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Escherichia coli K-12 substr. MG1655 Polypeptide: nitrite reductase, small subunit



Gene: nirD Accession Numbers: EG10655 (EcoCyc), b3366, ECK3354

Regulation Summary Diagram: ?

Component of: nitrite reductase (extended summary available)

Summary:
The nirD gene encodes the small subunit of the nitrite reductase. [Peakman90, Harborne92]

Gene Citations: [Peakman90a]

Locations: cytosol

Map Position: [3,494,573 -> 3,494,899] (75.32 centisomes)
Length: 327 bp / 108 aa

Molecular Weight of Polypeptide: 12.284 kD (from nucleotide sequence)

pI: 5.17

Unification Links: ASAP:ABE-0011005 , CGSC:35425 , EchoBASE:EB0649 , EcoGene:EG10655 , EcoliWiki:b3366 , ModBase:P0A9I8 , OU-Microarray:b3366 , PortEco:nirD , PR:PRO_000023391 , Pride:P0A9I8 , Protein Model Portal:P0A9I8 , RefSeq:NP_417825 , RegulonDB:EG10655 , SMR:P0A9I8 , String:511145.b3366 , UniProt:P0A9I8

Relationship Links: InterPro:IN-FAMILY:IPR012748 , InterPro:IN-FAMILY:IPR017881 , InterPro:IN-FAMILY:IPR017941 , PDB:Structure:2JO6 , Prosite:IN-FAMILY:PS51300

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Page90]
GO:0042128 - nitrate assimilation Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008942 - nitrite reductase [NAD(P)H] activity Inferred from experiment Inferred by computational analysis [GOA01a, Harborne92, Coleman78]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0009344 - nitrite reductase complex [NAD(P)H] Inferred from experiment [Harborne92]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for nirD knockouts: ?

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

Credits:
Last-Curated ? 30-Apr-2008 by Nolan L , Macquarie University


Subunit of: nitrite reductase

Synonyms: NirB

Subunit composition of nitrite reductase = [NirD][(NirB)2]
         nitrite reductase, small subunit = NirD (summary available)
         dimer of large subunit of nitrite reductase = (NirB)2
                 nitrite reductase, large subunit = NirB

Summary:
E. coli has two distinct nitrite reductases. Both enzymes reduce nitrite to ammonia. Their expresssion is complementary--with low concentrations of nitrate in the environment pentaheme nitrite reductase (NrfA) is made; with high concentrations of nitrate the NADH-dependent nitrite reductase (NirB) is made almost exclusively. At intermediate concentrations of nitrate, both are made. This regulation acts through the Nar regulatory circuit. Nitrite also induces the formation of both enzymes but it is a less effective inducer than nitrate by at least two orders of magnitude [Wang00].

NirB is located in the cytoplasm and does not generate a proton gradient. Its probable metabolic role is to detoxify nitrite. However, when cells are growing on high concentrations of nitrate (when NirB is active), nitrite nevertheless is excreted into the environment [Wang00].

NirB catalyzes the six-electron reduction of nitrite to ammonia and also catalyzes the two-electron reduction of hydroxylamine to ammonia. The prosthetic groups of nitrite reductase are FAD, an iron-sulfur cluster and siroheme [Jackson81, Macdonald85, Cammack82]. The product of the cysG gene is necessary for the synthesis of the siroheme prosthetic group of NirB. The reaction is active only during anaerobic growth and fulfills a dissimilatory rather than assimilatory role [Harborne92].

No NADH-dependent nitrite reductase activity was detected in E.coli strains lacking either NirB or NirD but a mixture of the two was as active as an extract from wild type [Harborne92]. Reconstitution of nitrite reductase activity in vitro required stoichiometric quantities of NirB and NirD, and NirD remained associated with NirB during the initial stages of enzyme purification suggesting that NirD is a structural subunit of the enzyme [Harborne92].

Locations: cytosol

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Page90]
Molecular Function: GO:0008942 - nitrite reductase [NAD(P)H] activity Inferred from experiment Inferred by computational analysis [GOA01, Coleman78, Jackson81a]
Cellular Component: GO:0009344 - nitrite reductase complex [NAD(P)H] Inferred from experiment [Harborne92]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA00]
GO:0005829 - cytosol

Credits:
Reviewed 17-Apr-2008 by Nolan L , Macquarie University
Last-Curated ? 30-Apr-2008 by Nolan L , Macquarie University


Enzymatic reaction of: nitrite reductase

Synonyms: nitrite reductase NADH, NADH:nitrite oxidoreductase

EC Number: 1.7.1.15

nitrite + 3 NADH + 5 H+ <=> ammonium + 3 NAD+ + 2 H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

Alternative Substrates for nitrite: ferricyanide [Jackson81 ] , oxidized DCPIP [Jackson81 ] , hydroxylamine [Jackson81 ]

Cofactors or Prosthetic Groups: siroheme [Jackson81], FAD [Jackson81], [FeS] iron-sulfur cluster [Jackson81, Cammack82]

Inhibitors (Unknown Mechanism): NAD+ [Comment 5] , p-chloromercuribenzoate [Coleman78] , sulfite [Coleman78] , arsenite [Coleman78] , hydrogen cyanide [Coleman78]

