|Gene:||ndh||Accession Numbers: EG10649 (MetaCyc), b1109, ECK1095|
Synonyms: NDH-2, NADH dhII, NADH dehydrogenase II, NQR, NADH-quinone reductase
Species: Escherichia coli K-12 substr. MG1655
NADH:quinone oxidoreductase II (NDH-2) is a type IIA NADH dehydrogenase that catalyzes the transfer of electrons from NADH to the quinone pool in the cytoplasmic membrane. NDH-2 is one of two distinct NADH dehydrogenases in E. coli. In contrast to NDH-1 (encoded by the nuo genes), NDH-2 utilizes NADH exclusively, and electron flow from NADH to ubiquinone does not generate an electrochemical gradient [Matsushita87, Hayashi89, Calhoun93].
During glucose limited aerobic growth E. coli directs electron flux through both NADH dehydrogenases [Calhoun93a]. Electron transport from NADH to oxygen is not affected in a strain lacking NDH-I but is significantly reduced in a strain lacking NDH-II; similarly nitrate respiration with NADH was only slightly affected in a strain lacking NDH-I but significantly reduced in a strain lacking NDH-II. This suggests that NDH-II is used preferentially in aerobic and nitrate respiration [Tran97].
NDH-2 is a strongly membrane-associated protein; it contains an FAD cofactor and copurifies with phospholipids [Young78, Jaworowski81, Campbell83]. Phosphatidylethanolamine appears to be required for full enzymatic activity in vivo [Mileykovskaya93]. The enzyme contains a thiolate-bound Cu(I) ion, and a putative copper binding site has been identified [Rapisarda02]. Heterooligomers of NDH-1 and NDH-2 have been identified by electrophoresis and sucrose gradient centrifugation is suggestive of a supramolecular organisation in the membrane [Sousa11].
NDH-2 can generate superoxide radicals and hydrogen peroxide by autooxidation of the FAD cofactor [Messner99] when the enzyme is overproduced or in the absence of quinones [Seaver04]. However, under regular growth conditions, it is not the primary source of intracellular hydrogen peroxide [Seaver04]. NDH-2 also has cupric reductase activity that is dependend on FAD or quinones. Under experimental conditions, the reductase activity was observed simultaneously with the dehydrogenase function linked to the respiratory chain [Rapisarda99]. NDH-2 mutants are more sensitive to copper toxicity; NDH-2 may have a role in copper homeostasis [RodriguezMontel06, Volentini11].
Sequence analysis predicts that NDH-2 contains four domains: a FAD binding domain containing a conserved FAD binding motif; and NADH binding domain with a conserved NADH binding motif, a membrane anchoring domain containing two predicted transmembrane regions and a copper binding domain containing two conserved cysteine residues that may be copper ligands [Rapisarda02]. Based on the remote similarity of NDH-2 to the SCOP family of FAD/NAD-linked reductases, a structural model of NDH-2 has been proposed [Schmid04].
The originally isolated ndh mutant [Young76] was not a single-locus mutant; it also contained a disruption of the nuo locus, encoding NDH-1 [Calhoun93]. Only strains containing mutations in both NADH dehydrogenases are unable to grow on mannitol as the sole source of carbon [Calhoun93]. Metabolic effects of an ndh null mutation alone and in combination with various other mutations have been investigated [Yun05].
ndh is subject to complex transcriptional regulation. Expression of ndh is repressed during anaerobic growth in an FNR dependent manner; expression of ndh varies during the growth cycle regulated by the transcription factors Fis and IHF [Spiro89, Green94, Green96, Green97, Meng97]. In an F1-ATPase-defective mutant, ndh transcription and NDH-2 activity is increased [Noda06].
