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Escherichia coli K-12 substr. MG1655 Polypeptide: nitrate reductase Z, β subunit




Gene: narY Accession Numbers: EG10647 (EcoCyc), b1467, ECK1461

Synonyms: chlZ

Regulation Summary Diagram

Regulation summary diagram for narY

Component of: nitrate reductase Z (extended summary available)

Summary:
narY encodes the β subunit of nitrate reductase Z; sequence analysis shows it has 75% identity with narH (which encodes the β subunit of nitrate reductase A); it is predicted to contain the iron-sulfur clusters [Blasco92] - one [3Fe-4S] cluster (FS4) and three [4Fe-4S] clusters (FS1, FS2 and FS3)

Gene Citations: [Bonnefoy94]

Locations: cytosol, inner membrane

Map Position: [1,535,333 <- 1,536,877] (33.09 centisomes, 119°)
Length: 1545 bp / 514 aa

Molecular Weight of Polypeptide: 58.558 kD (from nucleotide sequence)

pI: 5.91

Isozyme Sequence Similarity:
nitrate reductase A, β subunit: YES

Unification Links: ASAP:ABE-0004896, CGSC:32142, DIP:DIP-10323N, EchoBASE:EB0641, EcoGene:EG10647, EcoliWiki:b1467, Mint:MINT-1251788, ModBase:P19318, OU-Microarray:b1467, PortEco:narY, PR:PRO_000023363, Pride:P19318, Protein Model Portal:P19318, RefSeq:NP_415984, RegulonDB:EG10647, SMR:P19318, String:511145.b1467, Swiss-Model:P19318, UniProt:P19318

Relationship Links: InterPro:IN-FAMILY:IPR006547, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR029263, Pfam:IN-FAMILY:PF13247, Pfam:IN-FAMILY:PF14711, Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 223 (21 members)

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0009061 - anaerobic respiration [Iobbi87]
Inferred from experimentGO:0019645 - anaerobic electron transport chain [Iobbi87]
Inferred by computational analysisGO:0042126 - nitrate metabolic process [GOA01a]
Inferred by computational analysisGO:0042128 - nitrate assimilation [UniProtGOA11a]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rajagopala14, Butland05]
Inferred from experimentInferred by computational analysisGO:0008940 - nitrate reductase activity [GOA01, GOA01a, IobbiNivol90]
Inferred by computational analysisGO:0009055 - electron carrier activity [Blasco90]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, Blasco90]
Inferred by computational analysisGO:0051538 - 3 iron, 4 sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0009325 - nitrate reductase complex [GOA01a, IobbiNivol90]
Inferred by computational analysisGO:0005737 - cytoplasm [Gaudet10]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, Gaudet10]

MultiFun Terms: metabolismenergy metabolism, carbonanaerobic respiration
metabolismenergy production/transportelectron acceptors

Essentiality data for narY 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]

Credits:
Curated 29-Apr-2008 by Nolan L, Macquarie University
Last-Curated 07-Dec-2014 by Mackie A, Macquarie University


Subunit of: nitrate reductase Z

Synonyms: NRZ, quinol:nitrate oxidoreductase

Subunit composition of nitrate reductase Z = [NarY][NarZ][NarV]
         nitrate reductase Z, β subunit = NarY (summary available)
         nitrate reductase Z, α subunit = NarZ (summary available)
         nitrate reductase Z, γ subunit = NarV (summary available)

Summary:
Nitrate reductase Z (NRZ) is a membrane bound molybdoenzyme responsible for the weak nitrate reductase activity present when cells are grown aerobically in a nitrate containing medium [Iobbi87].

By homology whith nitrate reductase A, nitrate reductase Z is a heterotrimer composed of the α (NarZ), β (NarY) and γ (NarV) chains. A fourth polypeptide, encoded by narW, is required for the incorporation of the molybdenum cofactor into the α subunit [Blasco90, Blasco92].

NRZ is constitutively expressed in a strain which carries the operon on a multicopy plasmid [Iobbi87]; NRZ is repressed by Fnr in anaerobiosis; NRZ is only slightly induced by nitrate; NRZ may function during the aerobic to anaerobic transition when cells are growing in the presence of nitrate [IobbiNivol90]. During entry into stationary phase, transcription of the narZYWV operon is induced, and induction is mainly dependent on the alternative sigma factor RpoS [Chang99].

Nitrate reductase Z also has tellurite reductase activity in wild-type E. coli [Avazeri97].

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 but differentially regulated (reviewed by [Bonnefoy94]. The third nitrate reductase, Nap is located in the periplasm.

Citations: [Showe68]

Locations: inner membrane


GO Terms:
Biological Process:
Inferred from experimentGO:0009061 - anaerobic respiration [Iobbi87, IobbiNivol90]
Inferred from experimentGO:0019645 - anaerobic electron transport chain [Iobbi87]
Inferred by computational analysisGO:0006810 - transport [GOA00]
Molecular Function:
Inferred by computational analysisInferred from experimentGO:0008940 - nitrate reductase activity [Iobbi87, IobbiNivol90, Blasco92, GOA01a, GOA01]
Inferred from experimentGO:0009055 - electron carrier activity [Guigliarelli92, IobbiNivol90]
Inferred from experimentGO:0043546 - molybdopterin cofactor binding [Iobbi87, IobbiNivol90]
Inferred from experimentGO:0051536 - iron-sulfur cluster binding [IobbiNivol90]
Inferred from experimentGO:0051538 - 3 iron, 4 sulfur cluster binding [Guigliarelli92]
Inferred from experimentGO:0051539 - 4 iron, 4 sulfur cluster binding [Guigliarelli92]
Cellular Component:
Inferred by computational analysisInferred from experimentGO:0009325 - nitrate reductase complex [IobbiNivol90, GOA01a]
Inferred by computational analysisInferred from experimentGO:0016020 - membrane [Iobbi87, Blasco92, GOA00]
Inferred by curatorGO:0005886 - plasma membrane []

