FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2085562885> ?p ?o ?g. }

• W2085562885 endingPage "1433" @default.
• W2085562885 startingPage "1421" @default.
• W2085562885 abstract "Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNAGln is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNAGln is then matured into Gln-tRNAGln by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase—that of GatDE from Pyrococcus abyssi. The 3.0 Å resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a β hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE. Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNAGln is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNAGln is then matured into Gln-tRNAGln by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase—that of GatDE from Pyrococcus abyssi. The 3.0 Å resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a β hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE. The synthesis of aminoacylated tRNAs occupies a central place in the translation of the genetic information into proteins. In most organisms, the 20 amino acids are directly charged onto their cognate tRNAs by a set of 20 distinct aminoacyl-tRNA synthetases. However, besides these direct routes of aminoacylation, indirect routes also occur (White and Bayley, 1972White B.N. Bayley S.T. Further codon assignments in an extremely halophilic bacterium using a cell-free protein-synthesizing system and a ribosomal binding assay.Can. J. Biochem. 1972; 50: 600-609Crossref PubMed Scopus (25) Google Scholar, Wilcox, 1969Wilcox M. γ-Glutamyl phosphate attached to glutamine-specific tRNA.Eur. J. Biochem. 1969; 11: 405-412Crossref PubMed Scopus (60) Google Scholar, Wilcox and Nirenberg, 1968Wilcox M. Nirenberg M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein.Proc. Natl. Acad. Sci. USA. 1968; 61: 229-236Crossref PubMed Scopus (149) Google Scholar). Such pathways are based on the mischarging of certain tRNAs by aminoacyl-tRNA synthetases that have a relaxed specificity. Further modification of the mischarged tRNA by specialized enzymes ensures production of mature aminoacyl-tRNAs for translation. Genome sequences and other data show that these noncanonical routes of aminoacylation are widespread (Curnow et al., 1996Curnow A.W. Ibba M. Söll D. tRNA-dependant asparagine formation.Nature. 1996; 382: 589-590Crossref PubMed Scopus (132) Google Scholar, Gagnon et al., 1996Gagnon Y. Lacoste L. Champagne N. Lapointe J. Widespread use of the Glu-tRNAGln transamidation pathway among bacteria.J. Biol. Chem. 1996; 271: 14856-14863Crossref PubMed Scopus (59) Google Scholar, Schön et al., 1988Schön A. Kannangara C.G. Gough S. Söll D. Protein biosynthesis in organelles requires misaminoacylation of tRNA.Nature. 1988; 331: 187-190Crossref PubMed Scopus (177) Google Scholar, Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar). Their study is of increasing interest. On the one hand, these processes illustrate ways in which the number of amino acids used in protein synthesis may have increased during evolution. They also suggest evolutionary links between the metabolism of amino acids and protein synthesis. On the other hand, because these routes are specific markers of the majority of bacteria, they represent attractive targets for antibiotherapy (Decicco et al., 2001Decicco C.P. Nelson D.J. Luo Y. Shen L. Horiuchi K.Y. Amsler K.M. Foster L.A. Spitz S.M. Merrill J.J. Sizemore C.F. et al.Glutamyl-gamma-boronate inhibitors of bacterial Glu-tRNA(Gln) amidotransferase.Bioorg. Med. Chem. Lett. 2001; 11: 2561-2564Crossref PubMed Scopus (26) Google Scholar). Aminoacyl-tRNA maturation has been described for the biosyntheses of Gln-tRNAGln and Asn-tRNAAsn (Curnow et al., 1996Curnow A.W. Ibba M. Söll D. tRNA-dependant asparagine formation.Nature. 1996; 382: 589-590Crossref PubMed Scopus (132) Google Scholar, Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar), of selenocysteinyl-tRNASec (Böck, 2000Böck A. Biosynthesis of selenoproteins–an overview.Biofactors. 