Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Transporter: cytochrome bd-I terminal oxidase

Synonyms: cytochrome b558-d complex, cytochrome d complex, cytochrome bd complex, cytochrome d ubiquinol oxidase complex

Subunit composition of cytochrome bd-I terminal oxidase = [CydA][CydB][CydX]
         cytochrome bd-I terminal oxidase subunit I = CydA (summary available)
         cytochrome bd-I terminal oxidase subunit II = CydB (summary available)
         cytochrome bd-I terminal oxidase - CydX subunit = CydX (extended summary available)

Summary:
The E. coli K-12 genome contains gene clusters for 3 cytochrome oxidase enzymes - cytochrome bo oxidase (CyoABCD), cytochrome bd-I oxidase (CydABX) and cytochrome bd-II oxidase (AppCD). The three enzymes function as the major terminal oxidases in the aerobic respiratory chain of E. coli. Cytochrome bo oxidase genes (cyoABCD) are expressed when oxygen levels are high while cytochrome bd-I oxidase genes are expressed under oxygen limited conditions. Both enymes contribute to the generation of a proton motive force (PMF), cytochrome bo oxidase functions as a proton pump whilst cytochrome bd-I does not. Cytochrome bd-I catalyses ubiquinal oxidation with a H+/e- of 1 [Puustinen91]. The energetics of cytochrome bd-II are less clear: initial reports suggest that it does not contribute to PMF [Bekker09] - later work indicates that it generates PMF with an H+/e- of 0.94 [Borisov11].

Cytochrome bd-I terminal oxidase catalyses the two electron oxidation of ubiquinol and the four electron reduction of oxygen to water. Oxidation of ubiquinol releases two protons into the periplasmic space and two electrons are transferred through the heme cofactors to the oxygen reducing site. Four protons are taken up from the cytoplasm for oxygen reduction (see review by [Borisov11a] and references within). The protein is a heterodimer containing one copy each of subunit I (CydA) and subunit II (CydB) [Miller88a]. Copurification experiments suggest that CydX forms a complex with cytochrome bd-I [Vanorsdel13, Hoeser14]. Cytochrome bd-I contains 3 bound hemes: heme b558, heme b595 and heme d, present in a 1:1:1 ratio [Miller83b, Kita84, Miller86, Kita86, HataTanaka87, Rothery89, Meinhardt89]. Subunit I (CyaA) contains the heme b558 component and is the site of ubiquinol oxidation [Kranz84, Green84, Lorence87, Green86, Matsumoto06]. The heme b595 and heme d components form a binuclear centre where oxygen is reduced to water [Hill93]. Both subunits are required for binding of the heme b595 and heme d components [Newton91].

Expression of cydAB is negatively regulated by Fnr, induced by anaerobiosis via the ArcA/ArcB two-component regulatory system [Cotter90, Cotter97], and repressed by H-NS under aerobic conditions, resulting in maximal expression under microaerobic conditions [Tseng96, Govantes00a]. Expression is induced by iron limitation [Cotter92] and H2O2 exposure [Lindqvist00], and is sensitive to the level of DNA supercoiling [Bebbington01]. cydAB is upregulated when exposed to nitric oxide and cytochrome bd-1 confers resistance to nitric oxide stress when compared to cytochrome bo [Mason09].

GFP-tagged cytochrome bd-I terminal oxidase concentrates in mobile localised areas of the inner membrane of E. coli [Lenn08].

