Kinetic Characterization and Molecular Modeling of NAD(P)+-Dependent Succinic Semialdehyde Dehydrogenase from Bacillus subtilis as an Ortholog YneI

Park, Seong Ah; Park, Ye Song; Lee, Ki Seog

doi:10.4014/jmb.1402.02054

Cited by 16 publications

(9 citation statements)

References 21 publications

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“…Other than the physiological functional study of SSADH in vivo, there were many studies on its catalytical function and cofactor preference in recent years [19][20][21][22]. NADP + or NAD + was required as a hydride acceptor in the reaction of SSA to succinic acid catalyzed by SSADH.…”

Section: Introductionmentioning

confidence: 99%

Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142

Xie

Bai

et al. 2020

PLoS ONE

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As a ubiquitous enzyme, succinic semialdehyde dehydrogenase contributes significantly in many pathways including the tricarboxylic acid cycle and other metabolic processes such as detoxifying the accumulated succinic semialdehyde and surviving in nutrient-limiting conditions. Here the cce4228 gene encoding succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142 was cloned and the homogenous recombinant cce4228 protein was obtained by Ni-NTA affinity chromatography. Biochemical characterization revealed that cce4228 protein displayed optimal activity at presence of metal ions in basic condition. Although the binding affinity of cce4228 protein with NAD + was about 50-fold lower than that of cce4228 with NADP + , the catalytic efficiency of cce4228 protein towards succinic semialdehyde with saturated concentration of NADP + is same as that with saturated concentration of NAD + as its cofactors. Meanwhile, the catalytic activity of cce4228 was competitively inhibited by succinic semialdehyde substrate. Kinetic and structural analysis demonstrated that the conserved Cys262 and Glu228 residues were crucial for the catalytic activity of cce4228 protein and the Ser157 and Lys154 residues were determinants of cofactor preference.

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Section: Introductionmentioning

confidence: 99%

Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142

Xie

Bai

et al. 2020

PLoS ONE

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“…encoded by gabT and puuE, and also two succinate semialdehyde dehydrogenases (SSADH) encoded by gabD and sad 21,22 .…”

Section: Resultsmentioning

confidence: 99%

A Systems Approach Discovers the Role and Characteristics of Seven LysR Type Transcription Factors in Escherichia Coli

Rodionova

Palsson

Gao

et al. 2021

Preprint

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Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates the dhaKLM operon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

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“…Moreover, Drosophila melanogaster MalE-DmSSADH showed 7-fold higher activity in the presence of NAD + than NADP + ( Rothacker and Ilg, 2008 ). On the other hand, in the case of YneI, the SSADHs from Bacillus subtilis ( Park et al, 2014 ) and Salmonella typhimurium ( Zheng et al, 2013 ) showed differences in affinity for NAD + or NADP + , but their catalytic efficiency exhibited similar values in both cofactors.…”

Section: Resultsmentioning

confidence: 99%

Kinetic and Structural Characterization for Cofactor Preference of Succinic Semialdehyde Dehydrogenase from Streptococcus pyogenes

Jang¹,

Park²,

Min³

et al. 2014

Molecules and Cells

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The γ-Aminobutyric acid (GABA) that is found in prokaryotic and eukaryotic organisms has been used in various ways as a signaling molecule or a significant component generating metabolic energy under conditions of nutrient limitation or stress, through GABA catabolism. Succinic semialdehyde dehydrogenase (SSADH) catalyzes the oxidation of succinic semialdehyde to succinic acid in the final step of GABA catabolism. Here, we report the catalytic properties and two crystal structures of SSADH from Streptococcus pyogenes (SpSSADH) regarding its cofactor preference. Kinetic analysis showed that SpSSADH prefers NADP+ over NAD+ as a hydride acceptor. Moreover, the structures of SpSSADH were determined in an apo-form and in a binary complex with NADP+ at 1.6 Å and 2.1 Å resolutions, respectively. Both structures of SpSSADH showed dimeric conformation, containing a single cysteine residue in the catalytic loop of each subunit. Further structural analysis and sequence comparison of SpSSADH with other SSADHs revealed that Ser158 and Tyr188 in SpSSADH participate in the stabilization of the 2’-phosphate group of adenine-side ribose in NADP+. Our results provide structural insights into the cofactor preference of SpSSADH as the gram-positive bacterial SSADH.

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Kinetic Characterization and Molecular Modeling of NAD(P)+-Dependent Succinic Semialdehyde Dehydrogenase from Bacillus subtilis as an Ortholog YneI

Cited by 16 publications

References 21 publications

Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142

Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142

A Systems Approach Discovers the Role and Characteristics of Seven LysR Type Transcription Factors in Escherichia Coli

Kinetic and Structural Characterization for Cofactor Preference of Succinic Semialdehyde Dehydrogenase from Streptococcus pyogenes

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