Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions

In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).     

X-ray structure of a bacterial oligosaccharyltransferase

Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, organism development or host-pathogen interactions. The reaction is catalysed by oligosaccharyltransferase (OST), a membrane protein complex located in the endoplasmic reticulum. The central, catalytic enzyme of OST is the STT3 subunit, which has homologues in bacteria and archaea. Here we report the X-ray structure of a bacterial OST, the PglB protein of Campylobacter lari, in complex with an acceptor peptide. The structure defines the fold of STT3 proteins and provides insight into glycosylation sequon recognition and amide nitrogen activation, both of which are prerequisites for the formation of the N-glycosidic linkage. We also identified and validated catalytically important, acidic amino acid residues. Our results provide the molecular basis for understanding the mechanism of N-linked glycosylation.     

Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units

Electrostatic interactions are of considerable importance in protein structure and function, and in a variety of cellular and biochemical processes. Here we report three similar findings from highly refined atomic structures of periplasmic binding proteins. Hydrogen bonds, acting primarily through backbone peptide units, are mainly responsible for the involvement of the positively charged arginine 151 residue in the ligand site of the arabinose-binding protein, for the association between teh sulphate-binding protein and the completely buried sulphate dianion, and for the formation of the complex of the leucine/isoleucine/valine-binding protein with the leucine zwitterion. We propose a general mechanism in which the isolated charges on the various buried, desolvated ionic groups are stabilized by the polarized peptide units. This mechanism also has broad application to processes requiring binding of uncompensated ions and charged ligands and stabilization of enzyme reaction charged intermediates, as well as activation of catalytic residues.     

Protein biosynthesis in organelles requires misaminoacylation of tRNA

In the course of our studies on transfer RNA involvement in chlorophyll biosynthesis, we have determined the structure of chloroplast glutamate tRNA species. Barley chloroplasts contain in addition to a tRNA(Glu) species at least two other glutamate-accepting tRNAs. We now show that the sequences of these tRNAs differ significantly: they are differentially modified forms of tRNA(Gln) (as judged by their UUG anticodon). These mischarged Glu-tRNA(Gln) species can be converted in crude chloroplast extracts to Gln-tRNA(Gln). This reaction requires a specific amidotransferase and glutamine or asparagine as amide donors. Aminoacylation studies show that chloroplasts, plant and animal mitochondria, as well as cyanobacteria, lack any detectable glutaminyl-tRNA synthetase activity. Therefore, the requirement for glutamine in protein synthesis in these cells and organelles is provided by the conversion of glutamate attached to an 'incorrectly' charged tRNA. A similar situation has been described for several species of Gram-positive bacteria. Thus, it appears that the occurrence of this pathway of Gln-tRNA(Gln) formation is widespread among organisms and is a function conserved during evolution. These findings raise questions about the origin of organelles and about the evolution of the mechanisms maintaining accuracy in protein biosynthesis.     

A ratchet-like inter-subunit reorganization of the ribosome during translocation

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis following genetic instructions in all organisms. It is composed of two unequal subunits: the smaller subunit binds messenger RNA and the anticodon end of transfer RNAs, and helps to decode the mRNA; and the larger subunit interacts with the amino-acid-carrying end of tRNAs and catalyses the formation of the peptide bonds. After peptide-bond formation, elongation factor G (EF-G) binds to the ribosome, triggering the translocation of peptidyl-tRNA from its aminoacyl site to the peptidyl site, and movement of mRNA by one codon. Here we analyse three-dimensional cryo-electron microscopy maps of the Escherichia coli 70S ribosome in various functional states, and show that both EF-G binding and subsequent GTP hydrolysis lead to ratchet-like rotations of the small 30S subunit relative to the large 50S subunit. Furthermore, our finding indicates a two-step mechanism of translocation: first, relative rotation of the subunits and opening of the mRNA channel following binding of GTP to EF-G; and second, advance of the mRNA/(tRNA)2 complex in the direction of the rotation of the 30S subunit, following GTP hydrolysis.     

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A?site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A?site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P?site) on the 30S head and simultaneously establishes interaction with the exit site (E?site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain?IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process.     

Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase

The correct attachment of amino acids to their corresponding (cognate) transfer RNA catalysed by aminoacyl-tRNA synthetases is a key factor in ensuring the fidelity of protein biosynthesis. Previous studies have demonstrated that the interaction of Escherichia coli tRNA(Gln) with glutaminyl-tRNA synthetase (GlnRS) provides an excellent system to study this highly specific recognition process, also referred to as 'tRNA identity'. Accurate acylation of tRNA depends mainly on two principles: a set of nucleotides in the tRNA molecule (identity elements) responsible for proper discrimination by aminoacyl-tRNA synthetases and competition between different synthetases for tRNAs. Elements of glutamine identity are located in the anticodon and in the acceptor stem region, including the discriminator base. We report here the production of more than 20 tRNA(2Gln) mutants at positions likely to be involved in tRNA discrimination by the enzyme. Unmodified tRNA, containing the wild-type anticodon and U or G at its 5'-terminus, can be aminocylated by GlnRS with similar kinetic parameters to native tRNA(2Gln). By in vitro aminoacylation the mutant tRNAs showed decreases of up to 3 x 10(5)-fold in the specificity constant (kcat/KM)14 with the major contribution of kcat. Despite these large changes, some of these mutant tRNAs are efficient amber suppressors in vivo. Our results show that strong elements for glutamine identity reside in the anticodon region and in positions 2 and 3 of the acceptor stem, and that the contribution of different identity elements to the overall discrimination varies significantly. We discuss our data in the light of the crystal structure of the GlnRS:tRNA(Gln) complex.     

A model of synthetase/transfer RNA interaction as deduced by protein engineering

The recognition of transfer-RNA by their cognate aminoacyl-tRNA synthetases is the crucial step in the translation of the genetic code. In order to construct a structural model of the complex between the tyrosyl-tRNA synthetase (TyrTS) from Bacillus stearothermophilus and tRNATyr, 40 basic residues at the surface of the TyrTS dimer have been mutated by site-directed mutagenesis and heterodimers created in vitro by recombining subunits derived from different mutants. As reported here a cluster of basic residues (Arg 207-Lys 208) in the N-terminal domain of one TyrTS subunit interacts with the acceptor stem of tRNATyr and two separated clusters of basic residues (Arg 368-Arg 371; Arg 407-Arg 408-Lys 410-Lys 411) in the C-terminal domain of the other subunit interact with the anticodon arm. The TyrTS would thus clamp the tRNA in a fixed orientation. The precise alignment of the flexible... ACCA 3' end of the tRNA for attack on the tyrosyl adenylate is made by contacts closer to the catalytic groups of the enzyme, such as with Lys 151.     

Orientation of the peptide formation of N-phosphoryl amino acids in solution

The peptide formation of N-phosphoryl amino acids with amino acids proceeds in aqueous solution without any coupling reagents. After being separated in sephadex gel column, the phosphoryl dipeptides were analyzed by the electrospray ionization tandem mass spectrometry (ESIMS/ MS). The result demonstrates that phosphoryl dipeptides were detected in all the reaction systems. It is found that the formation of N-phosphoryl dipeptides is oriented: the N-terminal amino acid residues of the N-phosphoryl dipeptides are from N-phosphoryl amino acids, and the peptide elongation happened at the C-terminal. Only a-dipeptide, no b-dipeptide, is formed in the N-phosphoryl dipeptides, showing that a-carboxylic group is activated selectively by N-phosphorylation. Theoretical calculation shows that the peptide formation of N-phosphoryl amino acids might happen through a penta-coordinate carboxylic-phosphoric intermediate in solution. These results might give some clues to the study on the origin of proteins and protein biosynthesis.     

分离与克隆中国人TPO基因片段及序列分析

应用ＲＴＰＣＲ技术从中国人胎肝细胞中分离出１个５６６ｂｐ大小的基因片段,经过克隆、限制性内切酶鉴定和序列分析证实为ＴＰＯ的ｃＤＮＡ片段．与ＧｅｎＢａｎｋ中发表的人ＴＰＯｍＲＮＡ的序列比较同源性在８２％～９９％之间,仅有２个碱基不相同,在１７５位密码子（５２３～５２５位的碱基）分别是ＣＧＧ和ＣＡＡ,即精氨酸（Ｒ）的位置上,中国人是谷胺酰氨（Ｇ）．而与测得的韩国人序列比较,在相应位置的氨基酸是相同的     

TD1修饰绿色荧光蛋白透皮功能的研究

TD1作为一种含有11个氨基酸的短肽,具有良好的促进蛋白类大分子透皮的功能.过去的研究显示TD1可以有效协助胰岛素通过皮肤进入循环并最终降低血糖.在本研究中我们构建了一种TD1 N端修饰的GFP融合蛋白(TGFP). 我们的实验表明, 与TD1与GFP蛋白的混合物相比, TGFP具有更加良好的透皮功能.这一发现为透皮给药研究提供了一条新的途径,并对解释TD1透皮功能具有指导意义.     