Review: [Borisov11a]

Citations: [Mogi09, Borisov11b, Zhang01d, Borisov02, Mogi06, Yang07f, Borisov08, Sun96b, Rappaport10, Paulus12, Borisov13, Siletsky14, Belevich07a, Jasaitis00]

Locations: inner membrane

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Kita84, Miller85]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Kita84, Kobayashi99]
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Inferred from experiment [Miller83b, Kita84]
GO:0020037 - heme binding Inferred from experiment [Miller83b, Kita84]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment [Kita84]
GO:0070069 - cytochrome complex Inferred from experiment [Miller83b, Kita84]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Osborne99]
GO:0016021 - integral component of membrane Inferred by computational analysis [GOA00]

Credits:
Last-Curated ? 12-May-2014 by Mackie A , Macquarie University
Revised 12-May-2014 by Mackie A , Macquarie University


Enzymatic reaction of: cytochrome bd-I terminal oxidase

EC Number: 1.10.3.14

Alternative Substrates for an ubiquinol [Comment 1 ]: ubiquinol-1 , L-ascorbate , menadiol

In Pathways: NADH to cytochrome bd oxidase electron transfer I , succinate to cytochrome bd oxidase electron transfer , NADH to cytochrome bd oxidase electron transport II , pyruvate to cytochrome bd terminal oxidase electron transfer

Citations: [Fang89, Hill93, Kobayashi99]

Cofactors or Prosthetic Groups: heme d , protoheme IX

Activators (Unknown Mechanism): a phospholipid [Kita84]

Inhibitors (Unknown Mechanism): a gramicidin [Mogi08] , hydroxyquinoline N oxide [Helmward89, Kita86] , hydroxylamine [Kita86, Helmward89] , piericidin A [Helmward89, Kita86, Kita84] , potassium cyanide [Kita84] , azide [Kita84]

Kinetic Parameters:

Substrate
Km (μM)
Citations
oxygen
0.38
[Kita84]


Subunit of cytochrome bd-I terminal oxidase: cytochrome bd-I terminal oxidase subunit I

Synonyms: CydA, Cyd-1

Gene: cydA Accession Numbers: EG10173 (EcoCyc), b0733, ECK0721

Locations: inner membrane

Sequence Length: 522 AAs

Molecular Weight: 58.205 kD (from nucleotide sequence)

pI: 6.75

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Miller85, Kita84]
GO:0006119 - oxidative phosphorylation Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hoeser14, Stenberg05]
GO:0009055 - electron carrier activity Inferred from experiment [Kita84]
GO:0016679 - oxidoreductase activity, acting on diphenols and related substances as donors Inferred from experiment [Green86, Kita84]
GO:0020037 - heme binding Inferred from experiment [Green84, Green86, Fang89, Hill93]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07a, Daley05, Green84]
GO:0005887 - integral component of plasma membrane Inferred from experiment Inferred by computational analysis [Osborne99, Green86]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Newton91, Lasserre06]
GO:0070069 - cytochrome complex Inferred from experiment [Green84, Miller83b, Kita84]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]
GO:0031224 - intrinsic component of membrane Inferred by computational analysis [GOA00]

MultiFun Terms: cell structure membrane
metabolism energy production/transport electron acceptors

Unification Links: DIP:DIP-36181N , EcoCyc:CYDA-MONOMER , EcoliWiki:b0733 , EcoO157Cyc:CYDA-MONOMER , PR:PRO_000022361 , Pride:P0ABJ9 , Protein Model Portal:P0ABJ9 , RefSeq:NP_415261 , String:511145.b0733 , UniProt:P0ABJ9

Relationship Links: InterPro:IN-FAMILY:IPR002585 , Pfam:IN-FAMILY:PF01654

Summary:
cydA encodes subunit I of cytochrome bd-I terminal oxidase. CydA contains the heme b558 component of cytochrome bd-I and is the site of ubiquinol oxidation [Green84, Lorence87, Green86]. Purified, reconstituted CydA can be reduced by ubiquinol but it does not reduce molecular oxygen [Green86]. The CydA protein has nine transmembrane helices, the N-terminus is located in the periplasm and the C-terminus in the cytoplasm [Osborne99, Zhang04f]. A periplasmic loop (the Q-loop) located between transmembrane regions VI and VII is implicated in ubiquinol binding [Dueweke90, Dueweke91, Osborne99, Matsumoto06]. Histidine 19 and methionine 393 are the axial ligands for heme b558 [Fang89, Kaysser95, Spinner95]. Replacement of histidine 19 with leucine or arginine results in loss of the two heme components, heme b595 and heme d [Fang89].