Kinetic Parameters:

Substrate
Km (μM)
Citations
NADH
48.8
[Jackson82, BRENDA14]
nitrite
11.0
[Jackson82, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 102
[Peakman90, Bell89a, UniProt10a]
Alternate sequence: G → D; UniProt: (in Ref. 1 and 2);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3366 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10655; 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

Bell89a: Bell AI, Gaston KL, Cole JA, Busby SJ (1989). "Cloning of binding sequences for the Escherichia coli transcription activators, FNR and CRP: location of bases involved in discrimination between FNR and CRP." Nucleic Acids Res 17(10);3865-74. PMID: 2543955

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

Cammack82: Cammack R, Jackson RH, Cornish-Bowden A, Cole JA (1982). "Electron-spin-resonance studies of the NADH-dependent nitrite reductase from Escherichia coli K12." Biochem J 207(2);333-9. PMID: 6297458

Coleman78: Coleman KJ, Cornish-Bowden A, Cole JA (1978). "Purification and properties of nitrite reductase from Escherichia coli K12." Biochem J 1978;175(2);483-93. PMID: 217342

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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."

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."

Harborne92: Harborne NR, Griffiths L, Busby SJ, Cole JA (1992). "Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon." Mol Microbiol 1992;6(19);2805-13. PMID: 1435259

Jackson81: Jackson RH, Cornish-Bowden A, Cole JA (1981). "Prosthetic groups of the NADH-dependent nitrite reductase from Escherichia coli K12." Biochem J 1981;193(3);861-7. PMID: 7030314

Jackson81a: Jackson RH, Cole JA, Cornish-Bowden A (1981). "The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction." Biochem J 1981;199(1);171-8. PMID: 6279095

Jackson82: Jackson RH, Cole JA, Cornish-Bowden A (1982). "The steady state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K12. The reduction of single-electron acceptors." Biochem J 203(2);505-10. PMID: 6288003

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

Macdonald85: Macdonald H, Cole J (1985). "Molecular cloning and functional analysis of the cysG and nirB genes of Escherichia coli K12, two closely-linked genes required for NADH-dependent nitrite reductase activity." Mol Gen Genet 1985;200(2);328-34. PMID: 2993824

Page90: Page L, Griffiths L, Cole JA (1990). "Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria." Arch Microbiol 1990;154(4);349-54. PMID: 2173895

Peakman90: Peakman T, Crouzet J, Mayaux JF, Busby S, Mohan S, Harborne N, Wootton J, Nicolson R, Cole J (1990). "Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome." Eur J Biochem 1990;191(2);315-23. PMID: 2200672

Peakman90a: Peakman T, Busby S, Cole J (1990). "Transcriptional control of the cysG gene of Escherichia coli K-12 during aerobic and anaerobic growth." Eur J Biochem 1990;191(2);325-31. PMID: 2200673

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

Wang00: Wang H, Gunsalus RP (2000). "The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite." J Bacteriol 182(20);5813-22. PMID: 11004182

Other References Related to Gene Regulation

Browning00: Browning DF, Cole JA, Busby SJ (2000). "Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly." Mol Microbiol 37(5);1258-69. PMID: 10972841

Browning04a: Browning DF, Cole JA, Busby SJ (2004). "Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter." Mol Microbiol 53(1);203-15. PMID: 15225315

Browning08: Browning DF, Cole JA, Busby SJ (2008). "Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter." J Bacteriol 190(21);7258-67. PMID: 18757534

Darwin97: Darwin AJ, Tyson KL, Busby SJ, Stewart V (1997). "Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement." Mol Microbiol 1997;25(3);583-95. PMID: 9302020

Eiglmeier89: Eiglmeier K, Honore N, Iuchi S, Lin EC, Cole ST (1989). "Molecular genetic analysis of FNR-dependent promoters." Mol Microbiol 1989;3(7);869-78. PMID: 2677602

Jayaraman87: Jayaraman PS, Peakman TC, Busby SJ, Quincey RV, Cole JA (1987). "Location and sequence of the promoter of the gene for the NADH-dependent nitrite reductase of Escherichia coli and its regulation by oxygen, the Fnr protein and nitrite." J Mol Biol 196(4);781-8. PMID: 2445993

Jayaraman88: Jayaraman PS, Gaston KL, Cole JA, Busby SJ (1988). "The nirB promoter of Escherichia coli: location of nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite." Mol Microbiol 1988;2(4);527-30. PMID: 2845227

Stewart03a: Stewart V, Bledsoe PJ (2003). "Synthetic lac operator substitutions for studying the nitrate- and nitrite-responsive NarX-NarL and NarQ-NarP two-component regulatory systems of Escherichia coli K-12." J Bacteriol 185(7);2104-11. PMID: 12644479

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

Tyson97: Tyson K, Busby S, Cole J (1997). "Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein." Arch Microbiol 1997;168(3);240-4. PMID: 9382703

Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183

Wu98: Wu H, Tyson KL, Cole JA, Busby SJ (1998). "Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors." Mol Microbiol 1998;27(2);493-505. PMID: 9484902

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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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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