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Escherichia coli K-12 substr. MG1655 Polypeptide: dimethyl sulfoxide reductase, chain A



Gene: dmsA Accession Numbers: EG10232 (EcoCyc), b0894, ECK0885

Regulation Summary Diagram: ?

Component of: dimethyl sulfoxide reductase (summary available)

Summary:
This subunit contains the active site and the molybdenum cofactor [Rothery91].

DmsA contains a twin-arginine leader peptide which targets the protein to the membrane, although DmsA does not appear to be exported to the periplasm. The leader peptide is also essential for expression of DmsA and stability of the DmsAB dimer, and is cleaved between residues 45 and 46 [Bilous88, Sambasivarao00].

Gene Citations: [Tseng96, Tseng94]

Locations [Comment 1]: inner membrane

Map Position: [940,182 -> 942,626] (20.26 centisomes)
Length: 2445 bp / 814 aa

Molecular Weight of Polypeptide: 90.398 kD (from nucleotide sequence)

pI: 6.53

Unification Links: ASAP:ABE-0003044 , CGSC:17710 , DIP:DIP-9452N , EchoBASE:EB0228 , EcoGene:EG10232 , EcoliWiki:b0894 , Mint:MINT-8046334 , ModBase:P18775 , OU-Microarray:b0894 , PortEco:dmsA , PR:PRO_000022455 , Pride:P18775 , Protein Model Portal:P18775 , RefSeq:NP_415414 , RegulonDB:EG10232 , SMR:P18775 , String:511145.b0894 , UniProt:P18775

Relationship Links: InterPro:IN-FAMILY:IPR006311 , InterPro:IN-FAMILY:IPR006655 , InterPro:IN-FAMILY:IPR006656 , InterPro:IN-FAMILY:IPR006657 , InterPro:IN-FAMILY:IPR006963 , InterPro:IN-FAMILY:IPR009010 , InterPro:IN-FAMILY:IPR011888 , InterPro:IN-FAMILY:IPR019546 , InterPro:IN-FAMILY:IPR027467 , Pfam:IN-FAMILY:PF00384 , Pfam:IN-FAMILY:PF01568 , Pfam:IN-FAMILY:PF04879 , Prosite:IN-FAMILY:PS00490 , Prosite:IN-FAMILY:PS00551 , Prosite:IN-FAMILY:PS00932 , Prosite:IN-FAMILY:PS51318 , Prosite:IN-FAMILY:PS51669 , Smart:IN-FAMILY:SM00926

In Paralogous Gene Group: 222 (14 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Cotter89]
GO:0006810 - transport Inferred by computational analysis [GOA00]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005506 - iron ion binding Inferred from experiment [Rothery91]
GO:0005515 - protein binding Inferred from experiment [Chan10, Chan09, Kostecki10]
GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [GOA01a, Trieber94]
GO:0030151 - molybdenum ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Rothery91]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Rothery91]
GO:0009389 - dimethyl sulfoxide reductase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a, Gaudet10]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0009390 - dimethyl sulfoxide reductase complex Inferred from experiment [Weiner88]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, Gaudet10]

MultiFun Terms: cell structure membrane
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron acceptors

Essentiality data for dmsA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Credits:
Last-Curated ? 29-Apr-2008 by Nolan L , Macquarie University


Subunit of: dimethyl sulfoxide reductase

Synonyms: DMSO/TMAO reductase

Subunit composition of dimethyl sulfoxide reductase = [DmsA][DmsB][DmsC]
         dimethyl sulfoxide reductase, chain A = DmsA (summary available)
         dimethyl sulfoxide reductase, chain B = DmsB (summary available)
         dimethyl sulfoxide reductase, chain C = DmsC (summary available)

Summary:
Dimethyl sulfoxide (DMSO) reductase is a membrane-associated terminal electron transfer enzyme, catalyzing a step in an energy-transducing anaerobic electron transport chain. It reduces many other amine-N-oxides and methyl-sulfoxides, including trimethylamine N-oxide (TMAO), but is genetically distinct from other TMAO reductases [Cammack90, Sambasivarao91]. The enzyme contains a molybdenum cofactor, and four iron-sulfur clusters [Weiner88, Cammack90, Trieber94].

The enzyme functions anaerobically in the absence of nitrate (a preferred terminal electron acceptor). Anaerobiosis stimulates its expression 100-fold, an effect controlled by the Fnr regulatory protein [Cotter89].

