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Escherichia coli K-12 substr. MG1655 Enzyme: alkanesulfonate monooxygenase, FMNH2-dependent

Gene: ssuD Accession Numbers: G6477 (EcoCyc), b0935, ECK0926

Synonyms: ssi6, ycbN

Regulation Summary Diagram

Regulation summary diagram for ssuD

Subunit composition of alkanesulfonate monooxygenase, FMNH2-dependent = [SsuD]4
         alkanesulfonate monooxygenase, FMNH2-dependent = SsuD

E. coli can utilize alkanesulfonates as a sulfur source for growth. The ssuD gene encodes an FMNH2-dependent alkanesulfonate monooxygenase with a broad substrate range. It is able to desulfonate C-2 to C-10 unsubstituted alkanesulfonates, substituted ethanesulfonic acids, N-phenyltaurine, 4-phenyl-1-butanesulfonic acid and certain sulfonated buffers. The best substrates for the monooxygenase were decanesulfonic acid, octanesulfonic acid and 1,3-dioxo-2-isoindolineethanesulfonic acid [Eichhorn99].

The ssuE-encoded NADPH-dependent FMN reductase provides the alkanesulfonate monooxygenase with FMNH2. The reductase and monooxygenase act as a two-component system [Eichhorn99]. The presence of SsuD and the octanesulfonate substrate changes the kinetics of FMN reduction catalyzed by SsuE [Gao05]. Further studies showed the formation of a stable complex between SsuD and SsuE, which changes the flavin environment of FMN-bound SsuE [Abdurachim06]. These results support a model for direct transfer of the reduced flavin from SsuE to SsuD.

A crystal structure of the enzyme has been solved at 2.3 Å resolution. Comparison of the structure to the related structure of LuxA allowed identification of a possible active site [Eichhorn02]. Kinetic studies indicate that ordered substrate binding, with the reduced flavin binding first, is important for SsuD catalytic activity [Zhan08]. The Cys54 residue may be involved in stabilizing the C4a-(hydro)-peroxyflavin reaction intermediate [Carpenter10]. An R227A mutant lacks catalytic activity; Arg227 may therefore be involved in proton abstraction in the active site [Robbins12]. The conserved Arg298 residue (position 297 in the mature polypeptide, within a dynamic loop region near the active site) is important for catalytic activity [Eichhorn99, Carpenter11]. Conformational changes in this loop region are required for catalysis; it appears to protect the reduced flavin cosubstrate from unproductive oxidation [Xiong12]. Molecular dynamics simulations have been performed to study the interactions between the SsuD active site and the substrates as well as the flavin cosubstrate [Ferrario12].

An ssuD null mutant can not grow on methanesulfonate or L-cysteate as the sole source of sulfur [Eichhorn01].

ssuD shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. An ssuD deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Kri14].

SsuD: "sulfonate-sulfur utilization" [vanDer99]

Reviews: [vanderPloeg01, Ellis11]

Map Position: [994,066 <- 995,211] (21.43 centisomes, 77°)
Length: 1146 bp / 381 aa

Molecular Weight of Polypeptide: 41.736 kD (from nucleotide sequence), 41.2 kD (experimental) [Eichhorn99]

Molecular Weight of Multimer: 181 kD (experimental) [Eichhorn99]

Unification Links: ASAP:ABE-0003178, DIP:DIP-10928N, EchoBASE:EB3470, EcoGene:EG13706, EcoliWiki:b0935, ModBase:P80645, OU-Microarray:b0935, PortEco:ssuD, PR:PRO_000023996, Protein Model Portal:P80645, RefSeq:NP_415455, RegulonDB:G6477, SMR:P80645, String:511145.b0935, UniProt:P80645

Relationship Links: InterPro:IN-FAMILY:IPR011251, InterPro:IN-FAMILY:IPR019911, PDB:Structure:1M41, PDB:Structure:1NQK, Pfam:IN-FAMILY:PF00296

