Dimerization of Proline Dehydrogenase from Thermus thermophilus Is Crucial for Its Thermostability

Thermus thermophilus proline dehydrogenase ( TtProDH) catalyzes the first step in proline catabolism. The thermostable flavoenzyme consists of a distorted triosephosphate isomerase (TIM) barrel and three N‐terminal helices: αA, αB, and αC. Using maltose‐binding protein (MBP) fused constructs, it has been recently demonstrated that helix αC is crucial for TtProDH catalysis and for tetramerization through positioning of helix α8. Here, the structural features that determine the thermostability of TtProDH are reported. Selective disruption of two ion pairs in the dimerization interface of several MBP‐TtProDH variants result in the formation of monomers. The newly created monomers have improved catalytic properties but their melting temperatures are decreased by more than 20 °C. Sequence comparison suggests that one of the ion‐pairs involved in dimerization is unique for ProDHs from Thermus species. In summary, intermolecular ion‐pairs improve the thermostability of TtProDH and a trade‐off is made between thermostability and catalytic activity.     

Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase

Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are produced by aborted translation, to recycle tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its enzymatic activity is essential for bacterial viability. We have determined the crystal structure of Escherichia coli Pth in complex with the tRNA CCA-acceptor-TΨC domain, the enzyme-binding region of the tRNA moiety of the substrate, at 2.4 Å resolution. In combination with site-directed mutagenesis studies, the structure identified the amino acid residues involved in tRNA recognition. The structure also revealed that Pth interacts with the tRNA moiety through the backbone phosphates and riboses, and no base-specific interactions were observed, except for the interaction with the highly conserved base G53. This feature enables Pth to accept the diverse sequences of the elongator-tRNAs as substrate components. Furthermore, we propose an authentic Pth:peptidyl-tRNA complex model and a detailed mechanism for the hydrolysis reaction, based on the present crystal structure and the previous studies’ results.     

Idiosyncrasy and identity in the prokaryotic Phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP

The crystal structure of Phenylalanyl‐tRNA synthetase from E. coli (EcPheRS), a class II aminoacyl‐tRNA synthetase, complexed with phenylalanine and AMP was determined at 3.05 Å resolution. EcPheRS is a (αβ)₂ heterotetramer: the αβ heterodimer of EcPheRS consists of 11 structural domains. Three of them: the N‐terminus, A1 and A2 belong to the α‐subunit and B1‐B8 domains to the β subunit. The structure of EcPheRS revealed that architecture of four helix‐bundle interface, characteristic of class IIc heterotetrameric aaRSs, is changed: each of the two long helices belonging to CLM transformed into the coil‐short helix structural fragments. The N‐terminal domain of the α‐subunit in EcPheRS forms compact triple helix domain. This observation is contradictory to the structure of the apo form of TtPheRS, where N‐terminal domain was not detected in the electron density map. Comparison of EcPheRS structure with TtPheRS has uncovered significant rearrangements of the structural domains involved in tRNA^Phe binding/translocation. As it follows from modeling experiments, to achieve a tighter fit with anticodon loop of tRNA, a shift of ～5 Å is required for C‐terminal domain B8, and of ～6 to 7 Å for the whole N terminus. EcPheRSs have emerged as an important target for the incorporation of novel amino acids into genetic code. Further progress in design of novel compounds is anticipated based on the structural data of EcPheRS.     

In silico characterization of thermostable lipases

Thermostable lipases are of high priority for industrial applications as they are endowed with the capability of carrying out diversified reactions at elevated temperatures. Extremophiles are their potential source. Sequence and structure annotation of thermostable lipases can elucidate evolution of lipases from their mesophilic counterparts with enhanced thermostability hence better industrial potential. Sequence analysis highlighted the conserved residues in bacterial and fungal thermostable lipases. Higher frequency of AXXXA motif and poly Ala residues in lid domain of thermostable Bacillus lipases were distinguishing characteristics. Comparison of amino acid composition among thermostable and mesostable lipases brought into light the role of neutral, charged and aromatic amino acid residues in enhancement of thermostability. Structural annotation of thermostable lipases with that of mesostable lipases revealed some striking features which are increment of gamma turns in thermostable lipases; being first time reported in our paper, longer beta strands, lesser beta-branched residues in helices, increase in charged-neutral hydrogen bonding pair, hydrophobic-hydrophobic contact and differences in the N-cap and C-cap residues of the α helices. Conclusively, it can be stated that subtle changes in the arrangement of amino acid residues in the tertiary structure of lipases contributes to enhanced thermostability.     

