Structure and Function of a Regulated Archaeal Triosephosphate Isomerase Adapted to High Temperature

Walden, Helen; Taylor, G.L.; Lorentzen, Esben; Pohl, Ehmke; Lilie, Hauke; Schramm, Alexander; Knura, Thomas; Stubbe, K.; Tjaden, Britta; Hensel, Reinhard

doi:10.1016/j.jmb.2004.07.067

Cited by 33 publications

(37 citation statements)

References 58 publications

(55 reference statements)

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“…tenax, a preference in the formation of DHAP (anabolic function) was observed (K m of 0.9 mM and V max of 2,000 U/mg for DHAP; K m of 0.2 mM and V max of 9,500 U/mg for GAP) (140,147). The enzyme in solution showed an unusual equilibrium between inactive dimers and active tetramers that was shifted by the specific interaction with glycerol-1-phosphate dehydrogenase toward active tetramers, and a possible physiological function of protein-protein interactions in channeling thermolabile DHAP toward lipid biosynthesis was discussed (147).…”

Section: Thermoproteus Tenaxmentioning

confidence: 98%

“…TIM activity has been detected in crude extracts of many archaeal species (40-42, 70, 105, 128), and TIM sequences have been identified in apparently all archaeal genomes (36,43 (145)(146)(147)(148). The archaeal TIM sequences are shorter, by ϳ20 amino acids, than those of their bacterial/eukaryotic counterparts, comprising ϳ230 amino acids and ϳ250 to 260 amino acids, corresponding to ϳ24 kDa and 28 kDa, respectively (36,139).…”

Section: Triosephosphate Isomerasementioning

confidence: 99%

“…maritima is also a tetramer (149), and TIM from the mesophilic archaeon Methanobacterium bryantii is a homodimer, there appears to be a correlation between oligomerization and thermoadaptation. Therefore, TIMs became one of the model systems to study thermoadaptation of proteins, especially the stabilizing mechanism, through higher oligomerization states (146,147). However, the TIM from the hyperthermo- (138), which also has been described for some halophilic Archaea.…”

Section: Triosephosphate Isomerasementioning

confidence: 99%

“…tenax was found to exist in an equilibrium between inactive dimers and active tetramers, which is shifted to the tetrameric state through a specific interaction with glycerol-1-phosphate dehydrogenase. This observation was interpreted in physiological terms as a need to reduce the formation of thermolabile metabolic intermediates (GAP and DHAP) (140,147). TIMs are the archetypical (␤/␣) 8 barrel proteins or TIM barrels ( Fig.…”

Section: Triosephosphate Isomerasementioning

confidence: 99%

“…8): an 8-fold repeat of strand-turn-helix-turn units assembled into a cylinder of eight parallel ␤ strands surrounded by a layer of eight ␣ helices. The active site is located at the carboxyl end of the barrel (45,(146)(147)(148). The enzyme follows an enediolate intermediate mechanism (Glu144 [P. woesei numbering] acid/base catalyst) (150,151).…”

Section: Triosephosphate Isomerasementioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Thermoproteus Tenaxmentioning

confidence: 98%

Section: Triosephosphate Isomerasementioning

confidence: 99%

Section: Triosephosphate Isomerasementioning

confidence: 99%

Section: Triosephosphate Isomerasementioning

confidence: 99%

Section: Triosephosphate Isomerasementioning

confidence: 99%

See 3 more Smart Citations

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality

Katebi

Jernigan

2013

Protein Science

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Triosephosphate isomerase (TIM) catalyzes the reaction to convert dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and vice versa. In most organisms, its functional oligomeric state is a homodimer; however, tetramer formation in hyperthermophiles is required for functional activity. The tetrameric TIM structure also provides added stability to the structure, enabling it to function at more extreme temperatures. We apply Principal Component Analysis to find that the TIM structure space is clearly divided into two groups-the open and the closed TIM structures. The distribution of the structures in the open set is much sparser than that in the closed set, showing a greater conformational diversity of the open structures. We also apply the Elastic Network Model to four different TIM structures-an engineered monomeric structure, a dimeric structure from a mesophile-Trypanosoma brucei, and two tetrameric structures from hyperthermophiles Thermotoga maritima and Pyrococcus woesei. We find that dimerization not only stabilizes the structures, it also enhances their functional dynamics. Moreover, tetramerization of the hyperthermophilic structures increases their functional loop dynamics, enabling them to function in the destabilizing environment of extreme temperatures. Computations also show that the functional loop motions, especially loops 6 and 7, are highly coordinated. In summary, our computations reveal the underlying mechanism of the allosteric regulation of the functional loops of the TIM structures, and show that tetramerization of the structure as found in the hyperthermophilic organisms is required to maintain the coordination of the functional loops at a level similar to that in the dimeric mesophilic structure.

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AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase

et al. 2023

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Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple‐drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β‐fold with multiple secondary structure elements omitted or shortened compared with protein structures of similar proteins. The functional characterization of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity toward thermophilic and mesophilic bacteria strains containing Orn‐type or DAP‐type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterized with a temperature optimum at 85°C. The extraordinary high melting temperature T m 102.6°C confirms fold stability up to approximately 100°C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.

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Structure and Function of a Regulated Archaeal Triosephosphate Isomerase Adapted to High Temperature

Cited by 33 publications

References 58 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality

AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase

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