Citations: [Belevich05, Borisov08]

Essentiality data for cydA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of cytochrome bd-I terminal oxidase: cytochrome bd-I terminal oxidase subunit II

Synonyms: CydB, Cyd-2

Gene: cydB Accession Numbers: EG10174 (EcoCyc), b0734, ECK0722

Locations: inner membrane

Sequence Length: 379 AAs

Molecular Weight: 42.453 kD (from nucleotide sequence)

pI: 7.45

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Miller85, Kita84]
GO:0006119 - oxidative phosphorylation Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hoeser14, Stenberg05]
GO:0009055 - electron carrier activity Inferred from experiment [Kita84]
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Inferred from experiment [Kita84]
GO:0020037 - heme binding Inferred from experiment [Newton91, Hill93]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07a, Daley05]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Newton91]
GO:0070069 - cytochrome complex Inferred from experiment [Miller83b, Kita84, Green84]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Osborne99]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]
GO:0031224 - intrinsic component of membrane Inferred by computational analysis [GOA00]

MultiFun Terms: cell structure membrane
metabolism energy production/transport electron acceptors

Unification Links: EcoCyc:CYDB-MONOMER , EcoliWiki:b0734 , EcoO157Cyc:CYDB-MONOMER , PR:PRO_000022362 , Pride:P0ABK2 , Protein Model Portal:P0ABK2 , RefSeq:NP_415262 , String:511145.b0734 , UniProt:P0ABK2

Relationship Links: InterPro:IN-FAMILY:IPR003317 , Pfam:IN-FAMILY:PF02322

Summary:
cydB encodes subunit II of cytochrome bd-I terminal oxidase. Subunit II has eight predicted transmembrane helices; the N and C-termini are located in the cytoplasm [Osborne99]. Subunit I (encoded by cybA) and subunit II are both required for binding of the heme b595 and heme d components of cytochrome bd-I [Newton91].
A cydB mutant has a temperature sensitive growth phenotype [Wall92].

Essentiality data for cydB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
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]

Subunit of cytochrome bd-I terminal oxidase: cytochrome bd-I terminal oxidase - CydX subunit

Synonyms: YbgT

Gene: cydX Accession Numbers: G0-10441 (EcoCyc), b4515, ECK0723

Locations: inner membrane

Sequence Length: 37 AAs

Molecular Weight: 4.042 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006119 - oxidative phosphorylation Inferred by computational analysis [UniProtGOA12]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0016679 - oxidoreductase activity, acting on diphenols and related substances as donors Inferred from experiment [Vanorsdel13]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Fontaine11]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Hemm08]
GO:0019867 - outer membrane Inferred from experiment [Fontaine11]
GO:0070069 - cytochrome complex Inferred from experiment [Vanorsdel13]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Hoeser14]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

Gene Class: ORFs Conserved-ORFs

Unification Links: EcoliWiki:b4515 , RefSeq:YP_588444 , String:511145.b4515 , UniProt:P56100

Relationship Links: InterPro:IN-FAMILY:IPR011724 , InterPro:IN-FAMILY:IPR012994 , Pfam:IN-FAMILY:PF08173

Summary:
Copurification experiments suggest that CydX forms a complex with cytochrome bd-I terminal oxidase [Vanorsdel13, Hoeser14]. A strain lacking cydX is slow growing in aerobic liquid culture and on plates and has increased sensitivity to β-mercaptoethanol. A wild-type phenotype can be restored when cydX is expressed from a plasmid [Vanorsdel13]. Membrane extracts from a strain lacking cydX display reduced levels of N N N' N'-tetramethyl-p-phenylenediamine (TMPD) oxidation [Vanorsdel13]. Preparations of CydAB lacking CydX do not contain the di-heme centre (hemes b595 and d) suggesting that CydX may be involved in the assembly or stabilisation of the di-heme active centre [Hoeser14].