Crystal structure studies of NADP dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

NADP⁺ dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP⁺ was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH’s. And, small domain and clasp domain showing significant differences when compared to other IDH’s of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH’s. Also, helices/beta sheets are absent in the small domain, when compared to other IDH’s of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit–subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV.     

Insights into thermal resistance of proteins from the intrinsic stability of their α-helices

To investigate the role of α helices in protein thermostability, we compared energy characteristics of α helices from thermophilic and mesophilic proteins belonging to four protein families of known three-dimensional structure, for at least one member of each family. The changes in intrinsic free energy of α-helix formation were estimated using the statistical mechanical theory for describing helix/coil transitions in peptide helices [Munoz, V., Serrano, L. Nature Struc. Biol. 1:399–409, 1994; Munoz, V., Serrano, L. J. Mol. Biol. 245:275–296, 1995; Munoz, V., Serrano, L. J. Mol. Biol. 245:297–308, 1995]. Based on known sequences of mesophilic and thermophilic RecA proteins we found that (1) a high stability of α helices is necessary but is not a sufficient condition for thermostability of RecA proteins, (2) the total helix stability, rather than that of individual helices, is the factor determining protein thermostability, and (3) two facets of intrahelical interactions, the intrinsic helical propensities of amino acids and the side chain–side chain interactions, are the main contributors to protein thermostability. Similar analysis applied to families of L-lactate dehydrogenases, seryl-tRNA synthetases, and aspartate amino transferases led us to conclude that an enhanced total stability of α helices is a general feature of many thermophilic proteins. The magnitude of the observed decrease in intrinsic free energy on α-helix formation of several thermoresistant proteins was found to be sufficient to explain the experimentally determined increase of their thermostability. Free energies of intrahelical interactions of different RecA proteins calculated at three temperatures that are thought to be close to its normal environmental conditions were found to be approximately equal. This indicates that certain flexibility of RecA protein structure is an essential factor for protein function. All RecA proteins analyzed fell into three temperature-dependent classes of similar α-helix stability (ΔG_int = 45.0 ± 2.0 kcal/mol). These classes were consistent with the natural origin of the proteins. Based on the sequences of protein α helices with optimized arrangement of stabilizing interactions, a natural reserve of RecA protein thermoresistance was estimated to be sufficient for conformational stability of the protein at nearly 200°C. Proteins 29:309–320, 1997. © 1997 Wiley-Liss, Inc.     

Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity

Peptidyl-tRNA hydrolase (Pth) activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes. Here we report the crystallographic structure of the Homo sapiens Pth2 at a 2.0-A resolution as well as its catalytic properties. In contrast to the structure of Escherichia coli Pth, H. sapiens Pth2 has an alpha/beta fold with a four-stranded antiparallel beta-sheet in its core surrounded by two alpha-helices on each side. This arrangement of secondary structure elements generates a fold not previously reported. Its catalytic efficiency is comparable with that reported for the archaeal Sulfolobus solfataricus Pth2 and higher than that of the bacterial E. coli Pth. Several lines of evidence target the active site to two close loops with highly conserved residues. This active site architecture is unrelated to that of E. coli Pth. In addition, intermolecular contacts in the crystal asymmetric unit cell suggest a likely surface for protein-protein interactions related to the Pth2-mediated apoptosis.     

The structure of a thermally stable 3-phosphoglycerate kinase and a comparison with its mesophilic equivalent

The structure of the phosphoglycerate kinase (PGK) from Bacillus stearothermophilus, a moderate thermophile, has been determined and compared with that of its mesophilic equivalent from yeast. The Bacillus enzyme structure was solved by molecular replacement and improved using constrained rigid-body, molecular dynamics and conventional refinement procedures. The refinement residual, calculated using all the measured data between 8 and 1.65 Å, is 0.18(1). The stereo chemical deviations of the final model from ideality are 0.01 Å for both bonds and planes. The mid-point temperatures of the Bacillus and yeast enzymes are 67 and 53°C, respectively. Differential scanning calorimetry indicates that the energy difference (ΔΔG) between the mesophilic and thermophilic enzymes is of the order of 5 kcal mol^?1 at room temperature. The structure comparison indicates that the features most likely to be responsible for the increased thermal stability of the Bacillus enzyme are the increased internal hydrophobicity, additional ion pairs, and better α-helix stability resulting from the removal of helix destablising residues and extra helix–dipole/helix side chain ionic interactions. © 1993 Wiley-Liss, Inc.     

