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

Synonyms: CbdAB, AppCB

Subunit composition of cytochrome bd-II terminal oxidase = [AppC][AppB]
         cytochrome bd-II terminal oxidase subunit I = AppC (summary available)
         cytochrome bd-II terminal oxidase subunit II = AppB (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 (cydAB) are expressed under oxygen limited conditions and both enzymes contribute to the generation of a proton motive force (PMF). The physiological role of cytochrome bd-II is less certain. Initial experiments suggest that it does not contribute to PMF [Bekker09] however more recent work concludes that cytochrome bd-II is able to generate PMF via a mechanism similar to cytochrome bd-I [Borisov11].

The two subunits of cytochrome bd-II encoded by the appC and appB genes are structurally similar to the cytochrome bd-I terminal oxidase CydA and CydB subunits respectively [Dassa91]. The appCB-appA operon is under the control of the transcriptional activator AppY. It is induced upon entry into the stationary phase, as well as starvation for carbon and phosphate [Atlung97].

Cytochrome bd-II oxidase is active under glucose-limited aerobic conditions and expression of cytochrome bd-II oxidase as a sole terminal oxidase allows growth on a highly reduced substrate such as glycerol [Bekker09]. Flux analysis with respect to glucose catabolism and respiration suggests that an E. coli strain expressing cytochrome bd-II oxidase as a sole terminal oxidase synthesizes ATP by substrate level phosphorylation only and consequently does not translocate protons [Bekker09, Shepherd10]. PMF is generated in inverted membrane vesicles expressing cytochrome bd-II oxidase as a sole terminal oxidase [Borisov11]. The H+/e- stoichiometry for cytochrome bd-II oxidase is estimated to be 0.94 [Borisov11].

Review: [Borisov11a]

Locations: inner membrane

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Sturr96, Bekker09]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Sturr96, Bekker09]
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Inferred from experiment [Sturr96]
GO:0020037 - heme binding Inferred from experiment [Sturr96]
GO:0048038 - quinone binding Inferred from experiment [Sturr96]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment [Sturr96]
GO:0070069 - cytochrome complex Inferred from experiment [Sturr96]

Credits:
Last-Curated ? 23-Mar-2010 by Mackie A , Macquarie University


Enzymatic reaction of: cytochrome bd-II terminal oxidase

EC Number: 1.10.3.14

In Pathways: succinate to cytochrome bd oxidase electron transfer


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

Synonyms: CyxA, CbdA, AppC

Gene: appC Accession Numbers: EG11380 (EcoCyc), b0978, ECK0969

Locations: inner membrane

Sequence Length: 514 AAs

Molecular Weight: 57.92 kD (from nucleotide sequence)

Molecular Weight: 43.0 kD (experimental) [Sturr96]

pI: 7.28

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Sturr96, Bekker09]
GO:0006119 - oxidative phosphorylation Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Sturr96, Bekker09]
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Inferred from experiment [Sturr96]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05, Sturr96]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Lasserre06]
GO:0070069 - cytochrome complex Inferred from experiment [Sturr96]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

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

Unification Links: DIP:DIP-9119N , EcoCyc:APPC-MONOMER , EcoliWiki:b0978 , EcoO157Cyc:APPC-MONOMER , PR:PRO_000022111 , Pride:P26459 , Protein Model Portal:P26459 , RefSeq:NP_415497 , String:511145.b0978 , UniProt:P26459

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

Summary:
The appC encoded protein is subunit 1 of E. coli cytochrome bd-II terminal oxidase.

Essentiality data for appC 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 cytochrome bd-II terminal oxidase: cytochrome bd-II terminal oxidase subunit II

Synonyms: CyxB, AppB, CbdB

Gene: appB Accession Numbers: EG11379 (EcoCyc), b0979, ECK0970

Locations: inner membrane

Sequence Length: 378 AAs

Molecular Weight: 42.424 kD (from nucleotide sequence)

Molecular Weight: 27.0 kD (experimental) [Sturr96]

pI: 8.86

GO Terms:

Biological Process: GO:0019646 - aerobic electron transport chain Inferred from experiment [Sturr96]
GO:0006119 - oxidative phosphorylation Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Sturr96, Bekker09]
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Inferred from experiment [Sturr96]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05, Sturr96]
GO:0070069 - cytochrome complex Inferred from experiment [Sturr96]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

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

Unification Links: EcoCyc:APPB-MONOMER , EcoliWiki:b0979 , EcoO157Cyc:APPB-MONOMER , PR:PRO_000022110 , Protein Model Portal:P26458 , RefSeq:NP_415498 , String:511145.b0979 , UniProt:P26458

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

Summary:
The appB encoded protein is subunit II of E. coli cytochrome bd-II terminal oxidase.

Essentiality data for appB 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]

References

Atlung97: Atlung T, Knudsen K, Heerfordt L, Brondsted L (1997). "Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation." J Bacteriol 179(7);2141-6. PMID: 9079897

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

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

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

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

Dassa91: Dassa J, Fsihi H, Marck C, Dion M, Kieffer-Bontemps M, Boquet PL (1991). "A new oxygen-regulated operon in Escherichia coli comprises the genes for a putative third cytochrome oxidase and for pH 2.5 acid phosphatase (appA)." Mol Gen Genet 1991;229(3);341-52. PMID: 1658595

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

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

Shepherd10: Shepherd M, Sanguinetti G, Cook GM, Poole RK (2010). "Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism." J Biol Chem 285(24);18464-72. PMID: 20392690

Sturr96: Sturr MG, Krulwich TA, Hicks DB (1996). "Purification of a cytochrome bd terminal oxidase encoded by the Escherichia coli app locus from a delta cyo delta cyd strain complemented by genes from Bacillus firmus OF4." J Bacteriol 178(6);1742-9. PMID: 8626304

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."

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

Zhang07: 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


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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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