The cydX open reading frame contains a predicted transmembrane segment, and the protein can be found in the membrane fraction [Hemm08, Fontaine11]. Using a sucrose fractionation protocol CydX partitions into both the inner membrane and outer membrane fractions [Fontaine11]. Topology assays using GFP and PhoA fusion proteins suggest that CydX is oriented with the C-terminus in the cytoplasm [Fontaine11]. Translocation of CydX is impaired in both SecE depleted and YidC depleted E. coli strains [Fontaine11].

CydX is highly expressed during both exponential and stationary phase [Hemm08]. Expression of CydX is increased during oxygen-limited growth and under envelope stress induced by SDS/EDTA treatment [Hemm10].

CydX and AppX are paralogues and may have overlapping functions within E. coli K-12 [Vanorsdel13].

Essentiality data for cydX knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
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]

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

Bebbington01: Bebbington KJ, Williams HD (2001). "A role for DNA supercoiling in the regulation of the cytochrome bd oxidase of Escherichia coli." Microbiology 147(Pt 3);591-8. PMID: 11238966

Bekker09: Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ (2009). "Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase." J Bacteriol 191(17);5510-7. PMID: 19542282

Belevich05: Belevich I, Borisov VB, Zhang J, Yang K, Konstantinov AA, Gennis RB, Verkhovsky MI (2005). "Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site." Proc Natl Acad Sci U S A 102(10);3657-62. PMID: 15728392

Belevich07a: Belevich I, Borisov VB, Verkhovsky MI (2007). "Discovery of the true peroxy intermediate in the catalytic cycle of terminal oxidases by real-time measurement." J Biol Chem 282(39);28514-9. PMID: 17690093

Borisov02: Borisov VB, Liebl U, Rappaport F, Martin JL, Zhang J, Gennis RB, Konstantinov AA, Vos MH (2002). "Interactions between heme d and heme b595 in quinol oxidase bd from Escherichia coli: a photoselection study using femtosecond spectroscopy." Biochemistry 41(5);1654-62. PMID: 11814360

Borisov08: Borisov VB, Belevich I, Bloch DA, Mogi T, Verkhovsky MI (2008). "Glutamate 107 in subunit I of cytochrome bd from Escherichia coli is part of a transmembrane intraprotein pathway conducting protons from the cytoplasm to the heme b595/heme d active site." Biochemistry 47(30);7907-14. PMID: 18597483

Borisov11: Borisov VB, Murali R, Verkhovskaya ML, Bloch DA, Han H, Gennis RB, Verkhovsky MI (2011). "Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode." Proc Natl Acad Sci U S A 108(42);17320-4. PMID: 21987791

Borisov11a: Borisov VB, Gennis RB, Hemp J, Verkhovsky MI (2011). "The cytochrome bd respiratory oxygen reductases." Biochim Biophys Acta 1807(11);1398-413. PMID: 21756872

Borisov11b: Borisov VB, Forte E, Sarti P, Giuffre A (2011). "Catalytic intermediates of cytochrome bd terminal oxidase at steady-state: ferryl and oxy-ferrous species dominate." Biochim Biophys Acta 1807(5);503-9. PMID: 21352800

Borisov13: Borisov VB, Verkhovsky MI (2013). "Accommodation of CO in the di-heme active site of cytochrome bd terminal oxidase from Escherichia coli." J Inorg Biochem 118;65-7. PMID: 23123340

Cotter90: Cotter PA, Chepuri V, Gennis RB, Gunsalus RP (1990). "Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product." J Bacteriol 172(11);6333-8. PMID: 2172211

Cotter92: Cotter PA, Darie S, Gunsalus RP (1992). "The effect of iron limitation on expression of the aerobic and anaerobic electron transport pathway genes in Escherichia coli." FEMS Microbiol Lett 79(1-3);227-32. PMID: 1478458

Cotter97: Cotter PA, Melville SB, Albrecht JA, Gunsalus RP (1997). "Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation." Mol Microbiol 25(3);605-15. PMID: 9302022