Succinylchymotrypsin

Succinylchymotrypsin was prepared from succinylchymotrypsinogen with trypsin and purified by DEAE-Sephadex chromatography.

The total 15 lysyl and N-terminal amino residues of chymotrypsinogen were succinylated. About 23.5 out of 49 seryl and threonyl residues and none in the total 4 tyrosyl residues in succinylchymotrypsin were modified

The helix content of succinylchymotrypsin was about 8.4%.

The pK_app of N-terminal amino group in succinylchymotrypsin did not change and that of tyrosyl residues shifted to alkali side, in comparison with those of unmodified α-chymotrypsin.

The k_cat of succinylchymotrypsin increased and its Km did not change within experimental error, in comparison with those of α-chymotrypsin.     

Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus

The bacterial tRNA adenosine deaminase (TadA) generates inosine by deaminating the adenosine residue at the wobble position of tRNA(Arg-2). This modification is essential for the decoding system. In this study, we determined the crystal structure of Aquifex aeolicus TadA at a 1.8-A resolution. This is the first structure of a deaminase acting on tRNA. A. aeolicus TadA has an alpha/beta/alpha three-layered fold and forms a homodimer. The A. aeolicus TadA dimeric structure is completely different from the tetrameric structure of yeast CDD1, which deaminates mRNA and cytidine, but is similar to the dimeric structure of yeast cytosine deaminase. However, in the A. aeolicus TadA structure, the shapes of the C-terminal helix and the regions between the beta4 and beta5 strands are quite distinct from those of yeast cytosine deaminase and a large cavity is produced. This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop.     

Crystal structure of glucose-6-phosphate isomerase from Thermus thermophilus HB8 showing a snapshot of active dimeric state

Glucose-6-phosphate isomerase (GPI) is a glycolytic enzyme with ill-defined oligomeric state. In order to obtain insight into the correlation between oligomerization and the catalytic function of this enzyme, the crystal structure of GPI from the extreme thermophile Thermus thermophilus HB8 (TtGPI) has been determined at 1.95 Å resolution. The crystallographic asymmetric unit contains an apparent dimer. The core fold of protomer and the interprotomer spatial arrangement of the dimer are similar to those of already reported crystal structures of other GPIs. The active site is located on the dimer interface, and putative catalytic residues are well conserved among the GPIs. These results suggest that the observed dimeric state of TtGPI in the crystal is biologically relevant and that this enzyme uses a common catalytic mechanism for the isomerase reaction. Gel-filtration chromatography, chemical cross-linking, sedimentation equilibrium by analytical ultracentrifugation, and dynamic light-scattering experiments indicate that TtGPI exists in a dynamic equilibrium between monomeric and dimeric states in solution. Several factors potentially contributing to the thermal stability of TtGPI protomer were identified: (i) a decrease in denaturation entropy by the shorter polypeptide length and by amino acid composition, including the increased number of proline residues and a higher arginine-to-lysine ratio; (ii) a larger number of ion pairs; and (iii) a reduction in cavity volume. From these results, it is suggested that transient dimer formation is sufficient for the catalytic function and that the TtGPI protomer itself has intrinsically higher thermal stability.     

Five mutations in N-terminus confer thermostability on mesophilic xylanase

The termini of a pair of xylanases, one of mesophilic and one of thermophilic origin, was studied by molecular dissection and systematic mutagenesis. The thermostability of the mesophilic xylanase SoxB from Streptomyces olivaceovirdis was significantly improved by substituting its 33 N-terminal amino acid residues with the corresponding residues of the thermophilic xylanase TfxA from Thermomonospora fusca. Five amino acid substitutions, which clustered in one of the regions of the N-terminus, were discovered, for the first time, to account for the majority of the improvement in thermostability of SoxB. Further systematic mutagenesis and analysis of the five mutations demonstrated that comprehensive synergism of the five mutations was involved in conferring the thermostability on the SoxB. Moreover, when the five thermostabilizing mutations were introduced into two other G/11 xylanases, SlxB from Streptomyces lividans and AnxB from Aspergillus niger, their thermostabilities were also dramatically enhanced.     