Ndh: "NADH dehydrogenase" [Young76]
Locations: inner membrane
|Map Position: [1,165,308 -> 1,166,612]|
Molecular Weight of Polypeptide: 47.359 kD (from nucleotide sequence), 45.0 kD (experimental) [Young78 ]
Unification Links: ASAP:ABE-0003746 , CGSC:457 , DIP:DIP-10325N , EchoBASE:EB0643 , EcoGene:EG10649 , EcoliWiki:b1109 , ModBase:P00393 , OU-Microarray:b1109 , PortEco:ndh , PR:PRO_000023365 , Pride:P00393 , Protein Model Portal:P00393 , RefSeq:NP_415627 , RegulonDB:EG10649 , SMR:P00393 , String:511145.b1109 , UniProt:P00393
Relationship Links: InterPro:IN-FAMILY:IPR001327 , InterPro:IN-FAMILY:IPR013027 , InterPro:IN-FAMILY:IPR023753 , PDB:Structure:1OZK , Pfam:IN-FAMILY:PF00070 , Pfam:IN-FAMILY:PF07992 , Prints:IN-FAMILY:PR00368
Instance reactions of [an electron-transfer quinone[membrane] + NAD(P)H[in] + H+[in] → an electron-transfer quinol[membrane] + NAD(P)+[in]] (126.96.36.199):
|Biological Process:||GO:0009060 - aerobic respiration
GO:0009061 - anaerobic respiration [Tran97]
GO:0019646 - aerobic electron transport chain [Matsushita87, Jaworowski81a]
GO:0055070 - copper ion homeostasis [RodriguezMontel06, Volentini11]
GO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
|Molecular Function:||GO:0008137 - NADH dehydrogenase (ubiquinone) activity
GO:0050660 - flavin adenine dinucleotide binding [GOA01a, Hayashi89, Jaworowski81]
GO:0003954 - NADH dehydrogenase activity [GOA01]
GO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
|Cellular Component:||GO:0005886 - plasma membrane
[UniProtGOA11, UniProtGOA11a, Jaworowski81, Young78]
GO:0030964 - NADH dehydrogenase complex [Jaworowski81]
GO:0005887 - integral component of plasma membrane [RodriguezMontel06]
GO:0016020 - membrane [UniProtGOA11a]
|MultiFun Terms:||metabolism → energy metabolism, carbon → aerobic respiration|
|metabolism → energy production/transport → electron donors|
Enzymatic reaction of: NADH:ubiquinone oxidoreductase (NADH:quinone oxidoreductase II)
Synonyms: NADH dehydrogenase
EC Number: 188.8.131.52
Enzyme activity in vitro was generally measured with ubiquinone-1 as the electron acceptor. The physiological electron acceptor is expected to be ubiquinone-8.
The apparent Km for ubiquinone-1 is <5 µM. The enzyme has no detectable activity with NADPH as substrate [Jaworowski81a].
Enzymatic reaction of: NADH cupric reductase (NADH:quinone oxidoreductase II)
Synonyms: NADH-linked cupric reductase, cupric reductase
EC Number: 1.16.1.-
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
Reversibility of this reaction is unspecified.
The enzyme is specific for copper and does not reduce Fe(III) to Fe(II) [Rapisarda99].
|Chain||2 -> 434|
|Protein-Segment||6 -> 121|
|Flavin-Binding-Region||7 -> 42|
|Nucleotide-Phosphate-Binding-Region||7 -> 42|
|Protein-Segment||170 -> 278|
|Nucleotide-Phosphate-Binding-Region||171 -> 208|
|Protein-Binding-Region||305 -> 377|
10/20/97 Gene b1109 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10649; confirmed by SwissProt match.
Bjorklof00: Bjorklof K, Zickermann V, Finel M (2000). "Purification of the 45 kDa, membrane bound NADH dehydrogenase of Escherichia coli (NDH-2) and analysis of its interaction with ubiquinone analogues." FEBS Lett 467(1);105-10. PMID: 10664466
Calhoun93: Calhoun MW, Gennis RB (1993). "Demonstration of separate genetic loci encoding distinct membrane-bound respiratory NADH dehydrogenases in Escherichia coli." J Bacteriol 1993;175(10);3013-9. PMID: 8387992
Calhoun93a: Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM (1993). "Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain." J Bacteriol 175(10);3020-5. PMID: 8491720
Green96: Green J, Anjum MF, Guest JR (1996). "The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis." Mol Microbiol 20(5);1043-55. PMID: 8809757
Hayashi89: Hayashi M, Miyoshi T, Takashina S, Unemoto T (1989). "Purification of NADH-ferricyanide dehydrogenase and NADH-quinone reductase from Escherichia coli membranes and their roles in the respiratory chain." Biochim Biophys Acta 977(1);62-9. PMID: 2679883
Jaworowski81: Jaworowski A, Mayo G, Shaw DC, Campbell HD, Young IG (1981). "Characterization of the respiratory NADH dehydrogenase of Escherichia coli and reconstitution of NADH oxidase in ndh mutant membrane vesicles." Biochemistry 1981;20(12);3621-8. PMID: 7020757
Jaworowski81a: Jaworowski A, Campbell HD, Poulis MI, Young IG (1981). "Genetic identification and purification of the respiratory NADH dehydrogenase of Escherichia coli." Biochemistry 1981;20(7);2041-7. PMID: 6784762