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

Dueweke90: Dueweke TJ, Gennis RB (1990). "Epitopes of monoclonal antibodies which inhibit ubiquinol oxidase activity of Escherichia coli cytochrome d complex localize functional domain." J Biol Chem 265(8);4273-7. PMID: 1689724

Dueweke91: Dueweke TJ, Gennis RB (1991). "Proteolysis of the cytochrome d complex with trypsin and chymotrypsin localizes a quinol oxidase domain." Biochemistry 30(14);3401-6. PMID: 1707310

Fang89: Fang H, Lin RJ, Gennis RB (1989). "Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis." J Biol Chem 1989;264(14);8026-32. PMID: 2656671

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

Fontaine11: Fontaine F, Fuchs RT, Storz G (2011). "Membrane localization of small proteins in Escherichia coli." J Biol Chem 286(37);32464-74. PMID: 21778229

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."

Govantes00a: Govantes F, Orjalo AV, Gunsalus RP (2000). "Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon." Mol Microbiol 38(5);1061-73. PMID: 11123679

Green84: Green GN, Kranz RG, Lorence RM, Gennis RB (1984). "Identification of subunit I as the cytochrome b558 component of the cytochrome d terminal oxidase complex of Escherichia coli." J Biol Chem 259(12);7994-7. PMID: 6376497

Green86: Green GN, Lorence RM, Gennis RB (1986). "Specific overproduction and purification of the cytochrome b558 component of the cytochrome d complex from Escherichia coli." Biochemistry 25(9);2309-14. PMID: 3013298

HataTanaka87: Hata-Tanaka A, Matsuura K, Itoh S, Anraku Y (1987). "Electron flow and heme-heme interaction between cytochromes b-558, b-595 and d in a terminal oxidase of Escherichia coli." Biochim Biophys Acta 893(2);289-95. PMID: 3040093

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Hemm08: Hemm MR, Paul BJ, Schneider TD, Storz G, Rudd KE (2008). "Small membrane proteins found by comparative genomics and ribosome binding site models." Mol Microbiol 70(6);1487-501. PMID: 19121005

Hemm10: Hemm MR, Paul BJ, Miranda-Rios J, Zhang A, Soltanzad N, Storz G (2010). "Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies." J Bacteriol 192(1):46-58. PMID: 19734316

Hill93: Hill JJ, Alben JO, Gennis RB (1993). "Spectroscopic evidence for a heme-heme binuclear center in the cytochrome bd ubiquinol oxidase from Escherichia coli." Proc Natl Acad Sci U S A 1993;90(12);5863-7. PMID: 8516338

Hoeser14: Hoeser J, Hong S, Gehmann G, Gennis RB, Friedrich T (2014). "Subunit CydX of Escherichia coli cytochrome bd ubiquinol oxidase is essential for assembly and stability of the di-heme active site." FEBS Lett 588(9);1537-41. PMID: 24681096

Jasaitis00: Jasaitis A, Borisov VB, Belevich NP, Morgan JE, Konstantinov AA, Verkhovsky MI (2000). "Electrogenic reactions of cytochrome bd." Biochemistry 39(45);13800-9. PMID: 11076519

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

Kaysser95: Kaysser TM, Ghaim JB, Georgiou C, Gennis RB (1995). "Methionine-393 is an axial ligand of the heme b558 component of the cytochrome bd ubiquinol oxidase from Escherichia coli." Biochemistry 34(41);13491-501. PMID: 7577938

Kita84: Kita K, Konishi K, Anraku Y (1984). "Terminal oxidases of Escherichia coli aerobic respiratory chain. II. Purification and properties of cytochrome b558-d complex from cells grown with limited oxygen and evidence of branched electron-carrying systems." J Biol Chem 1984;259(5);3375-81. PMID: 6321507

Kita86: Kita K, Konishi K, Anraku Y (1986). "Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain." Methods Enzymol 1986;126;94-113. PMID: 2856144

Kobayashi99: Kobayashi K, Tagawa S, Mogi T (1999). "Electron transfer process in cytochrome bd-type ubiquinol oxidase from Escherichia coli revealed by pulse radiolysis." Biochemistry 1999;38(18);5913-7. PMID: 10231544