The importance of an extra loop in the B-domain of an α-amylase from B. stearothermophilus US100

To provide insight into the potential role of a loop in domain B of several bacterial α-amylases, molecular and structural investigation of Bacillus stearothermophilus α-amylase (Amy US100) was used as a model. Combination deletion mutants of G₂₁₃, I₂₁₄ and G₂₁₅, described as a loop-forming on the surface bacterial amylases, were subjected to biochemical and structural investigation. Thermoactivity, thermostability as well calcium requirement were studied for each mutant.Thus, deletion of one residue differently affects only the thermostability. Shortening the loop by deletion of G₂₁₃-I₂₁₄ or I₂₁₄-G₂₁₅ improved the thermostability and reduces calcium requirement. However, the deletion of three residues has a negative effect on thermostability and reduces the optimal temperature by 17 °C.The structural investigation showed that stabilizing deletions contribute to reinforce the architecture of domain B and the active site conformation. The deletion of three residues reduces the flexibility of this region and abolishes a denser hydrogen bond network.     

Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes

The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is comprised of four alpha-helices and a mixed beta-sheet consisting of four parallel and anti-parallel beta-strands, where the alpha-helices sandwich the beta-sheet. Sequence and structural comparison of AF2095 with proteins from Homo sapiens, Methanocaldococcus jannaschii, and Sulfolobus solfataricus reveals that AF2095 is a peptidyl-tRNA hydrolase (Pth2). This structural comparison also identifies putative catalytic residues and a tRNA interaction region for AF2095. The structure of AF2095 is also similar to the structure of protein TA0108 from archaea Thermoplasma acidophilum, which is deposited in the Protein Data Bank but not functionally annotated. The NMR structure of AF2095 has been further leveraged to obtain good-quality structural models for 55 other proteins. Although earlier studies have proposed that the Pth2 protein family is restricted to archeal and eukaryotic organisms, the similarity of the AF2095 structure to human Pth2, the conservation of key active-site residues, and the good quality of the resulting homology models demonstrate a large family of homologous Pth2 proteins that are conserved in eukaryotic, archaeal, and bacterial organisms, providing novel insights in the evolution of the Pth and Pth2 enzyme families.     

A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability

Aquifex pyrophilus is a flagellated hyperthermophilic eubacterial species that grows optimally at 85°C. The thermostable A. pyrophilus flagellar filament is primarily composed of a single protein called flagellin (FlaA). The N- and C-terminal sequence regions of FlaA are important for self-assembly and share high sequence similarity with mesophilic bacterial flagellins. We have developed a predictive 3D-structure of FlaA, using the published structure of mesophilic Salmonella typhimurium flagellin (FliC) as a template and analyzed it with respect to possible determinants of thermostability. A sequence comparison of FlaA and FliC revealed a +7.0% increase in FlaA hydrophobic residues, a +0.6% increase in charged residues and a corresponding decrease of −6.0% in polar residues. The FlaA N- and C-termini also have higher proportions of hydrophobic and charged residues at the expense of polar residues and higher non-polar surface areas. Thus, a predominant stabilizing factor in FlaA appears to be increased hydrophobicity, which often confers greater rigidity to proteins. Fewer intramolecular ion pairs were observed in FlaA than FliC, although an increase in the positive charge potential of the FlaA D0 and D1 domains was also observed; increased intermolecular salt bridges may also contribute to the thermal stability of the oligomeric flagellar fiber. Figure a Model 3D structure of thermostable A. pyrophilus FlaA flagellin. b 3D structure of mesophilic S. typhimurium FliC flagellin. α-helices are shown in red, β-sheets are shown in yellow, turns are shown in blue and coils are shown in green. Both the structures show domains D0, D1, D2 and D3. c, d Stereo view of surface charge distribution of FlaA. e, f Stereo view of surface charge distribution of FliC. The legend shows the scale for coloring of the charge spectrum. Blue represents positive charge, red represents negative charge and white represents neutral     

