Structure of triosephosphate isomerase (TIM) from<i>Methanocaldococcus jannaschii</i>

Gayathri, P.; Banerjee, Mousumi; Vijayalakshmi, A.; Azeez, Shamina; Balaram, Hemalatha; Balaram, Padmanabhan; Murthy, M.R.N.

doi:10.1107/s0907444906046488

Cited by 23 publications

(29 citation statements)

References 38 publications

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“…4B and 5). The 10-residue cluster is present in all of the TIMs sequenced to date, except in the archeabacterial enzymes, which are tetrameric and in which none of these residues are conserved (34,35). This conservation pattern suggests that their presence is not essential for monomer folding but may be essential for dimeric assembly and stability.…”

Section: The Crystal Structure Of the Mutant E104d Shows No Alteratiomentioning

confidence: 88%

Structural Basis of Human Triosephosphate Isomerase Deficiency

Rodríguez-Almazán

Arreola

Rodríguez-Larrea

et al. 2008

Journal of Biological Chemistry

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Human triosephosphate isomerase deficiency is a rare autosomal disease that causes premature death of homozygous individuals. The most frequent mutation that leads to this illness is in position 104, which involves a conservative change of a Glu for Asp. Despite the extensive work that has been carried out on the E104D mutant enzyme in hemolysates and whole cells, the molecular basis of this disease is poorly understood. Here, we show that the purified, recombinant mutant enzyme E104D, while exhibiting normal catalytic activity, shows impairments in the formation of active dimers and low thermostability and monomerizes under conditions in which the wild type retains its dimeric form. The crystal structure of the E104D mutant at 1.85 Å resolution showed that its global structure was similar to that of the wild type; however, residue 104 is part of a conserved cluster of 10 residues, five from each subunit. An analysis of the available high resolution structures of TIM dimers revealed that this cluster forms a cavity that possesses an elaborate conserved network of buried water molecules that bridge the two subunits. In the E104D mutant, a disruption of contacts of the amino acid side chains in the conserved cluster leads to a perturbation of the water network in which the water-protein and water-water interactions that join the two monomers are significantly weakened and diminished. Thus, the disruption of this solvent system would stand as the underlying cause of the deficiency.

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Section: The Crystal Structure Of the Mutant E104d Shows No Alteratiomentioning

confidence: 88%

Structural Basis of Human Triosephosphate Isomerase Deficiency

Rodríguez-Almazán

Arreola

Rodríguez-Larrea

et al. 2008

Journal of Biological Chemistry

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“…The second side chain oxygen atom of Glu97 makes a hydrogen bond to the e-amino group of Lys12 and a water molecule (W566), which in turn is hydrogen-bonded to the water molecule W633, which also interacts with the S73 backbone carbonyl group. These two water molecules are conserved in all TIM structures from diverse organisms, with the exceptions of the tetrameric enzymes from the thermophilic organisms Methanocaldococcus janaschii (PDB ID: 2H6R) [26] and Pyrococcus woesei (PDB ID: 1HG3). [27] In the E97Q mutant, the hydrogen-bonding interactions across the dimer interface are maintained.…”

Section: Analysis Of the Crystal Structuresmentioning

confidence: 99%

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

Samanta¹,

Murthy²,

Balaram³

et al. 2011

ChemBioChem

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An analysis of 503 available triosephosphate isomerase sequences revealed nine fully conserved residues. Of these, four residues-K12, H95, E97 and E165-are capable of proton transfer and are all arrayed around the dihydroxyacetone phosphate substrate in the three-dimensional structure. Specific roles have been assigned to the residues K12, H95 and E165, but the nature of the involvement of E97 has not been established. Kinetic and structural characterization is reported for the E97Q and E97D mutants of Plasmodium falciparum triosephosphate isomerase (Pf TIM). A 4000-fold reduction in k(cat) is observed for E97Q, whereas the E97D mutant shows a 100-fold reduction. The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and stability of the dimeric structure have been demonstrated by biophysical studies. Crystal structures of E97Q and E97D mutants have been determined at 2.0 Å resolution. In the case of the isosteric replacement of glutamic acid by glutamine in the E97Q mutant a large conformational change for the critical K12 side chain is observed, corresponding to a trans-to-gauche transition about the Cγ-Cδ (χ(3)) bond. In the E97D mutant, the K12 side chain maintains the wild-type orientation, but the hydrogen bond between K12 and D97 is lost. The results are interpreted as a direct role for E97 in the catalytic proton transfer cycle. The proposed mechanism eliminates the need to invoke the formation of the energetically unfavourable imidazolate anion at H95, a key feature of the classical mechanism.

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“…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%

“…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%

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

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

279

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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Structure of triosephosphate isomerase (TIM) fromMethanocaldococcus jannaschii

Cited by 23 publications

References 38 publications

Structural Basis of Human Triosephosphate Isomerase Deficiency

Structural Basis of Human Triosephosphate Isomerase Deficiency

Revisiting the Mechanism of the Triosephosphate Isomerase Reaction: The Role of the Fully Conserved Glutamic Acid 97 Residue

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

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