Crystal structure and stereochemical studies of KD(P)G aldolase from <i>Thermoproteus tenax</i>

Pauluhn, A.; Ahmed, Hatim; Lorentzen, Esben; Buchinger, Sebastian; Schomburg, Dietmar; Siebers, Bettina; Pohl, Ehmke

doi:10.1002/prot.21890

Cited by 14 publications

(10 citation statements)

References 34 publications

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“…On the basis of crystal structures of Sulfolobus and Thermoproteus KD(P)GAs, amino acids for substrate binding were identified, including two conserved arginines and a conserved tyrosine (Fig. 3), which were proposed to form a putative phosphate binding pocket (16,30; Gary Taylor [United Kingdom], unpublished results). These conserved amino acids are absent in KDGA from P. torridus, which might reflect its preference for nonphosphorylated substrate KDG.…”

Section: Discussionmentioning

confidence: 99%

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The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase

et al. 2010

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The pathway of glucose degradation in the thermoacidophilic euryarchaeon Picrophilus torridus has been studied by in vivo labeling experiments and enzyme analyses. After growth of P. torridus in the presence of [1-13 C]-and [3-13 C]glucose, the label was found only in the C-1 and C-3 positions, respectively, of the proteinogenic amino acid alanine, indicating the exclusive operation of an Entner-Doudoroff (ED)-type pathway in vivo. Cell extracts of P. torridus contained all enzyme activities of a nonphosphorylative ED pathway, which were not induced by glucose. Two key enzymes, gluconate dehydratase (GAD) and a novel 2-keto-3-deoxygluconate (KDG)-specific aldolase (KDGA), were characterized. GAD is a homooctamer of 44-kDa subunits, encoded by Pto0485. KDG aldolase, KDGA, is a homotetramer of 32-kDa subunits. This enzyme was highly specific for KDG with up to 2,000-fold-higher catalytic efficiency compared to 2-keto-3-deoxy-6-phosphogluconate (KDPG) and thus differs from the bifunctional KDG/KDPG aldolase, KD(P)GA of crenarchaea catalyzing the conversion of both KDG and KDPG with a preference for KDPG. The KDGA-encoding gene, kdgA, was identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) as Pto1279, and the correct translation start codon, an ATG 24 bp upstream of the annotated start codon of Pto1279, was determined by N-terminal amino acid analysis. The kdgA gene was functionally overexpressed in Escherichia coli. Phylogenetic analysis revealed that KDGA is only distantly related to KD(P)GA, both enzymes forming separate families within the dihydrodipicolinate synthase superfamily. From the data we conclude that P. torridus degrades glucose via a strictly nonphosphorylative ED pathway with a novel KDG-specific aldolase, thus excluding the operation of the branched ED pathway involving a bifunctional KD(P)GA as a key enzyme.Comparative analyses of sugar-degrading pathways in members of the domain Archaea revealed that all species analyzed so far degrade glucose and glucose polymers to pyruvate via modification of the classical Embden-Meyerhof (EM) and Entner-Doudoroff (ED) pathways found in bacteria and eukarya. Modified EM pathways were reported for hyperthermophilic archaea, including, e.g., the strictly fermentative Thermococcales and Desulfurococcales, the sulfur-reducing Thermoproteus tenax, and the microaerophilic Pyrobaculum aerophilum. These pathways differ from the classical EM pathway by the presence of several novel enzymes and enzyme families, catalyzing, e.g., the phosphorylation of glucose and fructose-6-phosphate, isomerization of glucose-6-phosphate, and oxidation of glyceraldehyde-3-phosphate (18,22,25).Modified ED pathways have been proposed for aerobic archaea, including halophiles, and thermoacidophilic crenarchaea, such as Sulfolobus species, and the euryarchaea Thermoplasma acidophilum and Picrophilus torridus. The anaerobic Thermoproteus tenax, which degrades glucose predominantly via a modified EM pathway, also utilizes-to a minor exte...