Kranz84: Kranz RG, Gennis RB (1984). "Characterization of the cytochrome d terminal oxidase complex of Escherichia coli using polyclonal and monoclonal antibodies." J Biol Chem 259(12);7998-8003. PMID: 6376498

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lenn08: Lenn T, Leake MC, Mullineaux CW (2008). "Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo." Mol Microbiol 70(6);1397-407. PMID: 19019148

Lindqvist00: Lindqvist A, Membrillo-Hernandez J, Poole RK, Cook GM (2000). "Roles of respiratory oxidases in protecting Escherichia coli K12 from oxidative stress." Antonie Van Leeuwenhoek 78(1);23-31. PMID: 11016692

Lorence87: Lorence RM, Carter K, Green GN, Gennis RB (1987). "Cytochrome b558 monitors the steady state redox state of the ubiquinone pool in the aerobic respiratory chain of Escherichia coli." J Biol Chem 262(22);10532-6. PMID: 3301837

Mason09: Mason MG, Shepherd M, Nicholls P, Dobbin PS, Dodsworth KS, Poole RK, Cooper CE (2009). "Cytochrome bd confers nitric oxide resistance to Escherichia coli." Nat Chem Biol 5(2);94-6. PMID: 19109594

Matsumoto06: Matsumoto Y, Murai M, Fujita D, Sakamoto K, Miyoshi H, Yoshida M, Mogi T (2006). "Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli." J Biol Chem 281(4);1905-12. PMID: 16299377

Meinhardt89: Meinhardt SW, Gennis RB, Ohnishi T (1989). "EPR studies of the cytochrome-d complex of Escherichia coli." Biochim Biophys Acta 975(1);175-84. PMID: 2544229

Miller83b: Miller MJ, Gennis RB (1983). "The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain." J Biol Chem 258(15);9159-65. PMID: 6307994

Miller85: Miller MJ, Gennis RB (1985). "The cytochrome d complex is a coupling site in the aerobic respiratory chain of Escherichia coli." J Biol Chem 260(26);14003-8. PMID: 2414286

Miller86: Miller MJ, Gennis RB (1986). "Purification and reconstitution of the cytochrome d terminal oxidase complex from Escherichia coli." Methods Enzymol 126;87-94. PMID: 2856143

Miller88a: Miller MJ, Hermodson M, Gennis RB (1988). "The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits." J Biol Chem 263(11);5235-40. PMID: 3281937

Mogi06: Mogi T, Endou S, Akimoto S, Morimoto-Tadokoro M, Miyoshi H (2006). "Glutamates 99 and 107 in transmembrane helix III of subunit I of cytochrome bd are critical for binding of the heme b595-d binuclear center and enzyme activity." Biochemistry 45(51);15785-92. PMID: 17176101

Mogi08: Mogi T, Ui H, Shiomi K, Omura S, Kita K (2008). "Gramicidin S identified as a potent inhibitor for cytochrome bd-type quinol oxidase." FEBS Lett 582(15);2299-302. PMID: 18519036

Mogi09: Mogi T (2009). "Probing the haem d-binding site in cytochrome bd quinol oxidase by site-directed mutagenesis." J Biochem 145(6);763-70. PMID: 19254926

Newton91: Newton G, Gennis RB (1991). "In vivo assembly of the cytochrome d terminal oxidase complex of Escherichia coli from genes encoding the two subunits expressed on separate plasmids." Biochim Biophys Acta 1089(1);8-12. PMID: 1851043

Osborne99: Osborne JP, Gennis RB (1999). "Sequence analysis of cytochrome bd oxidase suggests a revised topology for subunit I." Biochim Biophys Acta 1410(1);32-50. PMID: 10076013

Paulus12: Paulus A, Rossius SG, Dijk M, de Vries S (2012). "Oxoferryl-porphyrin radical catalytic intermediate in cytochrome bd oxidases protects cells from formation of reactive oxygen species." J Biol Chem 287(12);8830-8. PMID: 22287551

