Glycerol Dehydrogenase

Ruzheinikov, S.N.; Burke, J.; Sedelnikova, S.E.; Baker, Patrick J.; Taylor, Robert W.; Bullough, Per A.; Muir, N.M.; Gore, Michael G.; Rice, David W.

doi:10.1016/s0969-2126(01)00645-1

Cited by 104 publications

(91 citation statements)

References 49 publications

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“…The fold of TM0423 was predicted by FFAS (24) to be similar to that of dehydroquinate synthase from Aspergillus nidulans (25) with a Z score of 52. The recently published structure of the Bacillus stearothermophilus glycerol dehydrogenase (26) provided an even better model for TM0423, but was not available for molecular replacement at the time of data collection. In all, five native TM0423 crystals were screened.…”

Section: Resultsmentioning

confidence: 99%

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Lesley

Kühn

Godzik

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

378

358

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Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

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Section: Resultsmentioning

confidence: 99%

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Lesley

Kühn

Godzik

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

378

358

View full text Add to dashboard Cite

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“…4). Recently, the crystal structure of coenzyme NAD ϩ -dependent glycerol dehydrogenase (GlyDH) of Bacillus stearothermophilus was solved (32). This protein, which is 23% identical and 40% similar to MDH, partly contains the conserved motif A of family III ADHs, but with a Lys residue at the position of the Ser 97 residue of MDH.…”

Section: Resultsmentioning

confidence: 99%

Identification of a Magnesium-dependent NAD(P)(H)-binding Domain in the Nicotinoprotein Methanol Dehydrogenase from Bacillus methanolicus

Hektor

Kloosterman

Dijkhuizen

2002

Journal of Biological Chemistry

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؉ -dependent MDH activity. Also mutants G95A and S97G were both impaired in cofactor NAD(H) binding but retained coenzyme NAD ؉ -dependent MDH activity. Mutant G95A displayed a rather low MDH activity, whereas mutant S97G was insensitive to activator protein but displayed "fully activated" MDH reaction rates. The various roles of these amino acid residues in coenzyme and/or cofactor NAD(H) binding in MDH are discussed. Methanol dehydrogenase (MDH)1 of Bacillus methanolicus belongs to family III of NAD(P)-dependent alcohol dehydrogenases (ADHs) (2, 3), distinct from the zinc-containing medium chain dehydrogenases/reductases (family I) and the zinc-lacking short chain 32 ADHs (family II) (4, 5). The initial members of family III all were iron-dependent ADHs. In time, with an increasing number of member proteins characterized, it became clear that not all members were iron-dependent. Where investigated, other metals like zinc and magnesium also were found instead of iron (5). B. methanolicus MDH contains one Zn 2ϩ and one or two Mg 2ϩ ions/subunit (3). Identification of members of family III ADHs increasingly became based on overall sequence similarity. Three unique, conserved amino acid sequence motifs have been defined for this family, aiding in ADH classification (2, 6) ( Table I). Over 100 fully sequenced members of family III ADHs are now found in data bases. Many of these are putative proteins, with no biochemical data available.The genes encoding MDH of B. methanolicus, methanol:pnitroso-N,NЈ-dimethylaniline oxidoreductase (MNO) of Amycolatopsis methanolica, MNO of Mycobacterium gastri MB19, ADH of Desulfovibrio gigas, and ADH of Desulfovibrio HDv enzymes of B. methanolicus, A. methanolica, D. gigas, and Desulfovibrio HDv have been cloned and characterized by us (2).2 Classification of the M. gastri enzyme was based on Nterminal amino acid sequence analysis (Fig. 1A). Characterization of the five purified enzymes revealed that each of the proteins possesses a decameric quaternary structure (7-10). The first three are nicotinoproteins, containing a tightly but noncovalently bound NAD(P)(H)/subunit (8, 11). It is unknown whether other members of family III are nicotinoproteins as well. The bound NAD(P)(H) species of MDH and A. methanolica MNO act as cofactors; they become reduced when the enzymes oxidize primary alcohols to the respective aldehydes (8,11). B. methanolicus MDH requires a second, exogenous NAD ϩ for methanol oxidation, serving as a coenzyme and resulting in reoxidation of the NADH cofactor (11). These two NAD(H) molecules are not exchanged during the reaction (11). In vitro, the relatively low coenzyme NAD ϩ -dependent MDH activity is strongly stimulated by a M r 50,000 activator protein from the same organism, resulting in a 40-fold increase in the MDH turnover rate (11,12).Activator protein-mediated activation of MDH is characterized by hydrolytic removal of the NMN(H) moiety of cofactor NAD(H) and converts the Ping-Pong type of reaction mechanism of MDH to a ternary complex mechanism, implyin...

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“…The three-dimensional structure of the glycerol dehydrogenase protein of Bacillus stearothermophilus revealed that the nicotinamide group of its coenzyme NAD ϩ binds in a deep pocket formed by nine amino acid residues (32). In MDH, which is 23% identical and 40% similar to glycerol dehydrogenase, this pocket is also present; of these nine amino acid residues, six residues are identical and three are similar.…”

Section: Act-mediated Hydrolysis Of Mdh-bound Nad(h) Cofactor-the Datmentioning

confidence: 99%

Molecular, Biochemical, and Functional Characterization of a Nudix Hydrolase Protein That Stimulates the Activity of a Nicotinoprotein Alcohol Dehydrogenase

Kloosterman

Vrijbloed

Dijkhuizen

2002

Journal of Biological Chemistry

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Glycerol Dehydrogenase

Cited by 104 publications

References 49 publications

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Identification of a Magnesium-dependent NAD(P)(H)-binding Domain in the Nicotinoprotein Methanol Dehydrogenase from Bacillus methanolicus

Molecular, Biochemical, and Functional Characterization of a Nudix Hydrolase Protein That Stimulates the Activity of a Nicotinoprotein Alcohol Dehydrogenase

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