Locations [Comment 6]: inner membrane, cytosol

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Cotter89]
GO:0006810 - transport Inferred by computational analysis [GOA00]
Molecular Function: GO:0009389 - dimethyl sulfoxide reductase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0009390 - dimethyl sulfoxide reductase complex Inferred from experiment [Weiner88]
GO:0005829 - cytosol
GO:0005886 - plasma membrane
GO:0016020 - membrane Inferred by computational analysis [GOA00]

Credits:
Reviewed 16-Apr-2008 by Nolan L , Macquarie University
Last-Curated ? 29-Apr-2008 by Nolan L , Macquarie University


Enzymatic reaction of: dimethyl sulfoxide reductase

Synonyms: DMSO reductase

EC Number: 1.8.5.3

Alternative Substrates for dimethyl sulfoxide [Comment 7 ]: adenosine-N1-oxide [Weiner88 ] , pyridine-N-oxide [Weiner88 ] , nicotinic acid N-oxide [Weiner88 ] , picolinic acid-N-oxide [Weiner88 ] , α-picoline N-oxide [Weiner88 ] , hydroxypyridine N-oxide [Weiner88 ] , nicotinamide N-oxide [Weiner88 ] , 3-picoline N-oxide [Weiner88 ] , 4-picoline N-oxide [Weiner88 ] , trimethylamine N-oxide [Weiner88 ] , tetrahydrothiophene 1-oxide [Weiner88 ] , L-methionine S-oxide , methyl phenyl sulfoxide , phenyl sulfoxide , hydroxylamine , chlorate

In Pathways: formate to dimethyl sulfoxide electron transfer , NADH to dimethyl sulfoxide electron transfer

Summary:
The representation of the DMSO reductase complex indiates transfer of protons across the membrane where protons from MQH2 are moved from the cytoplasmic side to the periplasmic side of the cytoplasmic membrane. This representation has not been experimentally established and is therefore speculative.

Cofactors or Prosthetic Groups: Mo2+

Activators (Unknown Mechanism): Fe2+ [Weiner88]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
dimethyl sulfoxide
180.0
79.9
[SimalaGrant96, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 45
[Bilous88, UniProt11]
UniProt: Tat-type signal.
Mutagenesis-Variant 17
[Sambasivarao00, Kostecki10, UniProt12]
Alternate sequence: R → S; UniProt: Not targeted to the membrane, does not support anaerobic growth.
Chain 46 -> 814
[UniProt09]
UniProt: Anaerobic dimethyl sulfoxide reductase chain A;
Conserved-Region 56 -> 118
[UniProt13]
UniProt: 4Fe-4S Mo/W bis-MGD-type.
Mutagenesis-Variant 57
[Trieber94, Kostecki10, UniProt12]
Alternate sequence: K → D; UniProt: No alteration of the growth, expression, or catalytic activities.
Metal-Binding-Site 63
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 67
[Rothery99, Trieber94, Kostecki10, UniProt12]
Alternate sequence: C → S; UniProt: Electron transfer from the 4Fe-4S clusters of DmsB to the Mo-bisMGD of DmsA is blocked. Little effect on the coordination sphere of the molybdenum and only minor effects on its redox chemistry.
Metal-Binding-Site 67
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 71
[Trieber94, Kostecki10, UniProt12]
Alternate sequence: C → S; UniProt: Can not support growth.
Metal-Binding-Site 71
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 104
[Trieber94, Kostecki10, UniProt12]
Alternate sequence: C → S; UniProt: No alteration of the growth, expression, or catalytic activities.
Metal-Binding-Site 104
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 106
[Rothery99, Trieber94, Kostecki10, UniProt12]
Alternate sequence: R → S; UniProt: Electron transfer from the 4Fe-4S clusters of DmsB to the Mo-bisMGD of DmsA is blocked. Little effect on the coordination sphere of the molybdenum and only minor effects on its redox chemistry.
Protein-Segment 172 -> 176
[UniProt12a]
UniProt: Molybdopterin 1 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 205
[UniProt13]
UniProt: Molybdenum; Non-Experimental Qualifier: by similarity.
Protein-Segment 244 -> 245
[UniProt12a]
UniProt: Molybdopterin 2 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 270 -> 271
[UniProt12a]
UniProt: Molybdopterin 2 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 291 -> 293
[UniProt12a]
UniProt: Molybdopterin 2 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 386 -> 387
[UniProt12a]
UniProt: Molybdopterin 2 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 390
[UniProt12a]
UniProt: Molybdopterin 1; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 488
[UniProt12a]
UniProt: Molybdopterin 1; Non-Experimental Qualifier: by similarity.
Protein-Segment 512 -> 513
[UniProt12a]
UniProt: Molybdopterin 1 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 701
[UniProt12a]
UniProt: Molybdopterin 1 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 707 -> 709
[UniProt12a]
UniProt: Molybdopterin 1 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 788
[UniProt12a]
UniProt: Molybdopterin 1; Non-Experimental Qualifier: by similarity.
Protein-Segment 804 -> 805
[UniProt12a]
UniProt: Molybdopterin 1 binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Ingrid Keseler on Thu Mar 3, 2005:
Location of initiating methionine corrected according to Sambasivarao et al., J. Biol. Chem. 275: 22526-22531 (2000).
10/20/97 Gene b0894 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10232; confirmed by SwissProt match.