2000; 11: 77-78Crossref PubMed Scopus (95) Google Scholar), and very recently of Cys-tRNACys (Sauerwald et al., 2005Sauerwald A. Zhu W. Major T.A. Roy H. Palioura S. Jahn D. Whitman W.B. Yates 3rd, J.R. Ibba M. Söll D. RNA-dependent cysteine biosynthesis in archaea.Science. 2005; 307: 1969-1972Crossref PubMed Scopus (187) Google Scholar). In the case of Gln-tRNAGln, the indirect route is found in all archaea, in most bacteria, and in some eukaryotic organelles (Ibba et al., 2000Ibba M. Becker H.D. Stathopoulos C. Tumbula D.L. Söll D. The adaptator revisited.Trends Biochem. Sci. 2000; 25: 311-316Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar). The process begins with the formation of misacylated Glu-tRNAGln, catalyzed by a glutamyl-tRNA synthetase with specificity toward both tRNAGlu and tRNAGln. Glu-tRNAGln is then converted into Gln-tRNAGln by a tRNA-dependent amidotransferase, which uses either Gln or Asn as the amide donor and consumes ATP. In some organisms, similar pathways produce Asn-tRNAAsn from Asp-tRNAAsn (Curnow et al., 1996Curnow A.W. Ibba M. Söll D. tRNA-dependant asparagine formation.Nature. 1996; 382: 589-590Crossref PubMed Scopus (132) Google Scholar). In most cases, the presence of a tRNA-dependent amidotransferase is related to the absence of the corresponding aminoacyl-tRNA synthetase (GlnRS or AsnRS; Ibba et al., 2000Ibba M. Becker H.D. Stathopoulos C. Tumbula D.L. Söll D. The adaptator revisited.Trends Biochem. Sci. 2000; 25: 311-316Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar). However, in a few living cells, direct and indirect routes can coexist (Becker et al., 2000aBecker H.D. Bokkee M. Jacobi C. Raczniak G. Pelaschier J. Roy H. Klein S. Kern D. Söll D. The heterotrimeric Thermus thermophilus Asp-tRNAAsn amidotransferase can also generate Gln-tRNAGln.FEBS Lett. 2000; 476: 140-144Abstract Full Text Full Text PDF PubMed Scopus (37) Google Scholar, Becker et al., 2000bBecker H.D. Roy H. Moulinier L. Mazauric M.-H. Keith G. Kern D. Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase.Biochemistry. 2000; 39: 3216-3230Crossref PubMed Scopus (47) Google Scholar, Becker and Kern, 1998Becker H.D. Kern D. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways.Proc. Natl. Acad. Sci. USA. 1998; 95: 12832-12837Crossref PubMed Scopus (141) Google Scholar, Curnow et al., 1998Curnow A.W. Tumbula D.L. Pelaschier J.T. Min B. Söll D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis.Proc. Natl. Acad. Sci. USA. 1998; 95: 12838-12843Crossref PubMed Scopus (126) Google Scholar). Two types of amidotransferases (AdT) have been identified. The first one corresponds to heterotrimeric proteins encoded by genes named gatC, gatA, and gatB (Becker et al., 2000aBecker H.D. Bokkee M. Jacobi C. Raczniak G. Pelaschier J. Roy H. Klein S. Kern D. Söll D. The heterotrimeric Thermus thermophilus Asp-tRNAAsn amidotransferase can also generate Gln-tRNAGln.FEBS Lett. 2000; 476: 140-144Abstract Full Text Full Text PDF PubMed Scopus (37) Google Scholar, Curnow et al., 1997Curnow A.W. Hong K.-W. Yuan R. Kim S.-I. Martins O. Winkler W. Henkin T.M. Söll D. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation.Proc. Natl. Acad. Sci. USA. 1997; 94: 11819-11826Crossref PubMed Scopus (266) Google Scholar). These enzymes can transamidate both Asp-tRNAAsn and Glu-tRNAGln. They have therefore been named Asp/Glu-AdT (or GatCAB). They are encountered in bacteria as well as in archaea. The second type of amidotransferases is heterodimeric enzymes, described so far only in archaea (Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar). These amidotransferases, encoded by the gatD and gatE genes, are specific for the conversion of Glu-tRNAGln into Gln-tRNAGln. They are named Glu-AdT (or GatDE). The presence of GatDE is always associated with the absence of GlnRS. If AsnRS is also absent, an Asp/Glu-AdT can coexist with a Glu-AdT (Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar). Sequence homologies between the GatB and GatE proteins indicate that the two types of amidotransferases are evolutionarily linked (Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar). Additionally, GatA resembles amidases, whereas GatD is homologous to asparaginases (Borek and Jaskolski, 2001Borek D. Jaskolski M. Sequence analysis of enzymes with asparaginase activity.Acta Biochim. Pol. 2001; 48: 893-902PubMed Google Scholar, Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar, Yao et al., 2005Yao M. Yasutake Y. Morita H. Tanaka I. Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.Acta Crystallogr. 2005; D61: 294-301Google Scholar). Asp/Glu-AdT and Glu-AdT share a similar two-step mechanism for the conversion of Glu-tRNAGln into Gln-tRNAGln. In the first step, Glu-tRNAGln is activated into γ-phosphoryl-Glu-tRNAGln at the expense of ATP (2). In the second step, amidation of Glu-tRNAGln into Gln-tRNAGln occurs (3) (Feng et al., 2005Feng L. Sheppard K. Tumbula-Hansen D. Söll D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.J. Biol. Chem. 2005; 280: 8150-8155Crossref PubMed Scopus (46) Google Scholar, Horiuchi et al., 2001Horiuchi K.Y. Harpel M.R. Shen L. Luo Y. Rogers K.C. Copeland R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase.Biochemistry. 2001; 40: 6450-6457Crossref PubMed Scopus (38) Google Scholar). Glutamine or asparagine can be used as an amide donor (1).E+Gln(or Asn)→E+Glu(or Asp)+NH3(1) E+ATP+Glu-tRNAGln→Pγ-Glu-tRNAGln:E+ADP(2) Pγ-Glu-tRNAGln:E+NH3→Glu-tRNAGln+E+PI(3) Production of the ammonia group used for amidation takes place on GatA or GatD. GatB and GatE are involved in the activation of the tRNA. Indeed, GatE alone produces γ-phosphoryl-Glu-tRNAGln in the presence of ATP and of misacylated Glu-tRNAGln (Feng et al., 2005Feng L. Sheppard K. Tumbula-Hansen D. Söll D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.J. Biol. Chem. 2005; 280: 8150-8155Crossref PubMed Scopus (46) Google Scholar). The two reaction steps are tightly coupled, since the amidase activities of GatDE or GatCAB are highly dependent on the presence of Glu-tRNAGln and on its further activation into γ-phosphoryl-Glu-tRNAGln (Feng et al., 2005Feng L. Sheppard K. Tumbula-Hansen D. Söll D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.J. Biol. Chem. 2005; 280: 8150-8155Crossref PubMed Scopus (46) Google Scholar, Horiuchi et al., 2001Horiuchi K.Y. Harpel M.R. Shen L. Luo Y. Rogers K.C. Copeland R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase.Biochemistry. 2001; 40: 6450-6457Crossref PubMed Scopus (38) Google Scholar). This study describes the crystal structure of GatDE from the hyperthermophilic archaeon Pyrococcus abyssi at 3.0 Å resolution. This enzyme forms an α2β2 tetramer (240 kDa). In the tetramer, two GatD molecules form an intimate dimer, identical to that encountered in L-asparaginases (Jakob et al., 1997Jakob C.G. Lewinski K. LaCount M.W. Roberts J. Lebioda L. Ion binding induces closed conformation in Pseudomonas 7A glutaminase-asparaginase (PGA): crystal structure of the PGA-SO4(2-)-NH4+ complex at 1.7 A resolution.Biochemistry. 1997; 36: 923-931Crossref PubMed Scopus (27) Google Scholar, Lubkowski et al., 1994Lubkowski J. Wlodawer A. Housset D. Weber I.T. Ammon H.L. Murphy K.C. Swain A.L. Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase.Acta Crystallogr. D Biol. Crystallogr. 1994; 50: 826-832Crossref PubMed Scopus (40) Google Scholar, Sanches et al., 2003Sanches M. Barbosa J.A. de Oliveira R.T. Abrahao Neto J. Polikarpov I. Structural comparison of Escherichia coli L-asparaginase in two monoclinic space groups.Acta Crystallogr. 2003; D59: 416-422Google Scholar, Swain et al., 1993Swain A.L. Jaskolski M. Housset D. Rao J.K. Wlodawer A. Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.Proc. Natl. Acad. Sci. USA. 1993; 90: 1474-1478Crossref PubMed Scopus (247) Google Scholar, Yao et al., 2005Yao M. Yasutake Y. Morita H. Tanaka I. Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.Acta Crystallogr. 