A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO regulates caspase activity and apoptosis

X-linked inhibitor-of-apoptosis protein (XIAP) interacts with caspase-9 and inhibits its activity, whereas Smac (also known as DIABLO) relieves this inhibition through interaction with XIAP. Here we show that XIAP associates with the active caspase-9-Apaf-1 holoenzyme complex through binding to the amino terminus of the linker peptide on the small subunit of caspase-9, which becomes exposed after proteolytic processing of procaspase-9 at Asp315. Supporting this observation, point mutations that abrogate the proteolytic processing but not the catalytic activity of caspase-9, or deletion of the linker peptide, prevented caspase-9 association with XIAP and its concomitant inhibition. We note that the N-terminal four residues of caspase-9 linker peptide share significant homology with the N-terminal tetra-peptide in mature Smac and in the Drosophila proteins Hid/Grim/Reaper, defining a conserved class of IAP-binding motifs. Consistent with this finding, binding of the caspase-9 linker peptide and Smac to the BIR3 domain of XIAP is mutually exclusive, suggesting that Smac potentiates caspase-9 activity by disrupting the interaction of the linker peptide of caspase-9 with BIR3. Our studies reveal a mechanism in which binding to the BIR3 domain by two conserved peptides, one from Smac and the other one from caspase-9, has opposing effects on caspase activity and apoptosis.     

运动与部分条件性氨基酸代谢

介绍了两种条件性氨基酸———精氨酸 (Arg)和谷氨酰胺 (Gln)的生物功能 ,探讨了它们与运动的关系 .发现中强度长时间的运动训练会使Arg和Gln浓度下降 ,影响运动能力 ;适当补充Arg或Orn和BCAA或Gln ,可使Arg和Gln的浓度恢复和升高 ,改善由于运动引起的免疫系统和神经系统等功能的下降 ,延缓疲劳发生和促进疲劳恢复 .     

The structural basis of agonist-induced activation in constitutively active rhodopsin

G-protein-coupled receptors (GPCRs) comprise the largest family of membrane proteins in the human genome and mediate cellular responses to an extensive array of hormones, neurotransmitters and sensory stimuli. Although some crystal structures have been determined for GPCRs, most are for modified forms, showing little basal activity, and are bound to inverse agonists or antagonists. Consequently, these structures correspond to receptors in their inactive states. The visual pigment rhodopsin is the only GPCR for which structures exist that are thought to be in the active state. However, these structures are for the apoprotein, or opsin, form that does not contain the agonist all-trans retinal. Here we present a crystal structure at a resolution of 3 ? for the constitutively active rhodopsin mutant Glu 113 Gln in complex with a peptide derived from the carboxy terminus of the α-subunit of the G protein transducin. The protein is in an active conformation that retains retinal in the binding pocket after photoactivation. Comparison with the structure of ground-state rhodopsin suggests how translocation of the retinal β-ionone ring leads to a rotation of transmembrane helix 6, which is the critical conformational change on activation. A key feature of this conformational change is a reorganization of water-mediated hydrogen-bond networks between the retinal-binding pocket and three of the most conserved GPCR sequence motifs. We thus show how an agonist ligand can activate its GPCR.     

Different substrate-dependent transition states in the active site of the ribosome

The active site of the ribosome, the peptidyl transferase centre, catalyses two reactions, namely, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the release-factor-dependent hydrolysis of peptidyl-tRNA. Unlike peptide bond formation, peptide release is strongly impaired by mutations of nucleotides within the active site, in particular by base exchanges at position A2602 (refs 1, 2). The 2'-OH group of A76 of the peptidyl-tRNA substrate seems to have a key role in peptide release. According to computational analysis, the 2'-OH may take part in a concerted 'proton shuttle' by which the leaving group is protonated, in analogy to similar current models of peptide bond formation. Here we report kinetic solvent isotope effects and proton inventories (reaction rates measured in buffers with increasing content of deuterated water, D(2)O) of the two reactions catalysed by the active site of the Escherichia coli ribosome. The transition state of the release factor 2 (RF2)-dependent hydrolysis reaction is characterized by the rate-limiting formation of a single strong hydrogen bond. This finding argues against a concerted proton shuttle in the transition state of the hydrolysis reaction. In comparison, the proton inventory for peptide bond formation indicates the rate-limiting formation of three hydrogen bonds with about equal contributions, consistent with a concerted eight-membered proton shuttle in the transition state. Thus, the ribosome supports different rate-limiting transition states for the two reactions that take place in the peptidyl transferase centre.     