In Paralogous Gene Group: 226 (2 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Instance reactions of [an alkylsulfonate + FMNH2 + oxygen → an aldehyde + sulfite + FMN + H2O + 2 H+] (
i1: 3-(N-morpholino)propanesulfonate + FMNH2 + oxygen → 3-(N-morpholino)propanal + sulfite + FMN + H2O + 2 H+ (

i2: isethionate + FMNH2 + oxygen → glycolaldehyde + sulfite + FMN + H2O + 2 H+ (

i3: 1-butanesulfonate + FMNH2 + oxygen → butanal + sulfite + FMN + H2O + 2 H+ (

Genetic Regulation Schematic

Genetic regulation schematic for ssuD

GO Terms:
Biological Process:
Inferred from experimentGO:0009408 - response to heat [Kri14]
Inferred from experimentGO:0046306 - alkanesulfonate catabolic process [vanDer99]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Abdurachim06]
Inferred from experimentInferred by computational analysisGO:0008726 - alkanesulfonate monooxygenase activity [GOA06, GOA01, GOA01a, Eichhorn99]
Inferred from experimentGO:0042802 - identical protein binding [Eichhorn99]
Inferred by computational analysisGO:0004497 - monooxygenase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [GOA01a]

MultiFun Terms: metabolismmetabolism of other compoundssulfur metabolism

Essentiality data for ssuD knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Last-Curated 10-Apr-2013 by Keseler I, SRI International

Enzymatic reaction of: alkanesulfonate monooxygenase

Inferred from experiment

EC Number:

an alkylsulfonate + FMNH2 + oxygen → an aldehyde + sulfite + FMN + H2O + 2 H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for an alkylsulfonate: octanesulfonate [Eichhorn99], hexanesulfonate [Eichhorn99], n-phenyltaurine [Eichhorn99], 2-(4-pyridyl)ethanesulfonate [Eichhorn99], 1,3-dioxo-2-isoindolineethanesulfonate [Eichhorn99], 4-phenyl-1-butanesulfonate [Eichhorn99], 3-(N-morpholino)propanesulfonate [Eichhorn99], decanesulfonate [Eichhorn99]

In Pathways: two-component alkanesulfonate monooxygenase

Kinetic parameters have been measured for various substrates and range from a Km of 35 µM for decanesulfonic acid to a Km of 1110 µM for PIPES [Eichhorn99]. The dissociation constants for FMNH2 and FMN are 0.32 and 10.2 µM, respectively [Zhan08].

Kinetic Parameters:
Substrate Km (μM) kcat (sec-1) Vmax (µmol mg-1 min-1) Citations
hexanesulfonate 95.0 2.3 [Eichhorn99]
1,3-dioxo-2-isoindolineethanesulfonate 114.0 4.1 [Eichhorn99]
decanesulfonate 35.0 1.4 [Eichhorn99]
2-(4-pyridyl)ethanesulfonate 139.0 3.8 [Eichhorn99]
4-phenyl-1-butanesulfonate 110.0 1.8 [Eichhorn99]
octanesulfonate 0.86 [Zhan08]
octanesulfonate 44.0 1.6 [Eichhorn99]
3-(N-morpholino)propanesulfonate 617.0 4.1 [Eichhorn99]
n-phenyltaurine 237.0 4.6 [Eichhorn99]

pH(opt): 7.2-8.5 [Robbins12]

Enzymatic reaction of: isethionate monooxygenase (alkanesulfonate monooxygenase, FMNH2-dependent)

Inferred from experiment

EC Number:

isethionate + FMNH2 + oxygen → glycolaldehyde + sulfite + FMN + H2O + 2 H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Imported from MetaCyc 04-May-2012 by Caspi R, SRI International

Sequence Features

Protein sequence of alkanesulfonate monooxygenase, FMNH2-dependent with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Inferred from experiment[Quadroni96]
UniProt: Removed.
Chain 2 -> 381
Author statement[UniProt15]
UniProt: Alkanesulfonate monooxygenase.
Pfam PF00296 5 -> 326
Inferred by computational analysis[Finn14]
Bac_luciferase : Luciferase-like monooxygenase
Sequence-Conflict 19
Inferred by curator[Quadroni96, UniProt15]
UniProt: (in Ref. 5; AA sequence).
Mutagenesis-Variant 298
Inferred from experiment[Eichhorn99]
UniProt: Loss of activity.
Extrinsic-Sequence-Variant 298
Author statement[UniProt15]
UniProt: In strain: K12 / MC4100; inactive..

