Dynamic, Ligand-dependent Conformational Change Triggers Reaction of Ribose-1,5-bisphosphate Isomerase from Thermococcus kodakarensis KOD1

Nakamura, Akira; Fujihashi, M.; Aono, Riku; Sato, Takaaki; Nishiba, Y.; Yoshida, Shosuke; Yano, Ayumu; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio

doi:10.1074/jbc.m112.349423

Cited by 26 publications

(47 citation statements)

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“…In previous studies, the substrate (R15P) used in measuring R15P isomerase activity was prepared enzymatically from AMP and sodium phosphate using AMPpase (18,25). R15P isomerase displayed a specific activity of about 35 mol min Ϫ1 mg Ϫ1 , a level similar to those observed in the previous studies, when the AMPpase reaction mixture, which includes R15P as well as AMP, adenine, and phosphate (referred to here as E-R15P), was used as the substrate (Fig.…”

Section: Resultssupporting

confidence: 70%

“…Recombinant His 6 -tagged R15P isomerase and Rubisco were produced in E. coli and were purified as described previously (18). The recombinant AMPpase was expressed as described elsewhere (25).…”

Section: Methodsmentioning

confidence: 99%

“…The reaction is of interest because opening of the furanose ring cannot precede isomerization due to the phosphate group on the C-1 carbon. The structure of R15P isomerase revealed that the enzyme displayed a hexameric assembly (18). Crystal structures bound to the substrate/product and mutational studies indicated that Cys133 and Asp202 act as active-site residues in the enzyme and that the reaction proceeds via a cis-phosphoenolate intermediate.…”

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confidence: 99%

“…The enzymatic and structural features of type III Rubiscos have been reported previously (1,7,8,(15)(16)(17)34). As mentioned above, we have recently determined the 3-dimensional structure of T. kodakarensis R15P isomerase (18). However, no detailed biochemical characterization of the two novel enzymes, AMPpase and R15P isomerase, has been reported.…”

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confidence: 99%

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Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway

et al. 2012

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dAMP phosphorylase (AMPpase), ribose-1,5-bisphosphate (R15P) isomerase, and type III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to constitute a novel pathway involved in AMP metabolism in the Archaea. Here we performed a biochemical examination of AMPpase and R15P isomerase from Thermococcus kodakarensis. R15P isomerase was specific for the ␣-anomer of R15P and did not recognize other sugar compounds. We observed that activity was extremely low with the substrate R15P alone but was dramatically activated in the presence of AMP. Using AMP-activated R15P isomerase, we reevaluated the substrate specificity of AMPpase. AMPpase exhibited phosphorylase activity toward CMP and UMP in addition to AMP. The [S]-v plot (plot of velocity versus substrate concentration) of the enzyme toward AMP was sigmoidal, with an increase in activity observed at concentrations higher than approximately 3 mM. The behavior of the two enzymes toward AMP indicates that the pathway is intrinsically designed to prevent excess degradation of intracellular AMP. We further examined the formation of 3-phosphoglycerate from AMP, CMP, and UMP in T. kodakarensis cell extracts. 3-Phosphoglycerate generation was observed from AMP alone, and from CMP or UMP in the presence of dAMP, which also activates R15P isomerase. 3-Phosphoglycerate was not formed when 2-carboxyarabinitol 1,5-bisphosphate, a Rubisco inhibitor, was added. The results strongly suggest that these enzymes are actually involved in the conversion of nucleoside monophosphates to 3-phosphoglycerate in T. kodakarensis.A rchaea comprise the third domain of life and exhibit unique metabolic features that are not found in bacteria and eukaryotes. The metabolic enzymes and pathways utilized for glycolysis and pentose biosynthesis in many archaea differ from the classical Embden-Meyerhof (EM)/Entner-Doudoroff (ED) pathways (24,27,33,35) and the pentose phosphate pathway (11,19,28), respectively. A previous study of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (3, 9) suggested the presence of a novel pathway involved in nucleic acid metabolism (25). The pathway consists of a type III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and two novel enzymes, AMP phosphorylase (AMPpase) and ribose-1,5-bisphosphate (R15P) isomerase. In the first reaction of this pathway, catalyzed by AMPpase, the adenine base of AMP is released and is replaced by a phosphate group to generate R15P. In the following R15P isomerase reaction, R15P is converted to ribulose 1,5-bisphosphate (RuBP). In the final reaction, Rubisco catalyzes the conversion of RuBP, CO 2 , and H 2 O to 2 molecules of 3-phosphoglycerate (3-PGA), which is an intermediate of central sugar metabolism. Genome sequences indicate that this pathway is distributed broadly among the Archaea, including all members of the Thermococcales, Archaeoglobales, Methanomicrobiales, and Methanosarcinales. The pathway is also found in several members of the Halobacteriales, Methanococcales, Desulfurococcales...

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Section: Resultssupporting

confidence: 70%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway

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“…All three enzymes have been studied extensively, and the crystal structures from archaeal R1,5BP isomerase and type III RubisCOs have been reported (386)(387)(388)(389)(390)(391)(392)(393)(394)(395)(396). The conversion of nucleoside monophosphates to 3PG was also detected in crude extracts of Tco.…”

Section: Alternative Pathways For C 5 -C 3 Interconversionmentioning

confidence: 99%

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

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

280

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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An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research

Rashid

Aslam

2019

Folia Microbiol

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Dynamic, Ligand-dependent Conformational Change Triggers Reaction of Ribose-1,5-bisphosphate Isomerase from Thermococcus kodakarensis KOD1

Cited by 26 publications

References 41 publications

Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway

Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway

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

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research

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