2005; D61: 294-301Google Scholar). The GatD dimer binds two GatE molecules that do not interact. To our knowledge, the fold of GatE is original and cannot be related to that of any aminoacyl-tRNA synthetase, nor to that of any known tRNA binding enzyme. GatD shows an active site devoted to hydrolysis of the ammonia donor. The site for activation of Glu-tRNAGln is on GatE. Examination of the 3D structure gives insights into the way the protein subunits and their active sites can communicate. More generally, to our knowledge, this study is a first step toward description at the structural level of the mechanism of a misaminoacylated tRNA modifying enzyme. Such mechanisms are of particular importance in light of the participation of these enzymes in expansion of the repertoire of amino acids composing proteins and of their likely roles in evolution, before the emergence of some aminoacyl-tRNA synthetases. GatDE crystals containing selenomethionylated GatD subunit were used. They diffracted to 3.0 Å resolution. A two-wavelength data set, with a single crystal near the K absorption edge of selenium, was collected (Table 1). According to the homology of GatD with L-asparaginases, a molecular replacement solution was found. This solution was used to locate the methionine residues of GatD before phasing by MAD methods (see Experimental Procedures). Two GatD and two GatE molecules could readily be built in the asymmetric unit. After minimization cycles with CNS (Brunger et al., 1998Brunger A.T. Adams P.D. Clore G.M. DeLano W.L. Gros P. Grosse-Kunstleve R.W. Jiang J.S. Kuszewski J. Nilges M. Pannu N.S. et al.Crystallography & NMR system: a new software suite for macromolecular structure determination.Acta Crystallogr. D Biol. Crystallogr. 1998; 54: 905-921Crossref PubMed Scopus (16762) Google Scholar), the model was refined to an R factor of 21.7% (Rfree = 25.6%; Table 1). The final model shows two full GatD molecules (2 × 438 residues) with two GatE molecules (2 × 633 residues) lacking the C-terminal residues 513–633.Table 1Data Collection and Refinement StatisticsWavelength (Å)0.9758 (peak)0.9796 (edge)Space group and cell parameters (Å)P21, a = 102.7, b = 138.2, c = 134.4, β = 109.6°P21, a = 102.7, b = 138.2, c = 134.4, β = 109.6°Unique reflectionsaBijvoet mates are counted separately.137,974113,404Resolution (Å)3.03.2Completeness (%)98.7 (99.6)98.5 (99.8)RedundancyaBijvoet mates are counted separately.1.91.9Rsym (I) (%)bValues in parentheses are Rsym (I) in the highest shell of resolution.6.9 (37.4)6.2 (29.3)Mean figure of merit before solvent flattening0.3 (50–3.2 Å)R/RfreecRfree is calculated with 6% of the reflections. (%)21.7 (25.6)Rmsd bonds (Å)/angles (°)0.0075/1.45B values (Å2) protein/ligand/waterGatD 63, GatD* 63, GatE 58, GatE* 85/Asp-GatD 87, Asp-GatD* 61/water molecules 48a Bijvoet mates are counted separately.b Values in parentheses are Rsym (I) in the highest shell of resolution.c Rfree is calculated with 6% of the reflections. Open table in a new tab In the asymmetric unit, two GatD molecules are tightly packed together and form a compact dimeric structure. Two molecules of GatE are anchored on the GatD dimer. In the resulting tetramer, the two GatE molecules do not interact (Figure 1). The two NCS-related GatDE dimers are superimposable and have an rmsd value of 0.52 Å for 945 pairs of Cα atoms. According to molecular sieving experiments (see Experimental Procedures), the species that was crystallized also forms an α2β2 complex in solution. As will be discussed below, this tetrameric organization has functional significance. The GatE subunit from P. abyssi contains 633 amino acids. In the structure of GatE, all residues but residues comprising the C-terminal part (residues 513–633) are visible. The overall fold indicates three structural modules (Figure 1, Figure 2). The core domain includes the N-terminal part of the protein (residues 1–277) plus residues 411–452 (domain 1 [dark blue] in Figure 1, Figure 2). This domain is folded around a 10-stranded mixed β sheet. In