肽泡的形态特征及其成膜蛋白的特性

小麦(Triticum aestivum)贮存蛋白经过纯化获得其中35kD一种蛋白质。该蛋白质在一定浓度的有机溶剂系统中经过超声波处理或搅拌,可以制成囊泡,并能包裹分子量从0.4～150kD的不同化合物(染料及抗体)。这种肽泡具有良好的稳定性,经低温冷冻干燥后,可成鳞片状,加水后复溶仍然保持肽泡的稳定性。这种特性称为DRV(Dehydration Rehydration Vesicles)性质。该蛋白质经修饰制定肽泡能包裹水溶性化合物,如水溶性染料,或不经修饰可包裹脂溶性化合物。这种蛋白质是由16种疏水性氨基酸残基组成,其N-末端为苯丙氨酸。     

Orientation of the peptide formation of N-phosphoryl amino acids in solution

The peptide formation of N-phosphoryl amino acids with amino acids proceeds in aqueous solution without any coupling reagents. After being separated in sephadex gel column, the phosphoryl dipeptides were analyzed by the electrospray ionization tandem mass spectrometry (ESIMS/ MS). The result demonstrates that phosphoryl dipeptides were detected in all the reaction systems. It is found that the formation of N-phosphoryl dipeptides is oriented: the N-terminal amino acid residues of the N-phosphoryl dipeptides are from N-phosphoryl amino acids, and the peptide elongation happened at the C-terminal. Only a-dipeptide, no β-dipeptide, is formed in the N-phosphoryl dipeptides, showing that a-carboxylic group is activated selectively by N-phosphorylation. Theoretical calculation shows that the peptide formation of N-phosphoryl amino acids might happen through a penta-coordinate carboxylic-phosphoric intermediate in solution. These results might give some clues to the study on the origin of proteins and protein biosynthesis.     

光照条件对丛枝菌根真菌吸收外源氮产精氨酸的影响

以高粱（Sorghum bicolor L．Moench）为宿主植物,接种丛枝菌根（arbuscular mycorrhiza,AM）真菌Glomus intraradices,采用三室隔离培养盒,在菌丝室加浓度为4mmol／L的精氨酸（Arg）、谷氨酰胺（Gln）、尿素（Urea）和NH4NO3,分别在4800,13200和17600lx光照条件下培养,通过测定根外菌丝和菌根中精氨酸的含量,探究了光照条件对丛枝菌根真菌吸收不同外源氮产生精氨酸的影响．结果表明：不同光照条件下不同外源氮对根外菌丝和菌根中精氨酸含量的影响不同,4800lx光照下添加谷氨酰胺和17600lx光照下添加NH4NO3,根外菌丝和菌根中的精氨酸含量均高于同光照条件下其他外源氮处理;13200lx光照下,不同外源氮对根外菌丝中精氨酸含量的影响大小为Arg〉Gln〉Urea〉NH4NO3,对菌根中精氨酸含量的影响为Gln〉Arg〉Urea〉NH4NO3．强光照可以促进丛枝菌根真菌孢子量、根侵染和菌丝量的提高．在相同氮源处理下,光照强度的影响表现为17600lx〉13200lx〉4800lx．     

二(过碘酸)合银(Ⅲ)配离子氧化L-谷氨酰胺的反应动力学及机理

在碱性介质中,二(过碘酸)合银(Ⅲ)配离子([Ag(HIO6)2]5-)氧化Gln导致脱羧与脱氨而生成H2NCOCH2CH2CHO,氧化的产物由化学方法和质谱鉴定.动力学实验表明,氧化反应为总二级,对Ag(Ⅲ)和Gln各为一级,表观二级速率常数随[IO4-]tot增大而减小,随着离子强度的增大而增大,同[OH-]的变化几乎无关.所提出的反应机理包括[Ag(HIO6)2]5-与[Ag(HIO6)(OH)(H2O)]2-形成前期平衡;2种Ag(Ⅲ)的形态被Gln平行还原并且均为速率控制步骤.根据反应机理,导出了速率方程和速控步的速率常数值,计算出了活化参数,对电子转移方式进行了详尽的讨论.