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Abdurachim06: Abdurachim K, Ellis HR (2006). "Detection of protein-protein interactions in the alkanesulfonate monooxygenase system from Escherichia coli." J Bacteriol 188(23);8153-9. PMID: 16997955

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Carpenter10: Carpenter RA, Zhan X, Ellis HR (2010). "Catalytic role of a conserved cysteine residue in the desulfonation reaction by the alkanesulfonate monooxygenase enzyme." Biochim Biophys Acta 1804(1);97-105. PMID: 19770075

Carpenter11: Carpenter RA, Xiong J, Robbins JM, Ellis HR (2011). "Functional role of a conserved arginine residue located on a mobile loop of alkanesulfonate monooxygenase." Biochemistry 50(29);6469-77. PMID: 21671586

Eichhorn01: Eichhorn E, Leisinger T (2001). "Escherichia coli utilizes methanesulfonate and L-cysteate as sole sulfur sources for growth." FEMS Microbiol Lett 205(2);271-5. PMID: 11750815

Eichhorn02: Eichhorn E, Davey CA, Sargent DF, Leisinger T, Richmond TJ (2002). "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD." J Mol Biol 324(3);457-68. PMID: 12445781

Eichhorn99: Eichhorn E, van der Ploeg JR, Leisinger T (1999). "Characterization of a two-component alkanesulfonate monooxygenase from Escherichia coli." J Biol Chem 1999;274(38);26639-46. PMID: 10480865

Ellis11: Ellis HR (2011). "Mechanism for sulfur acquisition by the alkanesulfonate monooxygenase system." Bioorg Chem 39(5-6);178-84. PMID: 21880344

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Ferrario12: Ferrario V, Braiuca P, Tessaro P, Knapic L, Gruber C, Pleiss J, Ebert C, Eichhorn E, Gardossi L (2012). "Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase." J Biomol Struct Dyn 30(1);74-88. PMID: 22571434

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gao05: Gao B, Ellis HR (2005). "Altered mechanism of the alkanesulfonate FMN reductase with the monooxygenase enzyme." Biochem Biophys Res Commun 331(4);1137-45. PMID: 15882995

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kri14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Quadroni96: Quadroni M, Staudenmann W, Kertesz M, James P (1996). "Analysis of global responses by protein and peptide fingerprinting of proteins isolated by two-dimensional gel electrophoresis. Application to the sulfate-starvation response of Escherichia coli." Eur J Biochem 239(3);773-81. PMID: 8774726

Robbins12: Robbins JM, Ellis HR (2012). "Identification of critical steps governing the two-component alkanesulfonate monooxygenase catalytic mechanism." Biochemistry 51(32);6378-87. PMID: 22775358

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanDer99: van Der Ploeg JR, Iwanicka-Nowicka R, Bykowski T, Hryniewicz MM, Leisinger T (1999). "The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl." J Biol Chem 274(41);29358-65. PMID: 10506196

vanderPloeg01: van der Ploeg JR, Eichhorn E, Leisinger T (2001). "Sulfonate-sulfur metabolism and its regulation in Escherichia coli." Arch Microbiol 176(1-2);1-8. PMID: 11479697

Xiong12: Xiong J, Ellis HR (2012). "Deletional studies to investigate the functional role of a dynamic loop region of alkanesulfonate monooxygenase." Biochim Biophys Acta 1824(7);898-906. PMID: 22564769

Zhan08: Zhan X, Carpenter RA, Ellis HR (2008). "Catalytic importance of the substrate binding order for the FMNH2-dependent alkanesulfonate monooxygenase enzyme." Biochemistry 47(7);2221-30. PMID: 18198899

Other References Related to Gene Regulation

Bykowski02: Bykowski T, van der Ploeg JR, Iwanicka-Nowicka R, Hryniewicz MM (2002). "The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess." Mol Microbiol 43(5);1347-58. PMID: 11918818

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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