMBL
A0A3Q0P292_ECOLX
171
0
19442
TrEMBL
A0A449CDZ1_ECOLX
171
0
19471
TrEMBL
A0A2K3TQ94_ECOLX
171
0
19427
TrEMBL
A0A370YTU1_ECOLX
151
0
16868
TrEMBL
E2QQE1_ECOLX
171
0
19443
TrEMBL
A0A3K3INN3_ECOLX
171
0
19489
TrEMBL
A0A418H3G4_ECOLX
71
0
8046
TrEMBL
A0A3L0VXR5_ECOLX
169
0
18791
TrEMBL
A0A376I224_ECOLX
171
0
19364
TrEMBL
A0A418GS41_ECOLX
133
0
14997
TrEMBL
A0A210GFX1_ECOLX
171
0
19385
TrEMBL
A0A5E8HN61_ECOLX
171
0
19391
TrEMBL
A0A376D4K4_ECOLX
72
1
8043
TrEMBL
A0A0L1C2M1_ECOLX
171
0
19431
TrEMBL
A0A370YMZ1_ECOLX
171
0
19283
TrEMBL
Q6A197_ECOLX
142
0
16055
TrEMBL
A0A2T1LGJ0_ECOLX
171
0
19339
TrEMBL
A0A3W4SPP7_ECOLX
171
0
19446
TrEMBL
A0A4Y9C710_ECOLX
171
0
19189
TrEMBL
A0A0K4BFT8_ECOLX
171
0
19402
TrEMBL
A0A5P0LWU7_ECOLX
171
0
19389
TrEMBL
A0A376HPL1_ECOLX
171
0
19388
TrEMBL
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12500
-
3 * 12500
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
-
3 * 12500
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C41A
-
by site directed mutagenesis
C83D
-
by site directed mutagenesis
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Q-Sepharose Fast-Flow column chromatography and ultrafiltration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
as lsrR knockout by chromosomal gene replacement
LuxS variants are overexpressed in Escherichia coli in their Fe2+, Zn2+- and Co2+-substituted forms
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mutant LuxS variants are overexpressed in Escherichia coli in both Zn2+- and Co2+-substituted forms
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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rapid, selective, and sensitive liquid chromatography-tandem mass spectrometry assay for the simultaneous quantification of the metabolites and precursors of the activated methyl cycle. Analytes are extracted from Escherichia coli MG1655 and chemically derivatized as N(O,S)-iso-butyloxycarbonyl iso-butyl esters using iso-butyl chloroformate in an aqueous iso-butanol/pyridine environment. S-Adenosylmethionine, S-adenosylhomocysteine, S-ribosylhomocysteine, homocysteine, methionine, cystathionine, cysteine, and homoserine are quantified by liquid chromatography-positive ion tandem electrospray ionization mass spectrometry. Internal standards are isotopically labeled [13CD3]methionine and S-adenosylcysteine. Linearity of the assay is established up to a concentration of 700 microg/g cell dry weight for each analyte
medicine
autoinducer-2 promotes interspecies signaling, the autoinducer-3 activates enterohemorrhagic Escherichia coli virulence genes, knocking out luxS in the enterohemorrhagic human pathogen Escherichia coli reveals a defect in AI-3 production, but not in AI-2 production
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Anand, S.K.; Griffiths, M.W.
Quorum sensing and expression of virulence in Escherichia coli O157:H7
Int. J. Food Microbiol.
85
1-9
2003
Escherichia coli
Manually annotated by BRENDA team
Winzer, K.; Hardie, K.R.; Burgess, N.; Doherty, N.; Kirke, D.; Holden, M.T.; Linforth, R.; Cornell, K.A.; Taylor, A.J.; Hill, P.J.; Williams, P.
LuxS: its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2H)-furanone
Microbiology
148
909-922
2002
Escherichia coli, Neisseria meningitidis, no activity in Pseudomonas aeruginosa, Porphyromonas gingivalis, Staphylococcus aureus
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
Walters, M.; Sircili, M.P.; Sperandio, V.
AI-3 synthesis is not dependent on luxS in Escherichia coli
J. Bacteriol.
188
5668-5681
2006
Escherichia coli (Q8X902)
Manually annotated by BRENDA team
Shen, G.; Rajan, R.; Zhu, J.; Bell, C.E.; Pei, D.
Design and synthesis of substrate and intermediate analogue inhibitors of S-ribosylhomocysteinase
J. Med. Chem.
49
3003-3011
2006
Escherichia coli (P45578)
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
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
Halliday, N.M.; Hardie, K.R.; Williams, P.; Winzer, K.; Barrett, D.A.
Quantitative liquid chromatography-tandem mass spectrometry profiling of activated methyl cycle metabolites involved in LuxS-dependent quorum sensing in Escherichia coli
Anal. Biochem.
403
20-29
2010
Escherichia coli
Manually annotated by BRENDA team
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