Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2

Rapisarda, Viviana Andrea; Chehı́n, Rosana; Rivas, Javier De Las; Rodrı́guez-Montelongo, Luisa; Farı́as, Ricardo N.; Massa, Eddy M.

doi:10.1016/s0003-9861(02)00277-1

Cited by 54 publications

(36 citation statements)

References 32 publications

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“…Only E. coli NDH-2 has been reported to contain a Cu(I)-thiolate ligation domain. 19) The Gram-positive coryne-form bacterium Corynebacterium glutamicum is an amino acid producing strain used industrially for the production of L-lysine and Lglutamate. The respiratory chain of this bacterium consists of several different primary dehydrogenases, 20,21) such as NADH dehydrogenase, succinate dehydrogenase, L-lactate dehydrogenase, and malate: quinone oxidoreductase, and at least three terminal oxidases, CN-sensitive cytochrome aa 3 , 22,23) CN-resistant bypass oxidase, 20) and cytochrome bd.…”

Section: )mentioning

confidence: 99%

“…Although, since NDH-2 of E. coli has been shown to contain copper (Cu(I)), 19) luminescence spectroscopy was performed with the purified enzyme, no bands corresponding to Cu(I) were observed (data not shown). In addition, metal analysis using induced-coupled plasma atomic emission spectrometery indicated that purified NDH-2 did not contain any copper (data not shown).…”

Section: Spectral Analysis Of the Purified Enzymementioning

confidence: 99%

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Electron Transfer Ability from NADH to Menaquinone and from NADPH to Oxygen of Type II NADH Dehydrogenase ofCorynebacterium glutamicum

Nantapong

Otofuji

Migita

et al. 2005

Bioscience, Biotechnology, and Biochemistry

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Section: )mentioning

confidence: 99%

Section: Spectral Analysis Of the Purified Enzymementioning

confidence: 99%

Electron Transfer Ability from NADH to Menaquinone and from NADPH to Oxygen of Type II NADH Dehydrogenase ofCorynebacterium glutamicum

Nantapong

Otofuji

Migita

et al. 2005

Bioscience, Biotechnology, and Biochemistry

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“…Only relatively recently, the copper-reducing activity of Escherichia coli has been molecularly characterized. It has been shown that approximately 70 % of the copper reduction activity by cells was due to quinones and 10 % to copper reduction by the NADH dehydrogenase, NDH-2 (Rapisarda et al, 1999(Rapisarda et al, , 2002 Volentini et al, 2011). The Gram-positive bacteria Enterococcus hirae and Lactococcus lactis have also been reported to exhibit extracellular Cu 2+ reductase activities (Wunderli-Ye & Solioz, 1999;Rezaïki et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Non-enzymic copper reduction by menaquinone enhances copper toxicity in Lactococcus lactis IL1403

et al. 2013

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Lactococcus lactis possesses a pronounced extracellular Cu 2+ -reduction activity which leads to the accumulation of Cu + in the medium. The kinetics of this reaction were not saturable by increasing copper concentrations, suggesting a non-enzymic reaction. A copper-reductasedeficient mutant, isolated by random transposon mutagenesis, had an insertion in the menE gene, which encodes O-succinylbenzoic acid CoA ligase. This is a key enzyme in menaquinone biosynthesis. The DmenE mutant was deficient in short-chain menaquinones, and exogenously added menaquinone complemented the copper-reductase-deficient phenotype. Haem-induced respiration of wild-type L. lactis efficiently suppressed copper reduction, presumably by competition by the bd-type quinol oxidase for menaquinone. As expected, the DmenE mutant was respiration-deficient, but could be made respiration-proficient by supplementation with menaquinone. Growth of wild-type cells was more copper-sensitive than that of the DmenE mutant, due to the production of Cu + ions by the wild-type. This growth inhibition of the wild-type was strongly attenuated if Cu + was scavenged with the Cu(I) chelator bicinchoninic acid. These findings support a model whereby copper is non-enzymically reduced at the membrane by menaquinones. Respiration effectively competes for reduced quinones, which suppresses copper reduction. These findings highlight novel links between copper reduction, respiration and Cu + toxicity in L. lactis.

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“…Hydrophobicity has been shown to be important for metal-protein interactions such that metal binding sites usually appear in clusters with hydrophobic environment. High-affinity metal binding sites in some proteins are located at sequence segments with specific amino acid composition, and specific sequence motifs have been used for predicting metal-binding proteins [48][49][50]. It was also found that polarity and solvent accessibility of the binding site influences the functional properties of metal-binding proteins.…”

Section: Performance Of 3 Rd Layer Of Neural Networkmentioning

confidence: 99%

MetalloPred: A tool for hierarchical prediction of metal ion binding proteins using cluster of neural networks and sequence derived features

Naik¹,

Ranjan²,

Kesari³

et al. 2011

JBPC

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Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized protein. Particularly, with the avalanche of protein sequences generated in the post genomic era and since conventional techniques are time consuming and expensive, it is highly desirable to develop an automated method by which one can get a fast and accurate answer to these questions. Here, a top-down predictor, called MetalloPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1 st layer of the prediction engine is for identifying a query protein as metalloprotein or not; the 2 nd layer for the main functional class; and the 3 rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 60% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. MetalloPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of metal binding proteins. MetalloPred is freely available to be used in-house as a standalone and is accessible at http://www.juit.ac.in/assets/Metallopred/.

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Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2

Cited by 54 publications

References 32 publications

Electron Transfer Ability from NADH to Menaquinone and from NADPH to Oxygen of Type II NADH Dehydrogenase ofCorynebacterium glutamicum

Electron Transfer Ability from NADH to Menaquinone and from NADPH to Oxygen of Type II NADH Dehydrogenase ofCorynebacterium glutamicum

Non-enzymic copper reduction by menaquinone enhances copper toxicity in Lactococcus lactis IL1403

MetalloPred: A tool for hierarchical prediction of metal ion binding proteins using cluster of neural networks and sequence derived features

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