Escherichia coli K-12 substr. MG1655 Polypeptide: subunit of periplasmic nitrate reductase, cytochrome c550 protein

Gene: napB Accession Numbers: EG12061 (EcoCyc), b2203, ECK2195

Synonyms: yejY, cytochrome c-type protein

Regulation Summary Diagram: ?

Regulation summary diagram for napB

Component of: periplasmic nitrate reductase (extended summary available)

The napB gene encodes the periplasmic diheme cytochrome c550 protein; it receives electrons from the membrane-bound proteins and passes them to NapA [IobbiNivol94, Grove96a, Grove96, Cole96]. E. coli NapA and NapB proteins do not purify as a heterodimeric complex [Jepson07].

Gene Citations: [Darwin95]

Locations: periplasmic space

Map Position: [2,296,291 <- 2,296,740] (49.49 centisomes, 178°)
Length: 450 bp / 149 aa

Molecular Weight of Polypeptide: 16.297 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007283 , CGSC:36560 , EchoBASE:EB1991 , EcoGene:EG12061 , EcoliWiki:b2203 , ModBase:P0ABL3 , OU-Microarray:b2203 , PortEco:napB , PR:PRO_000023346 , Protein Model Portal:P0ABL3 , RefSeq:NP_416707 , RegulonDB:EG12061 , SMR:P0ABL3 , String:511145.b2203 , Swiss-Model:P0ABL3 , UniProt:P0ABL3

Relationship Links: InterPro:IN-FAMILY:IPR005591 , InterPro:IN-FAMILY:IPR011031 , InterPro:IN-FAMILY:IPR027406 , Pfam:IN-FAMILY:PF03892 , Prosite:IN-FAMILY:PS51008

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for napB

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Potter99a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09, Grove96a]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers cytochromes
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron acceptors

Essentiality data for napB 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]

Subunit of: periplasmic nitrate reductase

Synonyms: Nap

Subunit composition of periplasmic nitrate reductase = [NapB][NapC][(NapG)(NapH)][NapA]
         subunit of periplasmic nitrate reductase, cytochrome c550 protein = NapB (summary available)
         periplasmic nitrate reductase, cytochrome c protein = NapC (summary available)
         NapGH, alternative quinol dehydrogenase = (NapG)(NapH) (summary available)
                 ferredoxin-type protein = NapG (summary available)
                 ferredoxin-type protein = NapH (summary available)
         large subunit of periplasmic nitrate reductase, molybdoprotein = NapA (summary available)

E. coli K-12 contains three nitrate reductases. Two of them, nitrate reductase A (NRA) and nitrate reductase Z (NRZ), are membrane bound and biochemically similar. The third nitrate reductase, Nap, is located in the periplasm. It is induced by anaerobiosis through the mediation of the transcription factor Fnr and low concentrations of nitrate through the mediation of NarP [McNicholas02]. Nap is not itself a coupling site for generating proton motive force; acting as a terminal electron acceptor, it does support anaerobic respiration of various carbon sources [Stewart02].

The physiological role of Nap is that of mediating anaerobic respiration at the expense of low concentrations of nitrate. Owing to the periplasmic location of Nap, the cost of pumping nitrate into the cell is avoided. In addition, Nap has a significantly higher affinity for nitrate than NRA and is thus able to exploit the low concentrations of nitrate occuring in the natural environment of E. coli [Potter99]. Notably, several pathogenic bacterial species, such as Haemophilus influenzae, only contain orthologs of the periplasmic nitrate reductase [Potter99]. During glucose fermentation in the absence of menaquinone, a very low level of Nap activity appears to substitute for the redox-balancing role of fumarate reductase, which is dependent on menaquinone [Brondijk04].

The nap operon encodes seven proteins. The catalytic portion of the protein, consisting of the periplasmic NapA and NapB polypeptides, receives electrons via the membrane-bound cytochrome NapC from NapGH or directly from the quinone pool. The NapD polypeptide is required for enzyme activity and is thought to be involved in the post-translational assembly of the molybdoprotein NapA. NapF, NapG and NapH are predicted to encode iron-sulfur proteins and are not required for Nap activity; they do, however, contribute to the maximum rate of nitrate reduction. NapG and NapH facilitate electron transfer from ubiquinol via NapC to NapAB. [Brondijk04, Brondijk02, Potter99a, Cole96, Grove96, Grove96a, IobbiNivol94]

nap: nitrate reductase in the periplasm [Grove96]

Citations: [Dow14]

Locations: periplasmic space

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space

Enzymatic reaction of: ubiquinol:nitrate oxidoreductase (periplasmic) (periplasmic nitrate reductase)

EC Number:

Transport reaction diagram for ubiquinol:nitrate oxidoreductase (periplasmic)

In Pathways: nitrate reduction X (periplasmic, dissimilatory)

Cofactors or Prosthetic Groups: heme c [Jepson07], a [4Fe-4S] iron-sulfur cluster [Jepson07], bis(guanylyl molybdopterin cofactor) [Jepson07]

Enzymatic reaction of: menaquinol:nitrate oxidoreductase (periplasmic) (periplasmic nitrate reductase)

