Characterization of the nicotinamide adenine dinucleotides (NAD+ and NADP+) binding sites of the monomeric isocitrate dehydrogenases from Campylobacter species

Zhu, Guoping; Chen, Xuefei; Yang, Jing; Pei, Yunyun; Bian, Mingjie; Zhu, Guoping

doi:10.1016/j.biochi.2019.03.007

Cited by 5 publications

(6 citation statements)

References 27 publications

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“…The type III IDH subfamily was recently redefined through the addition of a novel monomeric NAD-IDH subgroup, which highly likely comprises the ancestral proteins of this subfamily ( Wang et al, 2015 ; Wang et al, 2019 ). To determine the evolutionary relationship between PtIDH2 and other IDH protein family members, a phylogenetic tree was reconstructed in MEGA7 using 42 IDH sequences.…”

Section: Resultsmentioning

confidence: 99%

“…It has been shown that monomeric NAD-IDHs, such as Campylobacter sp. IDH (CaIDH) and Campylobacter curvus IDH (CcIDH) ( Wang et al, 2015 ; Wang et al, 2019 ), primarily use polar, uncharged amino acids (Met583, Leu584, Asp595, and Ser644 for CaIDH) to bind the coenzyme NAD + . In contrast, the residues that bind the coenzyme NADP + in type III NADP-IDHs are positively charged (His and Arg).…”

Section: Resultsmentioning

confidence: 99%

“…In contrast, Leu584, Asp595, and Ser644 in CaIDH, which correspond, respectively, to the NADP + binding residues in AvIDH, are polar uncharged amino acids. The side chains of Asp and Leu form hydrogen bonds with the 2′ and 3′-hydroxyl groups of NAD + , such that the enzyme has a high affinity for this coenzyme ( Wang et al, 2015 ; Wang et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…IDHs are widely distributed in all living organisms, including archaea, bacteria, and eukaryotes. However, to date, type III IDHs, such as Azotobacter vinelandii IDH (AvIDH), Corynebacterium glutamicum IDH (CgIDH), Campylobacter concisus IDH ( Wang et al, 2019 ), and Methanococcoides methylutens IDH (MmIDH) ( Wang et al, 2020 ), have been identified only in prokaryotes. Over recent years, with the development of high-throughput genome sequencing technology, a large number of complete genome sequences from marine organisms have become available.…”

Section: Introductionmentioning

confidence: 99%

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Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

Huang

Zhao

et al. 2021

Front. Mol. Biosci.

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Isocitrate dehydrogenase (IDH) family of proteins is classified into three subfamilies, namely, types I, II, and III. Although IDHs are widely distributed in bacteria, archaea, and eukaryotes, all type III IDHs reported to date are found only in prokaryotes. Herein, a novel type III IDH subfamily member from the marine microalga Phaeodactylum tricornutum (PtIDH2) was overexpressed, purified, and characterized in detail for the first time. Relatively few eukaryotic genomes encode this type of IDH and PtIDH2 shares the highest homology with marine bacterial monomeric IDHs, suggesting that PtIDH2 originated through a horizontal gene transfer event between a marine alga and a bacterium. Size-exclusion chromatography revealed that the native PtIDH2 is a homotetramer (∼320 kDa) in solution, comprising four monomeric IDH-like subunits (80 kDa each). Enzymatic characterization showed that PtIDH2 is a bivalent metal ion-dependent enzyme and Mn2+ is the optimal activator. The recombinant PtIDH2 protein exhibited maximal activity at 35°C and pH 8.0 in the presence of Mn2+. Heat-inactivation analysis revealed that PtIDH2 is a cold-adapted enzyme. Kinetic analysis demonstrated that PtIDH2 is a completely NADP+-specific IDH with no detectable NAD+-associated catalytic activity. The three putative key NADP+-binding residues (His604, Arg615, and Arg664) in PtIDH2 were also evaluated by site-directed mutagenesis. The H604L/R615D/R664S triple mutant showed a 3.25-fold preference for NAD+ over NADP+, implying that the coenzyme specificity of PtIDH2 can be converted from NADP+ to NAD+ through rational engineering approaches. Additionally, the roles of the conserved residues Ala718 and Leu742 in the thermostability of PtIDH2 were also explored by site-directed mutagenesis. We found that the L742F mutant displayed higher thermostability than wild-type PtIDH2. This study expands the phylogeny of the IDH family and provides new insights into the evolution of IDHs.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

Huang

Zhao

et al. 2021

Front. Mol. Biosci.

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“…Nicotine amide adenine dinucleotide (NADH) is an important co-enzyme in living cells which has essential roles in biological systems [1][2][3]. As determination of NADH is helpful in diagnostic of many sicknesses such as cancer and diabetes, therefore a lot of scientists in all around the word are trying to develop accurate, precise and cost-effective methods for NADH monitoring [4].…”

Section: Introductionmentioning

confidence: 99%

Controlled Electrodeposition of Au‐Copper Oxide Nanocomposite on a Renewable Carbon Ceramic Electrode for Sensitive Determination of NADH in Serum Samples

Mohammad‐Rezaei

Golmohammadpour

2019

Electroanalysis

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In this study, a sensitive nicotinamide adenine dinucleotide (NADH) biosensor based on Au‐Copper oxide nanocomposite modified carbon ceramic electrode (Au−CuO/CCE) was introduced. The developed NADH biosensor was prepared by controlled electrodeposition of copper and Au nanoparticles on the surface of a renewable CCE and was turned to Au−CuO/CCE by cycling the potential in alkaline media. The prepared electrode was carefully characterized with scanning electron microscopy, X‐ray diffraction, atomic force microscopy and cyclic voltammetry techniques. According to scan rate study, surface coverage (Γ) of the fabricated Au−CuO/CCE was calculated to be 1.54×10−8 mol cm−2 which was 3 time more than CuO/CCE. The fabricated electrode is well stable which could be reliably utilized for the determination of NADH with amperometry technique over the concentration range of 1–29 μM with sensitivity and detection limit (S/N=3) of 0.1025 μA μM−1 and 0.09 μM respectively. The prepared biosensor was used for NADH determination in serum samples with fast response time and satisfactory analytical results.

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Molecular insights and functional analysis of isocitrate dehydrogenase in two gram-negative pathogenic bacteria

Xiong,

Su,

Han

et al. 2024

World J Microbiol Biotechnol

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Characterization of the nicotinamide adenine dinucleotides (NAD+ and NADP+) binding sites of the monomeric isocitrate dehydrogenases from Campylobacter species

Cited by 5 publications

References 27 publications

Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

Biochemical and Phylogenetic Characterization of a Novel NADP+-Specific Isocitrate Dehydrogenase From the Marine Microalga Phaeodactylum tricornutum

Controlled Electrodeposition of Au‐Copper Oxide Nanocomposite on a Renewable Carbon Ceramic Electrode for Sensitive Determination of NADH in Serum Samples

Molecular insights and functional analysis of isocitrate dehydrogenase in two gram-negative pathogenic bacteria

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