Credits:
Revised 07-Dec-2014 by Mackie A, Macquarie University
Last-Curated 29-Apr-2008 by Nolan L, Macquarie University


Enzymatic reaction of: nitrate reductase

Inferred from experiment

Synonyms: respiratory nitrate reductase, nitrite:(acceptor) oxidoreductase

EC Number: 1.7.5.1

Transport reaction diagram for nitrate reductase

Alternative Substrates for nitrate: chlorate [Iobbi87]

In Pathways: nitrate reduction III (dissimilatory), nitrate reduction VIII (dissimilatory), nitrate reduction IX (dissimilatory)

Cofactors or Prosthetic Groups: bis(guanylyl molybdopterin cofactor) [Iobbi87], an iron-sulfur cluster [Iobbi87]

Inhibitors (Unknown Mechanism): 2-n-heptyl-4-hydroxyquinoline-N-oxide [IobbiNivol90], p-chloromercuribenzoate [IobbiNivol90], azide [IobbiNivol90], potassium cyanide [Iobbi87]

Enzymatic reaction of: tellurite reductase (nitrate reductase Z)

Inferred from experiment

EC Number: 1.97.1.-

tellurite + an reduced unknown electron acceptor → Te0 + an oxidized unknown electron acceptor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Summary:
Tellurite reductase activity was measured with benzyl viologen as an electron donor [Avazeri97].


Sequence Features

Protein sequence of nitrate reductase Z, beta subunit with features indicated

Feature Class Location Common Name Citations Comment
Conserved-Region 7 -> 35  
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 1.
Metal-Binding-Site 16  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 16, 19, 22, 262 FS1
Inferred by computational analysisInferred by curator[Blasco90]
[4Fe-4S] coordination; FS1
Metal-Binding-Site 19  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 22  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 26  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 26, 243, 246, 258 FS2
Inferred by computational analysisInferred by curator[Blasco90]
[4Fe-4S] coordination, FS2
Conserved-Region 174 -> 205  
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 2.
Metal-Binding-Site 183  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 183, 186, 191, 226 FS3
Inferred by computational analysisInferred by curator[Blasco90]
[4Fe-4S] corodination, FS3
Metal-Binding-Site 186  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 191  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 195  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (3Fe-4S).
Metal-Binding-Site 195, 216, 219, 222 FS4
Inferred by computational analysisInferred by curator[Blasco90]
[3Fe-4S] coordination, FS4
Conserved-Region 207 -> 236  
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 3.
Metal-Binding-Site 216  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (3Fe-4S).
Metal-Binding-Site 222  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (3Fe-4S).
Metal-Binding-Site 226  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 243  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 246  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 258  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 262  
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Sequence-Conflict 325 -> 326  
Inferred by curator[Blasco90, UniProt15]
UniProt: (in Ref. 1; CAA34965).


Sequence Pfam Features

Protein sequence of nitrate reductase Z, beta subunit with features indicated

Feature Class Location Citations Comment
Pfam PF13247 175 -> 271
Inferred by computational analysis[Finn14]
Fer4_11 : 4Fe-4S dicluster domain
Pfam PF14711 358 -> 436
Inferred by computational analysis[Finn14]
Nitr_red_bet_C : Respiratory nitrate reductase beta C-terminal


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

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b1467 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10647; confirmed by SwissProt match.


References

Avazeri97: Avazeri C, Turner RJ, Pommier J, Weiner JH, Giordano G, Vermeglio A (1997). "Tellurite reductase activity of nitrate reductase is responsible for the basal resistance of Escherichia coli to tellurite." Microbiology 143 ( Pt 4);1181-9. PMID: 9141681

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

Blasco90: Blasco F, Iobbi C, Ratouchniak J, Bonnefoy V, Chippaux M (1990). "Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon." Mol Gen Genet 1990;222(1);104-11. PMID: 2233673

Blasco92: Blasco F, Pommier J, Augier V, Chippaux M, Giordano G (1992). "Involvement of the narJ or narW gene product in the formation of active nitrate reductase in Escherichia coli." Mol Microbiol 1992;6(2);221-30. PMID: 1545706

Bonnefoy94: Bonnefoy V, Demoss JA (1994). "Nitrate reductases in Escherichia coli." Antonie Van Leeuwenhoek 1994;66(1-3);47-56. PMID: 7747940

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chang99: Chang L, Wei LI, Audia JP, Morton RA, Schellhorn HE (1999). "Expression of the Escherichia coli NRZ nitrate reductase is highly growth phase dependent and is controlled by RpoS, the alternative vegetative sigma factor." Mol Microbiol 34(4);756-66. PMID: 10564515

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

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

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."

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."

Guigliarelli92: Guigliarelli B, Asso M, More C, Augier V, Blasco F, Pommier J, Giordano G, Bertrand P (1992). "EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism." Eur J Biochem 207(1);61-8. PMID: 1321049

Iobbi87: Iobbi C, Santini CL, Bonnefoy V, Giordano G (1987). "Biochemical and immunological evidence for a second nitrate reductase in Escherichia coli K12." Eur J Biochem 1987;168(2);451-9. PMID: 3311749

IobbiNivol90: Iobbi-Nivol C, Santini CL, Blasco F, Giordano G (1990). "Purification and further characterization of the second nitrate reductase of Escherichia coli K12." Eur J Biochem 188(3);679-87. PMID: 2139607

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Showe68: Showe MK, DeMoss JA (1968). "Localization and regulation of synthesis of nitrate reductase in Escherichia coli." J Bacteriol 95(4);1305-13. PMID: 4869216

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


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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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