Crystal Structure of Methanocaldococcus jannaschii Trm4 Complexed with Sinefungin

tRNA:m⁵C methyltransferase Trm4 generates the modified nucleotide 5-methylcytidine in archaeal and eukaryotic tRNA molecules, using S-adenosyl-l-methionine (AdoMet) as methyl donor. Most archaea and eukaryotes possess several Trm4 homologs, including those related to diseases, while the archaeon Methanocaldococcus jannaschii has only one gene encoding a Trm4 homolog, MJ0026. The recombinant MJ0026 protein catalyzed AdoMet-dependent methyltransferase activity on tRNA in vitro and was shown to be the M. jannaschii Trm4. We determined the crystal structures of the substrate-free M. jannaschii Trm4 and its complex with sinefungin at 1.27 Å and 2.3 Å resolutions, respectively. This AdoMet analog is bound in a negatively charged pocket near helix α8. This helix can adopt two different conformations, thereby controlling the entry of AdoMet into the active site. Adjacent to the sinefungin-bound pocket, highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. The structure explains the roles of several conserved residues that were reportedly involved in the enzymatic activity or stability of Trm4p from the yeast Saccharomyces cerevisiae. We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4.     

Molecular dynamics study of structure and stability of a model coiled coil

This paper employs methods used earlier to study helix propensity in a model α-helix. The methods are extended to simulations of a motif structure of the α-helical coiled coil, i.e., a structure with a simple amino acid sequence, containing only alanine, leucine, and valine, with leucine and valine forming hydrophobic contacts in the helix interface (positions “d” and “a”). Dynamic simulations of the model coiled-coil structure reproduce characteristic features of the coiled-coil motif seen in experimental studies. Free energy simulations were used to assess the change in stability of the model when a leucine pair or a valine pair in the helix interface was replaced with an alanine pair. A leucine pair at position d was found to contribute 3.4 kcal/mol to the stability of the coiled coil relative to an alanine pair, and a valine pair at postion a was found to contribute 0.8 kcal/mol relative to an alanine pair. The value for the leucine pair agrees with reports in two experimental studies with molecules having different amino sequence. The value for the valine pair is reasonable given the smaller size of the valine side chain and the intrinsic low helix propensity of valine. No experimental value was available for comparison. © 1993 Wiley-Liss, Inc.     

Crystal structures of Entamoeba histolytica lysyl-tRNA synthetase reveal conformational changes upon lysine binding and a specific helix bundle domain

The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ligands to generate snapshots of the lysine-adenylate formation. The residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate, as observed in bacterial KRS. The Entamoeba EMAPII-like polypeptide is not resolved in the crystals, but another Entamoeba-specific insertion could be modeled as a small helix bundle that may contribute to tRNA binding through interaction with the tRNA hinge.     

The N-terminal region is crucial for the thermostability of the G-domain of Bacillus stearothermophilus EF-Tu

Bacterial elongation factor Tu (EF-Tu) is a model monomeric G protein composed of three covalently linked domains. Previously, we evaluated the contributions of individual domains to the thermostability of EF-Tu from the thermophilic bacterium Bacillus stearothermophilus. We showed that domain 1 (G-domain) sets up the basal level of thermostability for the whole protein. Here we chose to locate the thermostability determinants distinguishing the thermophilic domain 1 from a mesophilic domain 1. By an approach of systematically swapping protein regions differing between G-domains from mesophilic Bacillus subtilis and thermophilic B. stearothermophilus, we demonstrate that a small portion of the protein, the N-terminal 12 amino acid residues, plays a key role in the thermostability of this domain. We suggest that the thermostabilizing effect of the N-terminal region could be mediated by stabilizing the functionally important effector region. Finally, we demonstrate that the effect of the N-terminal region is significant also for the thermostability of the full-length EF-Tu.     

Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments

Constants of the helix–coil transition for all natural amino acid residues are evaluated on the basis of thermodynamic parameters obtained in paper I of this series. The specific effects at the termini of the helices are also considered as well as the parameters controlling the formation of β-bends in the unfolded protein chain. Evaluated s constants of the helix–coil transition agree with the experimental data on helix–coil transitions of synthetic polypeptides in water. Only a very qualitative correlation exists between s constants (both experimental and theoretical) and the occurrence of corresponding residues in internal turns of α-helices in globular proteins: residues with s > 1 occur in helices as a rule more often than residues with s < 1. At the same time a direct correlation is demonstrated between theoretical parameters of residue incorporation into α-helical termini and β-bends in an unfolded polypeptide chain and the occurrence of residues in corresponding positions of the globular protein secondary structures.