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Section: Discussionmentioning

confidence: 99%

“…In fact, the bifunctional KD(P)GA showed a higher catalytic efficiency for KDPG than for KDG (1,14). Crystal structures of bifunctional KD(P)GAs of S. solfataricus and T. tenax have been reported (16,27,30; G. Taylor [United Kingdom], unpublished data).…”

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confidence: 99%

The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase

et al. 2010

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“…acidocaldarius, and Tpt. tenax have been reported (295)(296)(297)(298). They belong to the protein family of Schiff base-forming class I aldolases, in which the archaeal KD(P)G aldolases appear to belong to a distinct subgroup of enzymes (SCOP database).…”

Section: -Keto-3-deoxy-(6-phospho)gluconate Aldolase [Kd(p)ga]mentioning

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

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266

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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“…In accordance with the low sequence identity, the aldolases from these archaea differ from H. volcanii KDPGA in several aspects: (i) they belong to the dihydrodipicolinate synthase (DHDPS)-like family of the class I aldolase superfamily, (ii) they constitute homotetrameric proteins composed of ϳ32-kDa subunits, and (iii) they show substrate promiscuity for KDPGal/KDGal (S. solfataricus) and KDGal (P. torridus) (3,7,44). However, the substrate promiscuity of KDG/KDPG aldolase from T. tenax is still unclear (45).…”

Section: Fig 5 Growth Analysis Of the H Volcanii Gad Deletion Mutantmentioning

confidence: 99%

Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase

et al. 2016

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The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. So far, the key enzymes of this pathway, glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (KDPGA), have not been characterized, and their functional involvement in glucose degradation has not been demonstrated. Here we report that the genes HVO_1083 and HVO_0950 encode GDH and KDPGA, respectively. The recombinant enzymes show high specificity for glucose and KDPG and did not convert the corresponding C 4 epimers galactose and 2-keto-3-deoxy-6-phosphogalactonate at significant rates. Growth studies of knockout mutants indicate the functional involvement of both GDH and KDPGA in glucose degradation. GAD was purified from H. volcanii, and the encoding gene, gad, was identified as HVO_1488. GAD catalyzed the specific dehydration of gluconate and did not utilize galactonate at significant rates. A knockout mutant of GAD lost the ability to grow on glucose, indicating the essential involvement of GAD in glucose degradation. However, following a prolonged incubation period, growth of the ⌬gad mutant on glucose was recovered. Evidence is presented that under these conditions, GAD was functionally replaced by xylonate dehydratase (XAD), which uses both xylonate and gluconate as substrates. Together, the characterization of key enzymes and analyses of the respective knockout mutants present conclusive evidence for the in vivo operation of the spED pathway for glucose degradation in H. volcanii. IMPORTANCEThe work presented here describes the identification and characterization of the key enzymes glucose dehydrogenase, gluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase and their encoding genes of the proposed semiphosphorylative Entner-Doudoroff pathway in the haloarchaeon Haloferax volcanii. The functional involvement of the three enzymes was proven by analyses of the corresponding knockout mutants. These results provide evidence for the in vivo operation of the semiphosphorylative Entner-Doudoroff pathway in haloarchaea and thus expand our understanding of the unusual sugar degradation pathways in the domain Archaea. Glucose degradation in thermoacidophilic and halophilic archaea has been proposed to proceed via modified versions of the classical Entner-Doudoroff (ED) pathway of bacteria (1, 2) (Fig. 1). For the thermoacidophilic euryarchaeon Picrophilus torridus, a nonphosphorylative ED (npED) pathway was reported (3). Accordingly, glucose is converted to 2-keto-3-deoxygluconate (KDG) via glucose dehydrogenase (GDH) and gluconate dehydratase (GAD). KDG is then cleaved by a KDG aldolase to pyruvate and glyceraldehyde (GA), which is converted to a second molecule of pyruvate via glyceraldehyde dehydrogenase, 2-phosphoglycerate forming glycerate kinase, enolase, and pyruvate kinase. The pathway was proposed to be promiscuous, being involved in the degradation of both D-glucose and its C 4 epimer ...

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Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax

Cited by 14 publications

References 34 publications

The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase

The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase

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

Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase

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