Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix

Kawakami, Retsuo; Sakuraba, Haruhiko; Goda, Shuichiro; Tsuge, Hideaki; Ohshima, Toshihisa

doi:10.1016/j.bbapap.2009.06.014

Cited by 13 publications

(12 citation statements)

References 46 publications

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“…It has been reported that oxaloacetate and NAD do not interact directly and oxaloacetate binding does not induce any conformational changes in protein structure in A. arcticum (Kim et al, 1999). In addition, substrate specificity is provided by an arginine residue near position 100 (Dym et al, 1995;Lee et al, 2001;Kawakami et al, 2009) (Kim et al, 1999). In E. coli, Arg 81 is in the NAD binding domain, and Arg 153 is present at the catalytic site (Hall et al, 1992).…”

Section: Crystallization Cofactor Binding Sites and Catalytic Domainsmentioning

confidence: 99%

“…In proteins obtained from hyperthermophiles, the preferential use of NADPH as the cofactor is due to the presence of glycine at position 33 (Lee et al, 2001) and the dual specificity for the cofactor results from alanine at position 53 in Methanobacterium jannaschii (Kawakami et al, 2009). The NAD + specificity of hyperthermophilic Chloroflexus aurantiacus is determined by Asp 32 , which is similar to other MDHs in which the specificity is given by Asp or Glu (Dalhus et al, 2002 , and a loop formed by residues 90-100 is also important (Kim et al, 1999 , and Met 227 .…”

Section: Crystallization Cofactor Binding Sites and Catalytic Domainsmentioning

confidence: 99%

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Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase

Takahashi-Íñiguez

Aburto-Rodríguez

Vilchis-González

et al. 2016

J. Zhejiang Univ. Sci. B

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Abstract:Malate dehydrogenase (MDH) is an enzyme widely distributed among living organisms and is a key protein in the central oxidative pathway. It catalyzes the interconversion between malate and oxaloacetate using NAD + or NADP + as a cofactor. Surprisingly, this enzyme has been extensively studied in eukaryotes but there are few reports about this enzyme in prokaryotes. It is necessary to review the relevant information to gain a better understanding of the function of this enzyme. Our review of the data generated from studies in bacteria shows much diversity in their molecular properties, including weight, oligomeric states, cofactor and substrate binding affinities, as well as differences in the direction of the enzymatic reaction. Furthermore, due to the importance of its function, the transcription and activity of this enzyme are rigorously regulated. Crystal structures of MDH from different bacterial sources led to the identification of the regions involved in substrate and cofactor binding and the residues important for the dimer-dimer interface. This structural information allows one to make direct modifications to improve the enzyme catalysis by increasing its activity, cofactor binding capacity, substrate specificity, and thermostability. A comparative analysis of the phylogenetic reconstruction of MDH reveals interesting facts about its evolutionary history, dividing this superfamily of proteins into two principle clades and establishing relationships between MDHs from different cellular compartments from archaea, bacteria, and eukaryotes.

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Section: Crystallization Cofactor Binding Sites and Catalytic Domainsmentioning

confidence: 99%

Section: Crystallization Cofactor Binding Sites and Catalytic Domainsmentioning

confidence: 99%

Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase

Takahashi-Íñiguez

Aburto-Rodríguez

Vilchis-González

et al. 2016

J. Zhejiang Univ. Sci. B

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“…[23], Streptomyces coelicolor [20] and higher plant cytosols [19] have a dimeric structure, whereas those in Bacillus sp. [17], Flavobacterium frigidimaris [24], and Aeropyrum pernix [25] have a tetrameric structure. Analytical gel filtration chromatography revealed that MDH from T. thermophilus was a dimer, which is consistent with the quaternary structure of the Thermus genus [21], [22].…”

Section: Discussionmentioning

confidence: 99%

Crystal Structures and Molecular Dynamics Simulations of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion for Co-Substrate Binding

et al. 2013

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Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60°C and specific activity of about 2,600 U/mg with optimal temperature of 90°C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity.

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“…MDH_AERPE is a homotetrameric protein with a molecular mass of about 110 kDa. 47 Homotetrameric MDH has also been characterized from the hyperthermophilic Archaea Methanocaldococcus jannaschii, and from a dimer MDH from the hyperthermophilic Archaea Arhaeoglobus fulgidus; the dimer MDH from A. fulgidus lacks the sequence that mediates the dimer-dimer interaction. 48 Structural comparisons of MDHs have revealed that the hyperthermostability of MDH_AERPE appears to be attributable to its smaller cavity volume and larger number of ion pairs and ion-pair networks.…”

Section: 4 Dehydrogenasesmentioning

confidence: 99%

“…48 Structural comparisons of MDHs have revealed that the hyperthermostability of MDH_AERPE appears to be attributable to its smaller cavity volume and larger number of ion pairs and ion-pair networks. 47 Protein Q9YC65 from the methanolic extract (an NADP-dependent glutamate dehydrogenase) was identified in two spots, spot ID5 and spot ID10, with slightly different pIs, of 6.42 and 6.50, respectively, but the same molecular masses (Figure 1, Table 1). This might have resulted from post-translational modifications, such as glycosylation, phosphorylation or proteolytic cleavage, which have been seen to occur with proteins in Archaea.…”

Section: 4 Dehydrogenasesmentioning

confidence: 99%

Antioxidative Activity of Methanolic and Water Extracts from the Hyperthermophilic Archaeon Aeropyrum pernix K1

Skrt

Jamnik²,

Ulrih

2018

ACSi

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The hyperthermophilic archaeon Aeropyrum pernix has adapted to optimal growth under high temperatures in saline environments and under oxidizing conditions. In the present study, we focused on the antioxidative activity of proteins from A. pernix K1. Following high temperature methanol and water extractions of the protein from the biomass of A. pernix K1, the total sulphydryl groups and radical scavenging activities were investigated. The total protein in the methanolic extract was 36% lower and showed 10% fewer sulphydryl groups than that from the water extract. However, the radical scavenging activity of the water extract was four-fold greater than for the methanolic extract. The proteins of both of these extracts were separated by two-dimensional electrophoresis, and selected proteins were identified using mass spectrometry. The majority of these identified proteins were intracellular proteins, such as those involved in oxidative stress responses and osmotic stress responses, and proteins with hydrolase and dehydrogenase activities. These proteins are also common to most organisms, and included putative uncharacterized proteins.

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Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix

Cited by 13 publications

References 46 publications

Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase

Function, kinetic properties, crystallization, and regulation of microbial malate dehydrogenase

Crystal Structures and Molecular Dynamics Simulations of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion for Co-Substrate Binding

Antioxidative Activity of Methanolic and Water Extracts from the Hyperthermophilic Archaeon Aeropyrum pernix K1

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