the sheet, 8 strands are antiparallel, while Eβ11 and Eβ16 are parallel (Figure 2A). The β sheet is twisted and rolled. Its convex side is packed on three α helices (Eα3–Eα5, Figure 2A). The C end of Eα3 is packed on the N-terminal part of Eα4, and, similarly, the C end of Eα4 is packed on the N-terminal part of Eα5. Helix Eα12 interacts with the C terminus of Eα3. The space between the β sheet and the helices is completely filled with hydrophobic side chains. The overall structure is bent, thereby forming a half torus. This torus is extended by an overhanging subdomain formed by a 4-stranded mixed β sheet carrying a protruding α helix (Eα1). This overhanging domain is tightly associated with the main domain of GatE. In particular, the Eβ4-Eβ5 loop of the core domain dips inside the subdomain. Overall, the core of GatE has the shape of a cradle, with the overhanging subdomain forming the top. Notably, the elongated peptide joining Eβ17 to Eβ18 resembles a handle bridging the two sides of the cradle. To our knowledge, such a domain structure represents a new fold. No significant homolog could be detected by using the DALI database (www.ebi.ac.uk/dali). A bundle of four small, antiparallel α helices (residues 459–512) is appended at the C terminus of the cradle domain. This bundle makes few contacts with the core of the protein (Figure 1, Figure 2). The C-terminal part of GatE (residues 513–633) is not visible in the electron density. However, residues 591–628 present sequence similarities with the C end (residues 111–148) of a Bacillus subtilis protein, named Yqey, of unknown function (44.7% identities, 65.8% similarities for 38 residues). Hence, residues 591–633 of GatE might also form two antiparallel α helices, as in the case of the Yqey C-terminal peptide (PDB ID 1ng6 ). Between the Eα5 helix and the Eβ16 strand of the cradle domain, an α/β domain is inserted. It is made of a curved antiparallel β sheet surrounded by α helices (domain 2 [cyan] in Figure 2A). The folding of this domain strongly resembles an insertion domain found in bacterial AspRS (residues 278–412 in Thermus thermophilus AspRS; Delarue et al., 1994Delarue M. Poterszman A. Nikonov S. Garber M. Moras D. Thierry J.C. Crystal structure of a prokaryotic aspartyl tRNA-synthetase.EMBO J. 1994; 13: 3219-3229Crossref PubMed Scopus (89) Google Scholar). The two modules are superimposable and have an rmsd of 2.1 Å for 117 pairs of Cα atoms. Sequence homologies between the compared domains indicate nearly 20% identical residues, scattered throughout the structure. The resemblance between AspRS and GatE is strictly limited to the insertion domain. In particular, when the two modules are superimposed, the catalytic domain of AspRS does not fit on GatE. These data strongly suggest that the insertion domain of bacterial AspRS and that of GatE are evolutionarily related. The loop linking Eβ14 and Eα10 is, however, 7 residues shorter in GatE compared to AspRS. Notably, in all GatE sequences, this region carries a specific conserved sequence, 347GϕϕHxDELPHxYGϕ359 (Figure 2B). In the overall structure of GatE, the AspRS-like insertion domain makes contacts with the cradle domain through packing interactions of Eα9 with Eβ17, and through electrostatic interactions of E336 (Eα9) with R261 (Eα5) and R412 (Eβ16). An additional contact involves D339 (Eα9) and the main chain NH of Y422 (Eβ17). A multiple sequence alignment was performed by using 21 GatE sequences as well as 173 sequences of the GatB paralog (Figure 2B). Residues of the cradle domain are conserved in GatE and GatB proteins. The AspRS-like domain is only present in GatE. In GatB, it is replaced by a short region of about 20 residues. The C-terminal part of GatE (from Eα12), and that of GatB, displays much more variability. GatE and GatB are thought to share the same mechanism for the ATP-dependent activation of Glu-tRNAGln. This activation leads to the formation of a γ-phosphoryl-Glu-tRNAGln intermediate. This intermediate is further attacked by an ammonium ion, produced by the GatD subunit upon hydrolysis of glutamine or asparagine (Wilcox, 1969Wilcox M. γ-Glutamyl phosphate attached to glutamine-specific tRNA.Eur. J. Biochem. 