Structural Investigation of Cold Activity and Regulation of Aspartate Carbamoyltransferase from the Extreme Psychrophilic Bacterium Moritella profunda

Vos, Dirk De; Xu, Ying; Hulpiau, Paco; Vergauwen, Bjorn; Beeumen, Jozef J. Van

doi:10.1016/j.jmb.2006.09.064

Cited by 20 publications

(12 citation statements)

References 69 publications

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“…21.5b, the backbone structure of this enzyme (PDB ID: 3vmk) completely overlaps with that of the normal homolog from S. oneidensis strain MR-1 (PDB ID: 3vmj) (Nagae et al 2012), which was collected from Oneida Lake (Venkateswaran et al 1999). Similar structural conservation was also observed in other deep-sea enzymes such as aspartate carbamoyltransferase from M. profunda (De Vos et al 2007), '-glucosidase from Geobacillus sp. strain HTA-462 (Shirai et al 2008), Cu/Zn superoxide dismutase from the deep-sea yeast Cryptococcus liquefaciens strain N6 (Teh et al 2008), and superoxide dismutase from the deep-sea worm Alvinella pompejana (Shin et al 2009), as found for other hyperthermophilic enzymes (Vieille and Zeikus 2001).…”

Section: Primary and Tertiary Structures Of Deep-sea Dhfrssupporting

confidence: 56%

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Ohmae

Gekko

Kato

2015

Subcellular Biochemistry

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In order to elucidate the molecular adaptation mechanisms of enzymes to the high hydrostatic pressure of the deep sea, we cloned, purified, and characterized more than ten dihydrofolate reductases (DHFRs) from bacteria living in deep-sea and ambient atmospheric pressure environments. The nucleotide and amino acid sequences of these DHFRs indicate the deep-sea bacteria are adapted to their environments after the differentiation of their genus from ancestors inhabiting atmospheric pressure environments. In particular, the backbone structure of the deep-sea DHFR from Moritella profunda (mpDHFR) almost overlapped with the normal homolog from Escherichia coli (ecDHFR). Thus, those of other DHFRs would also overlap on the basis of their sequence similarities. However, the structural stability of both DHFRs was quite different: compared to ecDHFR, mpDHFR was more thermally stable but less stable against urea and pressure unfolding. The smaller volume changes due to unfolding suggest that the native structure of mpDHFR has a smaller cavity and/or enhanced hydration compared to ecDHFR. High hydrostatic pressure reduced the enzymatic activity of many DHFRs, but three deep-sea DHFRs and the D27E mutant of ecDHFR exhibited pressure-dependent activation. The inverted activation volumes from positive to negative values indicate the modification of their structural dynamics, conversion of the rate-determining step of the enzymatic reaction, and different contributions of the cavity and hydration to the transition-state structure. Since the cavity and hydration depend on amino acid side chains, DHFRs would adapt to the deep-sea environment by regulating the cavity and hydration by substituting their amino acid side chains without altering their backbone structure. The results of this study clearly indicate that the cavity and hydration play important roles in the adaptation of enzymes to the deep-sea environment.

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Section: Primary and Tertiary Structures Of Deep-sea Dhfrssupporting

confidence: 56%

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Ohmae

Gekko

Kato

2015

Subcellular Biochemistry

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“…Conversely, there is no change in the numbers of isoleucine and glycine residues, which would be expected to decrease and increase, respectively, for both adaptations; fewer serine residues (expected to increase in piezophilic enzymes) and more tyrosine residues (expected to decrease in piezophilic enzymes) were found; and there is no trend towards smaller amino acids. MpDHFR had a higher proportion of negatively charged amino acids, mainly due to an increased number of glutamate residues as also seen in aspartate transcarbamoylase from M. profunda ,19 combined with the reduction in the number of lysine residues.…”

Section: Resultsmentioning

confidence: 88%

“…Alternatively, pressure adaptation may not be intrinsic to MpDHFR, but may be brought about within the M. profunda cell by external factors such as chaperone proteins or osmolytes 16. Furthermore, it is known that “ it is not uncommon to encounter enzymes that are functionally compatible with the constraints of certain environments without being specifically adapted to them ” 19. MpDHFR might simply be “good enough” for its purpose within the context of the whole organism, with no strong selective pressure forcing it to adapt to the high pressures it encounters.…”

Section: Discussionmentioning

confidence: 99%

Are the Catalytic Properties of Enzymes from Piezophilic Organisms Pressure Adapted?

et al. 2009

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We report the crystal structure of dihydrofolate reductase (DHFR) from the psychropiezophilic bacterium Moritella profunda, which was isolated from the deep ocean at 2 degrees C and 280 bar. The structure is typical of a chromosomal DHFR and we were unable to identify any obvious structural features that would suggest pressure adaptation. In particular, the core regions of the enzyme are virtually identical to those of the DHFR from the mesophile Escherichia coli. The steady-state rate at pH 9, which is limited by hydride transfer at atmospheric pressure, is roughly constant between 1 and 750 bar, falling at higher pressures. However, the value of K(M) increases with increasing pressure, and as a result k(cat)/K(M) decreases over the entire pressure range studied. Isotope effect studies showed that increasing the pressure causes a change in the rate-limiting step of the reaction. We therefore see no evidence of pressure adaptation in either the structure or the activity of this enzyme.

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“…As a result of such a better accessibility, cold-active enzymes can accommodate substrates at lower energy cost, as far as the conformational changes are concerned, and therefore reduce the activation energy required for the formation of the enzyme-substrate complex [170]. The larger active site may also facilitate easier release and exit of products and thus may alleviate the effect of a rate-limiting step on the reaction rate [134, 171]. …”

Section: Cold-adapted Activitymentioning

confidence: 99%

Psychrophilic Enzymes: From Folding to Function and Biotechnology

2013

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Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.

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Structural Investigation of Cold Activity and Regulation of Aspartate Carbamoyltransferase from the Extreme Psychrophilic Bacterium Moritella profunda

Cited by 20 publications

References 69 publications

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Environmental Adaptation of Dihydrofolate Reductase from Deep-Sea Bacteria

Are the Catalytic Properties of Enzymes from Piezophilic Organisms Pressure Adapted?

Psychrophilic Enzymes: From Folding to Function and Biotechnology

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