References

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

Bilous88: Bilous PT, Cole ST, Anderson WF, Weiner JH (1988). "Nucleotide sequence of the dmsABC operon encoding the anaerobic dimethylsulphoxide reductase of Escherichia coli." Mol Microbiol 2(6);785-95. PMID: 3062312

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Cammack90: Cammack R, Weiner JH (1990). "Electron paramagnetic resonance spectroscopic characterization of dimethyl sulfoxide reductase of Escherichia coli." Biochemistry 1990;29(36);8410-6. PMID: 2174699

Chan09: Chan CS, Chang L, Rommens KL, Turner RJ (2009). "Differential interactions between Tat-specific redox enzyme peptides and their chaperones." J Bacteriol 191(7):2091-101. PMID: 19151138

Chan10: Chan CS, Chang L, Winstone TM, Turner RJ (2010). "Comparing system-specific chaperone interactions with their Tat dependent redox enzyme substrates." FEBS Lett 584(22);4553-8. PMID: 20974141

Cotter89: Cotter PA, Gunsalus RP (1989). "Oxygen, nitrate, and molybdenum regulation of dmsABC gene expression in Escherichia coli." J Bacteriol 171(7);3817-23. PMID: 2544558

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

GOA00: GOA (2000). "Gene Ontology annotation based on Swiss-Prot keyword mapping."

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

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

Kostecki10: Kostecki JS, Li H, Turner RJ, DeLisa MP (2010). "Visualizing interactions along the Escherichia coli twin-arginine translocation pathway using protein fragment complementation." PLoS One 5(2);e9225. PMID: 20169075

Rothery91: Rothery RA, Weiner JH (1991). "Alteration of the iron-sulfur cluster composition of Escherichia coli dimethyl sulfoxide reductase by site-directed mutagenesis." Biochemistry 1991;30(34);8296-305. PMID: 1653010

Rothery99: Rothery RA, Trieber CA, Weiner JH (1999). "Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase." J Biol Chem 274(19);13002-9. PMID: 10224050

Sambasivarao00: Sambasivarao D, Turner RJ, Simala-Grant JL, Shaw G, Hu J, Weiner JH (2000). "Multiple roles for the twin arginine leader sequence of dimethyl sulfoxide reductase of Escherichia coli." J Biol Chem 275(29);22526-31. PMID: 10801884

Sambasivarao90: Sambasivarao D, Scraba DG, Trieber C, Weiner JH (1990). "Organization of dimethyl sulfoxide reductase in the plasma membrane of Escherichia coli." J Bacteriol 1990;172(10);5938-48. PMID: 2170332

Sambasivarao91: Sambasivarao D, Weiner JH (1991). "Dimethyl sulfoxide reductase of Escherichia coli: an investigation of function and assembly by use of in vivo complementation." J Bacteriol 1991;173(19);5935-43. PMID: 1917829

SimalaGrant96: Simala-Grant JL, Weiner JH (1996). "Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase." Microbiology 142 ( Pt 11);3231-9. PMID: 8969520

Trieber94: Trieber CA, Rothery RA, Weiner JH (1994). "Multiple pathways of electron transfer in dimethyl sulfoxide reductase of Escherichia coli." J Biol Chem 1994;269(10);7103-9. PMID: 8125918

Tseng94: Tseng CP, Hansen AK, Cotter P, Gunsalus RP (1994). "Effect of cell growth rate on expression of the anaerobic respiratory pathway operons frdABCD, dmsABC, and narGHJI of Escherichia coli." J Bacteriol 1994;176(21);6599-605. PMID: 7961411

Tseng96: Tseng CP, Albrecht J, Gunsalus RP (1996). "Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli." J Bacteriol 1996;178(4);1094-8. PMID: 8576043

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Weiner88: Weiner JH, MacIsaac DP, Bishop RE, Bilous PT (1988). "Purification and properties of Escherichia coli dimethyl sulfoxide reductase, an iron-sulfur molybdoenzyme with broad substrate specificity." J Bacteriol 1988;170(4);1505-10. PMID: 3280546

Other References Related to Gene Regulation

Bearson02: Bearson SM, Albrecht JA, Gunsalus RP (2002). "Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions." BMC Microbiol 2(1);13. PMID: 12079504

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Lamberg00: Lamberg KE, Kiley PJ (2000). "FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3." Mol Microbiol 38(4);817-27. PMID: 11115116

McNicholas98: McNicholas PM, Chiang RC, Gunsalus RP (1998). "Anaerobic regulation of the Escherichia coli dmsABC operon requires the molybdate-responsive regulator ModE." Mol Microbiol 27(1);197-208. PMID: 9466267

Melville96: Melville SB, Gunsalus RP (1996). "Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes." Proc Natl Acad Sci U S A 93(3);1226-31. PMID: 8577745

Pruss01: Pruss BM, Liu X, Hendrickson W, Matsumura P (2001). "FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions." FEMS Microbiol Lett 2001;197(1);91-7. PMID: 11287152

Tyson93: Tyson KL, Bell AI, Cole JA, Busby SJ (1993). "Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL." Mol Microbiol 1993;7(1);151-7. PMID: 8437517

Zhang13: Zhang HK, Lu H, Wang J, Liu GF, Zhou JT, Xu MY (2013). "Global transcriptome analysis of Escherichia coli exposed to immobilized anthraquinone-2-sulfonate and azo dye under anaerobic conditions." Appl Microbiol Biotechnol 97(15);6895-905. PMID: 23820558


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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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