1969; 11: 405-412Crossref PubMed Scopus (60) Google Scholar; Feng et al., 2005Feng L. Sheppard K. Tumbula-Hansen D. Söll D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.J. Biol. Chem. 2005; 280: 8150-8155Crossref PubMed Scopus (46) Google Scholar, Horiuchi et al., 2001Horiuchi K.Y. Harpel M.R. Shen L. Luo Y. Rogers K.C. Copeland R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase.Biochemistry. 2001; 40: 6450-6457Crossref PubMed Scopus (38) Google Scholar). Recently, it was shown that GatE alone can activate Glu-tRNAGln, thus indicating that GatE is a tRNA-dependent kinase (Feng et al., 2005Feng L. Sheppard K. Tumbula-Hansen D. Söll D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.J. Biol. Chem. 2005; 280: 8150-8155Crossref PubMed Scopus (46) Google Scholar). Remarkably, the residues strictly conserved in both the GatE and GatB proteins (dark blue in Figure 2B) are located on the concave side of the twisted sheet (the inside of the cradle, Figure 3A ). The side chains of most of the conserved residues are oriented toward the same region. This strongly suggests that this region is the enzyme center where ATP and the 3′ end of Glu-tRNAGln make contact (Figure 3). In the second step, sequence conservation was analyzed by using the 21 GatE sequences only. Two additional clusters of conserved residues appear on the 3D structure (Figure 3B). One lies at the interface between the GatE and GatD subunits. The importance of this cluster will be discussed below. The second cluster is located within the AspRS-like domain. In the structure of E. coli tRNAAsp complexed to E. coli AspRS, this domain makes contacts with the acceptor arm of the tRNA molecule through water-mediated interactions (Eiler et al., 1999Eiler S. Dock-Bregeon A. Moulinier L. Thierry J.C. Moras D. Synthesis of aspartyl-tRNA(Asp) in Escherichia coli—a snapshot of the second step.EMBO J. 1999; 18: 6532-6541Crossref PubMed Scopus (147) Google Scholar). Possibly, the AspRS-like domain in GatE has the capacity to interact with the acceptor arm of Glu-tRNAGln. Archaeal Glu-Adt recognizes Glu-tRNAGln, not Glu-tRNAGlu nor Asp-tRNAAsn. All archaeal tRNAsGln have an A1-U72 base pair that distinguishes them from most elongator tRNAs, including archaeal tRNAsGlu and tRNAsAsn, which possess G1-C72 (Marck and Grosjean, 2002Marck C. Grosjean H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.RNA. 2002; 8: 1189-1232Crossref PubMed Scopus (268) Google Scholar). In contrast, archaeal Asp/Glu-AdTs are able to process Asp-tRNAAsn with a G1-C72 base pair, as well as Glu-tRNAGln with an A1-U72 one. Possibly, an A1-U72 base pair in tRNAGln is at the origin of tRNA substrate selection by Glu-AdT. In this context, the AspRS-like domain, found in GatE and not in GatB, and containing the 347GϕϕHxDELPHxYGϕ359 signature sequence, is a plausible candidate to participate in the selection of tRNAGln by GatE, for instance by recognizing the 5′ end of the tRNA (Figure 2, Figure 3). As expected from sequence alignments (Borek and Jaskolski, 2001Borek D. Jaskolski M. Sequence analysis of enzymes with asparaginase activity.Acta Biochim. Pol. 2001; 48: 893-902PubMed Google Scholar, Tumbula et al., 2000Tumbula D.L. Becker H.D. Chang W.Z. Söll D. Domain-specific recruitment of amide amino acids for protein synthesis.Nature. 2000; 407: 106-110Crossref PubMed Scopus (129) Google Scholar), the part of the 3D structure of GatD starting at residue 90 is highly homologous to those of protomers of type I or II L-asparaginases. Accordingly, in GatD, the L-asparaginase-like structure contains two domains (Figure 4A ). Domain 1 (residues 90–302) is built around a flavodoxine fold, and domain 2 contains four parallel β strands flanked on one side by three α helices (Lubkowski et al., 1994Lubkowski J. Wlodawer A. Housset D. Weber I.T. Ammon H.L. Murphy K.C. Swain A.L. Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase.Acta Crystallogr. D Biol. Crystallogr. 1994; 50: 826-832Crossref PubMed Scopus (40) Google Scholar, Swain et al., 1993Swain A.L. Jaskolski M. Housset D. Rao J.K. Wlodawer A. Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.Proc. Natl. Acad. Sci. USA. 1993; 90: 1474-1478Crossref PubMed Scopus (247) Google Scholar). Appended to this asparaginase-like core, GatD exhibits an idiosyncratic N-terminal open β barrel formed by five antiparallel β sheets and capped by an α helix. The barrel is attached to the core domain through an elongated linker peptide of 18 residues. A search for this barrel with DALI revealed the presence of similar folds in several multimeric proteins (e.g., heptameric archaeal Sm protein, PDB ID 1i8f ). The N-terminal domain of GatD participates in the anchoring of GatE, as we will see below. The best superimposition of the structure of the GatD protomer is obtained with the recently determined structure of the more closely sequence-related type I L-asparaginase from Pyrococcus horikoshii (Yao et al., 2005Yao M. Yasutake Y. Morita H. Tanaka I. Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.Acta Crystallogr. 2005; D61: 294-301Google Scholar; rmsd = 1.2 Å for 286 pairs of Cα atoms compared). GatD and the P. horikoshii type I L-asparaginase differ from type II L-asparaginases by two main features: (i) region 372–383 (GatD numbering) is an α helix (Dα10) in GatD, but is an extended peptide in type II L-asparaginases, (ii) region 287–304 in GatD is a loop, whose conformation is conserved in the P. horikoshii type I L-asparaginase. The same loop is shifted in the structures of type II L-asparaginases. Type I and type II L-asparaginases exist as intimate homodimers. In type II L-asparaginases, homodimers further assemble to give homotetramers (Borek and Jaskolski, 2001Borek D. Jaskolski M. Sequence analysis of enzymes with asparaginase activity.Acta Biochim. Pol. 2001; 48: 893-902PubMed Google Scholar). Within the crystal, the two NCS-related GatD molecules are closely assembled in the exact same way as type I L-asparaginase protomers (Figure 1A). Type I L-asparaginase from P. horikoshii and GatD homodimers are superimposable with an rmsd of 1.46 Å for 574 pairs of Cα atoms compared. The regions involved in the interface between the two GatD protomers are highly complementary. The contact surface is 1975 Å2. Domain 2 of one subunit is packed on both domain 1* and domain 2* of the second subunit (Figure 1A; the GatD molecule related by NCS to the reference molecule will now be noted with an asterisk). The two domains 2 are associated via salt bridges between side chains of residues belonging to Dβ18 and D*β18 of both subunits and via Van der Waals contacts between side chains of residues of the two Dα8 and D*α8 helices. The N-terminal parts of the D*α8, D*α9, and D*α10 helices of domain 2* face" @default.
• W2085562885 created "2016-06-24" @default.
• W2085562885 creator A5008230653 @default.
• W2085562885 creator A5036765563 @default.
• W2085562885 creator A5043636136 @default.
• W2085562885 creator A5047001938 @default.
• W2085562885 date "2005-10-01" @default.
• W2085562885 modified "2023-10-16" @default.
• W2085562885 title "Structural Basis for tRNA-Dependent Amidotransferase Function" @default.
• W2085562885 cites W1591680814 @default.
• W2085562885 cites W1625216564 @default.
• W2085562885 cites W1697265935 @default.
• W2085562885 cites W1970128456 @default.
• W2085562885 cites W1970212713 @default.
• W2085562885 cites W1973363547 @default.
• W2085562885 cites W1975278321 @default.
• W2085562885 cites W1979428706 @default.
• W2085562885 cites W1986083824 @default.
• W2085562885 cites W1986191025 @default.
• W2085562885 cites W1989837277 @default.
• W2085562885 cites W1990236079 @default.
• W2085562885 cites W1995017064 @default.
• W2085562885 cites W1996109843 @default.
• W2085562885 cites W1996322339 @default.