EC Number:

Transport reaction diagram for menaquinol:nitrate oxidoreductase (periplasmic)

Sequence Features

Protein sequence of subunit of periplasmic nitrate reductase, cytochrome c550 protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 27
[Thomas99a, UniProt11a]
Chain 28 -> 149
UniProt: Diheme cytochrome c napB;
Metal-Binding-Site 69
UniProt: Iron (heme C 1 axial ligand); via tele nitrogen; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 83
UniProt: Heme 1 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 86
UniProt: Heme 1 (covalent); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 87
UniProt: Iron (heme 1 axial ligand); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 104
UniProt: Iron (heme C 2 axial ligand); via tele nitrogen; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 123
UniProt: Heme 2 (covalent); Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 126
UniProt: Heme 2 (covalent); Non-Experimental Qualifier: by similarity;
Sequence-Conflict 127 -> 149
[Richterich93, UniProt15]
UniProt: (in Ref. 1; AAA16395).
Metal-Binding-Site 127
UniProt: Iron (heme 2 axial ligand); Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2203 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12061; confirmed by SwissProt match.


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

Brondijk02: Brondijk TH, Fiegen D, Richardson DJ, Cole JA (2002). "Roles of NapF, NapG and NapH, subunits of the Escherichia coli periplasmic nitrate reductase, in ubiquinol oxidation." Mol Microbiol 44(1);245-55. PMID: 11967083

Brondijk04: Brondijk TH, Nilavongse A, Filenko N, Richardson DJ, Cole JA (2004). "NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing." Biochem J 379(Pt 1);47-55. PMID: 14674886

Cole96: Cole J (1996). "Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation?." FEMS Microbiol Lett 1996;136(1);1-11. PMID: 8919448

Darwin95: Darwin AJ, Stewart V (1995). "Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site." J Mol Biol 1995;251(1);15-29. PMID: 7643383

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

Dow14: Dow JM, Grahl S, Ward R, Evans R, Byron O, Norman DG, Palmer T, Sargent F (2014). "Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone." FEBS J 281(1);246-60. PMID: 24314029

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

Grove96: Grove J, Tanapongpipat S, Thomas G, Griffiths L, Crooke H, Cole J (1996). "Escherichia coli K-12 genes essential for the synthesis of c-type cytochromes and a third nitrate reductase located in the periplasm." Mol Microbiol 1996;19(3);467-81. PMID: 8830238

Grove96a: Grove J, Busby S, Cole J (1996). "The role of the genes nrf EFG and ccmFH in cytochrome c biosynthesis in Escherichia coli." Mol Gen Genet 1996;252(3);332-41. PMID: 8842153

IobbiNivol94: Iobbi-Nivol C, Crooke H, Griffiths L, Grove J, Hussain H, Pommier J, Mejean V, Cole JA (1994). "A reassessment of the range of c-type cytochromes synthesized by Escherichia coli K-12." FEMS Microbiol Lett 1994;119(1-2);89-94. PMID: 8039676

Jepson07: Jepson BJ, Mohan S, Clarke TA, Gates AJ, Cole JA, Butler CS, Butt JN, Hemmings AM, Richardson DJ (2007). "Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli." J Biol Chem 282(9);6425-37. PMID: 17130127

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

McNicholas02: McNicholas PM, Gunsalus RP (2002). "The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability." J Bacteriol 184(12);3253-9. PMID: 12029041

Potter99: Potter LC, Millington P, Griffiths L, Thomas GH, Cole JA (1999). "Competition between Escherichia coli strains expressing either a periplasmic or a membrane-bound nitrate reductase: does Nap confer a selective advantage during nitrate-limited growth?." Biochem J 344 Pt 1;77-84. PMID: 10548536

Potter99a: Potter LC, Cole JA (1999). "Essential roles for the products of the napABCD genes, but not napFGH, in periplasmic nitrate reduction by Escherichia coli K-12." Biochem J 1999;344 Pt 1;69-76. PMID: 10548535

Richterich93: Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. (1993). Data submission to EMBL/GenBank/DDBJ databases on 1993-10.

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Stewart02: Stewart V, Lu Y, Darwin AJ (2002). "Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12." J Bacteriol 184(5);1314-23. PMID: 11844760

Thomas99a: Thomas G, Potter L, Cole JA (1999). "The periplasmic nitrate reductase from Escherichia coli: a heterodimeric molybdoprotein with a double-arginine signal sequence and an unusual leader peptide cleavage site." FEMS Microbiol Lett 1999;174(1);167-71. PMID: 10234835

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: 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.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

Other References Related to Gene Regulation

Choe93: Choe M, Reznikoff WS (1993). "Identification of the regulatory sequence of anaerobically expressed locus aeg-46.5." J Bacteriol 1993;175(4);1165-72. PMID: 8432709

Darwin98: Darwin AJ, Ziegelhoffer EC, Kiley PJ, Stewart V (1998). "Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro." J Bacteriol 1998;180(16);4192-8. PMID: 9696769

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

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

Stewart03: Stewart V, Bledsoe PJ, Williams SB (2003). "Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12." J Bacteriol 185(19);5862-70. PMID: 13129959

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

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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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