Puustinen91: Puustinen A, Finel M, Haltia T, Gennis RB, Wikstrom M (1991). "Properties of the two terminal oxidases of Escherichia coli." Biochemistry 30(16);3936-42. PMID: 1850294

Rappaport10: Rappaport F, Zhang J, Vos MH, Gennis RB, Borisov VB (2010). "Heme-heme and heme-ligand interactions in the di-heme oxygen-reducing site of cytochrome bd from Escherichia coli revealed by nanosecond absorption spectroscopy." Biochim Biophys Acta 1797(9);1657-64. PMID: 20529691

Rothery89: Rothery RA, Ingledew WJ (1989). "The cytochromes of anaerobically grown Escherichia coli. An electron-paramagnetic-resonance study of the cytochrome bd complex in situ." Biochem J 261(2);437-43. PMID: 2549971

Siletsky14: Siletsky SA, Zaspa AA, Poole RK, Borisov VB (2014). "Microsecond Time-Resolved Absorption Spectroscopy Used to Study CO Compounds of Cytochrome bd from Escherichia coli." PLoS One 9(4);e95617. PMID: 24755641

Spinner95: Spinner F, Cheesman MR, Thomson AJ, Kaysser T, Gennis RB, Peng Q, Peterson J (1995). "The haem b558 component of the cytochrome bd quinol oxidase complex from Escherichia coli has histidine-methionine axial ligation." Biochem J 308 ( Pt 2);641-4. PMID: 7772053

Stenberg05: Stenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, von Heijne G, Daley DO (2005). "Protein complexes of the Escherichia coli cell envelope." J Biol Chem 280(41);34409-19. PMID: 16079137

Sun96b: Sun J, Kahlow MA, Kaysser TM, Osborne JP, Hill JJ, Rohlfs RJ, Hille R, Gennis RB, Loehr TM (1996). "Resonance Raman spectroscopic identification of a histidine ligand of b595 and the nature of the ligation of chlorin d in the fully reduced Escherichia coli cytochrome bd oxidase." Biochemistry 35(7);2403-12. PMID: 8652583

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

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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Vanorsdel13: Vanorsdel CE, Bhatt S, Allen RJ, Brenner EP, Hobson JJ, Jamil A, Haynes BM, Genson AM, Hemm MR (2013). "The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome bd Oxidase Complex and Is Required for Cytochrome bd Oxidase Activity." J Bacteriol 195(16);3640-50. PMID: 23749980

Wall92: Wall D, Delaney JM, Fayet O, Lipinska B, Yamamoto T, Georgopoulos C (1992). "arc-dependent thermal regulation and extragenic suppression of the Escherichia coli cytochrome d operon." J Bacteriol 174(20);6554-62. PMID: 1328158

Yang07f: Yang K, Zhang J, Vakkasoglu AS, Hielscher R, Osborne JP, Hemp J, Miyoshi H, Hellwig P, Gennis RB (2007). "Glutamate 107 in subunit I of the cytochrome bd quinol oxidase from Escherichia coli is protonated and near the heme d/heme b595 binuclear center." Biochemistry 46(11);3270-8. PMID: 17305364

Zhang01d: Zhang J, Hellwig P, Osborne JP, Huang HW, Moenne-Loccoz P, Konstantinov AA, Gennis RB (2001). "Site-directed mutation of the highly conserved region near the Q-loop of the cytochrome bd quinol oxidase from Escherichia coli specifically perturbs heme b595." Biochemistry 40(29);8548-56. PMID: 11456494

Zhang04f: Zhang J, Barquera B, Gennis RB (2004). "Gene fusions with beta-lactamase show that subunit I of the cytochrome bd quinol oxidase from E. coli has nine transmembrane helices with the O2 reactive site near the periplasmic surface." FEBS Lett 561(1-3);58-62. PMID: 15013751

Zhang07a: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


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 18.5 on Sat Nov 22, 2014, BIOCYC14A.