• W2085562885 cites W2001641653 @default.
• W2085562885 cites W2005747480 @default.
• W2085562885 cites W2013083986 @default.
• W2085562885 cites W2018645572 @default.
• W2085562885 cites W2026762857 @default.
• W2085562885 cites W2049521571 @default.
• W2085562885 cites W2052100738 @default.
• W2085562885 cites W2066479660 @default.
• W2085562885 cites W2071304873 @default.
• W2085562885 cites W207730650 @default.
• W2085562885 cites W2077411406 @default.
• W2085562885 cites W2080020379 @default.
• W2085562885 cites W2083691392 @default.
• W2085562885 cites W2091969321 @default.
• W2085562885 cites W2095389444 @default.
• W2085562885 cites W2119662144 @default.
• W2085562885 cites W2122602899 @default.
• W2085562885 cites W2125181056 @default.
• W2085562885 cites W2127272780 @default.
• W2085562885 cites W2134482660 @default.
• W2085562885 cites W2147302373 @default.
• W2085562885 cites W2150956643 @default.
• W2085562885 cites W2157503621 @default.
• W2085562885 cites W2161743998 @default.
• W2085562885 doi "https://doi.org/10.1016/j.str.2005.06.016" @default.
• W2085562885 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16216574" @default.
• W2085562885 hasPublicationYear "2005" @default.
• W2085562885 type Work @default.
• W2085562885 sameAs 2085562885 @default.
• W2085562885 citedByCount "42" @default.
• W2085562885 countsByYear W20855628852013 @default.
• W2085562885 countsByYear W20855628852014 @default.
• W2085562885 countsByYear W20855628852015 @default.
• W2085562885 countsByYear W20855628852016 @default.
• W2085562885 countsByYear W20855628852017 @default.
• W2085562885 countsByYear W20855628852021 @default.
• W2085562885 countsByYear W20855628852023 @default.
• W2085562885 crossrefType "journal-article" @default.
• W2085562885 hasAuthorship W2085562885A5008230653 @default.
• W2085562885 hasAuthorship W2085562885A5036765563 @default.
• W2085562885 hasAuthorship W2085562885A5043636136 @default.
• W2085562885 hasAuthorship W2085562885A5047001938 @default.
• W2085562885 hasBestOaLocation W20855628851 @default.
• W2085562885 hasConcept C104317684 @default.
• W2085562885 hasConcept C14036430 @default.
• W2085562885 hasConcept C153957851 @default.
• W2085562885 hasConcept C185592680 @default.
• W2085562885 hasConcept C2779349466 @default.
• W2085562885 hasConcept C515207424 @default.
• W2085562885 hasConcept C54355233 @default.
• W2085562885 hasConcept C55493867 @default.
• W2085562885 hasConcept C67705224 @default.
• W2085562885 hasConcept C70721500 @default.
• W2085562885 hasConcept C75972863 @default.
• W2085562885 hasConcept C86803240 @default.
• W2085562885 hasConceptScore W2085562885C104317684 @default.
• W2085562885 hasConceptScore W2085562885C14036430 @default.
• W2085562885 hasConceptScore W2085562885C153957851 @default.
• W2085562885 hasConceptScore W2085562885C185592680 @default.
• W2085562885 hasConceptScore W2085562885C2779349466 @default.
• W2085562885 hasConceptScore W2085562885C515207424 @default.
• W2085562885 hasConceptScore W2085562885C54355233 @default.
• W2085562885 hasConceptScore W2085562885C55493867 @default.
• W2085562885 hasConceptScore W2085562885C67705224 @default.
• W2085562885 hasConceptScore W2085562885C70721500 @default.
• W2085562885 hasConceptScore W2085562885C75972863 @default.
• W2085562885 hasConceptScore W2085562885C86803240 @default.
• W2085562885 hasIssue "10" @default.
• W2085562885 hasLocation W20855628851 @default.
• W2085562885 hasLocation W20855628852 @default.
• W2085562885 hasLocation W20855628853 @default.
• W2085562885 hasLocation W20855628854 @default.
• W2085562885 hasOpenAccess W2085562885 @default.
• W2085562885 hasPrimaryLocation W20855628851 @default.

• next