Messner99: Messner KR, Imlay JA (1999). "The identification of primary sites of superoxide and hydrogen peroxide formation in the aerobic respiratory chain and sulfite reductase complex of Escherichia coli." J Biol Chem 274(15);10119-28. PMID: 10187794
Mileykovskaya93: Mileykovskaya EI, Dowhan W (1993). "Alterations in the electron transfer chain in mutant strains of Escherichia coli lacking phosphatidylethanolamine." J Biol Chem 268(33);24824-31. PMID: 8227044
Noda06: Noda S, Takezawa Y, Mizutani T, Asakura T, Nishiumi E, Onoe K, Wada M, Tomita F, Matsushita K, Yokota A (2006). "Alterations of cellular physiology in Escherichia coli in response to oxidative phosphorylation impaired by defective F1-ATPase." J Bacteriol 188(19);6869-76. PMID: 16980490
Noguchi04: Noguchi Y, Nakai Y, Shimba N, Toyosaki H, Kawahara Y, Sugimoto S, Suzuki E (2004). "The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system." J Biochem 136(4);509-15. PMID: 15625321
Poulis81: Poulis MI, Shaw DC, Campbell HD, Young IG (1981). "In vitro synthesis of the respiratory NADH dehydrogenase of Escherichia coli. Role of UUG as initiation codon." Biochemistry 20(14);4178-85. PMID: 7025892
Rapisarda02: Rapisarda VA, Chehin RN, De Las Rivas J, Rodriguez-Montelongo L, Farias RN, Massa EM (2002). "Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2." Arch Biochem Biophys 405(1);87-94. PMID: 12176061
Rapisarda02a: Rapisarda VA, Volentini SI, Farias RN, Massa EM (2002). "Quenching of bathocuproine disulfonate fluorescence by Cu(I) as a basis for copper quantification." Anal Biochem 307(1);105-9. PMID: 12137786
Rapisarda99: Rapisarda VA, Montelongo LR, Farias RN, Massa EM (1999). "Characterization of an NADH-linked cupric reductase activity from the Escherichia coli respiratory chain." Arch Biochem Biophys 1999;370(2);143-50. PMID: 10510271
RodriguezMontel06: Rodriguez-Montelongo L, Volentini SI, Farias RN, Massa EM, Rapisarda VA (2006). "The Cu(II)-reductase NADH dehydrogenase-2 of Escherichia coli improves the bacterial growth in extreme copper concentrations and increases the resistance to the damage caused by copper and hydroperoxide." Arch Biochem Biophys 451(1);1-7. PMID: 16759635
RodriguezMontel95: Rodriguez-Montelongo L, Farias RN, Massa EM (1995). "Sites of electron transfer to membrane-bound copper and hydroperoxide-induced damage in the respiratory chain of Escherichia coli." Arch Biochem Biophys 323(1);19-26. PMID: 7487066
Schmid04: Schmid R, Gerloff DL (2004). "Functional properties of the alternative NADH:ubiquinone oxidoreductase from E. coli through comparative 3-D modelling." FEBS Lett 578(1-2);163-8. PMID: 15581635
Sousa11: Sousa PM, Silva ST, Hood BL, Charro N, Carita JN, Vaz F, Penque D, Conrads TP, Melo AM (2011). "Supramolecular organizations in the aerobic respiratory chain of Escherichia coli." Biochimie 93(3);418-25. PMID: 21040753
Spiro89: Spiro S, Roberts RE, Guest JR (1989). "FNR-dependent repression of the ndh gene of Escherichia coli and metal ion requirement for FNR-regulated gene expression." Mol Microbiol 3(5);601-8. PMID: 2503680
Thomson81: Thomson JW, Shapiro BM (1981). "The respiratory chain NADH dehydrogenase of Escherichia coli. Isolation of an NADH:quinone oxidoreductase from membranes and comparison with the membrane-bound NADH:dichlorophenolindophenol oxidoreductase." J Biol Chem 256(6);3077-84. PMID: 7009604
Tran97: Tran QH, Bongaerts J, Vlad D, Unden G (1997). "Requirement for the proton-pumping NADH dehydrogenase I of Escherichia coli in respiration of NADH to fumarate and its bioenergetic implications." Eur J Biochem 244(1);155-60. PMID: 9063459
Volentini11: Volentini SI, Farias RN, Rodriguez-Montelongo L, Rapisarda VA (2011). "Cu(II)-reduction by Escherichia coli cells is dependent on respiratory chain components." Biometals 24(5);827-35. PMID: 21390523
Young81: Young IG, Rogers BL, Campbell HD, Jaworowski A, Shaw DC (1981). "Nucleotide sequence coding for the respiratory NADH dehydrogenase of Escherichia coli. UUG initiation codon." Eur J Biochem 116(1);165-70. PMID: 6265208
Yun05: Yun NR, San KY, Bennett GN (2005). "Enhancement of lactate and succinate formation in adhE or pta-ackA mutants of NADH dehydrogenase-deficient Escherichia coli." J Appl Microbiol 99(6);1404-12. PMID: 16313413
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