From hyperthermophiles to psychrophiles: the structural basis of temperature stability of the amino acid dehydrogenases

Baker, Patrick J.

doi:10.1042/bst0320264

Cited by 8 publications

(4 citation statements)

References 42 publications

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“…Such trends are not apparent when comparing TnIYD to HsIYD and HhIYD other than the gain of hydrophobic residues (W82, F88) in the active site of TnIYD, and even these substitutions are not universal in all homologues from thermophiles. An increase in the number of salt bridges is another common strategy for achieving thermal stability ( 38 , 39 , 40 ), but a similar number of salt bridges is observed within HsIYD and TnIYD. Instead, the thermal stability of TnIYD likely derives from its minimal sequence that is shared by homologues from other thermophilic Bacteria as well as thermophilic Archaea and distinct from those of mesophiles from all three domains of life ( 4 ).…”

Section: Discussionmentioning

confidence: 96%

The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana

Sun

Bing²,

Spisak³

et al. 2021

Journal of Biological Chemistry

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The nitroreductase superfamily of enzymes encompasses many flavin mononucleotide (FMN)-dependent catalysts promoting a wide range of reactions. All share a common core consisting of an FMN-binding domain, and individual subgroups additionally contain one to three sequence extensions radiating from defined positions within this core to support their unique catalytic properties. To identify the minimum structure required for activity in the iodotyrosine deiodinase subgroup of this superfamily, attention was directed to a representative from the thermophilic organism Thermotoga neapolitana (TnIYD). This representative was selected based on its status as an outlier of the subgroup arising from its deficiency in certain standard motifs evident in all homologues from mesophiles. We found that TnIYD lacked a typical N-terminal sequence and one of its two characteristic sequence extensions, neither of which was found to be necessary for activity. We also show that TnIYD efficiently promotes dehalogenation of iodo-, bromo-, and chlorotyrosine, analogous to related deiodinases (IYDs) from humans and other mesophiles. In addition, 2-iodophenol is a weak substrate for TnIYD as it was for all other IYDs characterized to date. Consistent with enzymes from thermophilic organisms, we observed that TnIYD adopts a compact fold and low surface area compared with IYDs from mesophilic organisms. The insights gained from our investigations on TnIYD demonstrate the advantages of focusing on sequences that diverge from conventional standards to uncover the minimum essentials for activity. We conclude that TnIYD now represents a superior starting structure for future efforts to engineer a stable dehalogenase targeting halophenols of environmental concern.

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Section: Discussionmentioning

confidence: 96%

The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana

Sun

Bing²,

Spisak³

et al. 2021

Journal of Biological Chemistry

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“…Furthermore, Arg and Tyr are significantly more abundant, whereas Cys and Ser are less frequent in thermophilic proteins. 26,40,41 Proteins from meso-and thermophiles also significantly differ by their aliphatic index, which is directly related to the content of aliphatic residues Ala, Ile, Leu, and Val. 42,43 At the level of secondary structure, the thermophilic proteins are characterized by a greater amount of R-helical structure, avoiding Pro in their R-helices to a greater extent than mesophilic proteins.…”

Section: Discussionmentioning

confidence: 99%

“…It is known that the thermophilic polypeptides in comparison with their mesophilic homologues possess increased amount of salt bridges and side chain-side chain hydrogen bonds. Furthermore, Arg and Tyr are significantly more abundant, whereas Cys and Ser are less frequent in thermophilic proteins. ,, Proteins from meso- and thermophiles also significantly differ by their aliphatic index, which is directly related to the content of aliphatic residues Ala, Ile, Leu, and Val. , At the level of secondary structure, the thermophilic proteins are characterized by a greater amount of α-helical structure, avoiding Pro in their α-helices to a greater extent than mesophilic proteins. Overall, evolutionary pressure led to the increased internal hydrophobicity and increased external polarity of thermophilic proteins .…”

Section: Discussionmentioning

confidence: 99%

Improving Solubility ofShewanellaoneidensisMR-1 andClostridiumthermocellumJW-20 Proteins Expressed intoEsherichiacoli

Kataeva

Chang

et al. 2005

J. Proteome Res.

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Low solubility of proteins overexpressed in E. coli is a frequent problem in high-throughput structural genomics. To improve solubility of proteins from mesophilic Shewanella oneidensis MR-1 and thermophilic Clostridium thermocellum JW20, an approach was attempted that included a fusion of the target protein to a maltose-binding protein (MBP) and a decrease of induction temperature. The MBP was selected as the most efficient solubilizing carrier when compared to a glutathione S-transferase and a Nus A protein. A tobacco etch virus (TEV) protease recognition site was introduced between fused proteins using a double polymerase-chain reaction and four primers. In this way, 79 S. oneidensis proteins have been expressed in one case with an N-terminal 30-residue tag and in another case as a fusion protein with MBP. A foreign tag might significantly affect the properties of the target polypeptide. At 37 degrees C and 18 degrees C induction temperatures, only 5 and 17 tagged proteins were soluble, respectively. In fusion with MBP 4, 34, and 38 proteins were soluble upon induction at 37 degrees, 28 degrees, and 18 degrees C, respectively. The MBP is assumed to increase stability and solubility of a target protein by changing both the mechanism and the cooperativity of folding/unfolding. The 66 C. thermocellum proteins were expressed as fusion proteins with MBP. Induction at 37 degrees, 28 degrees, and 18 degrees C produced 34, 57, and 60 soluble proteins, respectively. The higher solubility of C. thermocellum proteins in comparison with the S. oneidensis proteins under similar conditions of induction correlates with the thermophilicity of the host. The two-factor Wilkinson-Harrison statistical model was used to identify soluble and insoluble proteins. Theoretical and experimental data showed good agreement for S. oneidensis proteins; however, the model failed to identify soluble/insoluble Clostridium proteins. A suggestion has been made that the Wilkinson-Harrison model is not applicable to C. thermocellum proteins because it did not account for the peculiarities of protein sequences from thermophiles.

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“…An increase in the number of charged residues has been described specifically in alpha helices, organized in a way to form stabilizing ion pairs (Das and Gerstein, 2000;Chakravarty et al, 2002). In general, increased ion pair networks have also been observed particularly in hyperthermophilic organisms (and, to a lesser extend, in thermophilic organisms) through a higher number of salt bridges (Baker, 2004;Karshikoff and Ladenstein, 2001).…”

Section: Introductionmentioning

confidence: 96%

Prediction of potential thermostable proteins in Xylella fastidiosa

Linden

Rêgo

Araújo

et al. 2006

Journal of Theoretical Biology

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From hyperthermophiles to psychrophiles: the structural basis of temperature stability of the amino acid dehydrogenases

Cited by 8 publications

References 42 publications

The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana

The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana

Improving Solubility ofShewanellaoneidensisMR-1 andClostridiumthermocellumJW-20 Proteins Expressed intoEsherichiacoli

Prediction of potential thermostable proteins in Xylella fastidiosa

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