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

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

Essentiality data for narY 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:
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: GO:0009061 - anaerobic respiration Inferred from experiment [Iobbi87, IobbiNivol90]
GO:0019645 - anaerobic electron transport chain Inferred from experiment [Iobbi87]
GO:0006810 - transport Inferred by computational analysis [GOA00]
Molecular Function: GO:0008940 - nitrate reductase activity Inferred by computational analysis Inferred from experiment [Iobbi87, IobbiNivol90, Blasco92, GOA01, GOA01a]
GO:0009055 - electron carrier activity Inferred from experiment [Guigliarelli92, IobbiNivol90]
GO:0043546 - molybdopterin cofactor binding Inferred from experiment [Iobbi87, IobbiNivol90]
GO:0051536 - iron-sulfur cluster binding Inferred from experiment [IobbiNivol90]
GO:0051538 - 3 iron, 4 sulfur cluster binding Inferred from experiment [Guigliarelli92]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment [Guigliarelli92]
Cellular Component: GO:0009325 - nitrate reductase complex Inferred by computational analysis Inferred from experiment [IobbiNivol90, GOA01]
GO:0016020 - membrane Inferred by computational analysis Inferred from experiment [Iobbi87, Blasco92, GOA00]
GO:0005886 - plasma membrane Inferred by curator

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

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)

EC Number: 1.97.1.-

tellurite + an reduced unknown electron acceptor <=> Te0 + an oxidized unknown electron acceptor

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 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  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 16, 19, 22, 262 FS1
[Blasco90]
[4Fe-4S] coordination; FS1
Metal-Binding-Site 16  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 19  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 22  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 26, 243, 246, 258 FS2
[Blasco90]
[4Fe-4S] coordination, FS2
Metal-Binding-Site 26  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 174 -> 205  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 183, 186, 191, 226 FS3
[Blasco90]
[4Fe-4S] corodination, FS3
Metal-Binding-Site 183  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 186  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 191  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 195, 216, 219, 222 FS4
[Blasco90]
[3Fe-4S] coordination, FS4
Metal-Binding-Site 195  
[UniProt10]
UniProt: Iron-sulfur 4 (3Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 207 -> 236  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Metal-Binding-Site 216  
[UniProt10]
UniProt: Iron-sulfur 4 (3Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 222  
[UniProt10]
UniProt: Iron-sulfur 4 (3Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 226  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 243  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 246  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 258  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 262  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Sequence-Conflict 325 -> 326  
[Blasco90, UniProt10a]
UniProt: (in Ref. 1; CAA34965);


Gene Local Context (not to 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

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

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.

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Sep 4, 2015, biocyc14.