Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate

The second messenger hydrogen peroxide is required for optimal activation of numerous signal transduction pathways, particularly those mediated by protein tyrosine kinases. One mechanism by which hydrogen peroxide regulates cellular processes is the transient inhibition of protein tyrosine phosphatases through the reversible oxidization of their catalytic cysteine, which suppresses protein dephosphorylation. Here we describe a structural analysis of the redox-dependent regulation of protein tyrosine phosphatase 1B (PTP1B), which is reversibly inhibited by oxidation after cells are stimulated with insulin and epidermal growth factor. The sulphenic acid intermediate produced in response to PTP1B oxidation is rapidly converted into a previously unknown sulphenyl-amide species, in which the sulphur atom of the catalytic cysteine is covalently linked to the main chain nitrogen of an adjacent residue. Oxidation of PTP1B to the sulphenyl-amide form is accompanied by large conformational changes in the catalytic site that inhibit substrate binding. We propose that this unusual protein modification both protects the active-site cysteine residue of PTP1B from irreversible oxidation to sulphonic acid and permits redox regulation of the enzyme by promoting its reversible reduction by thiols.     

Tracking kinesin-driven movements with nanometre-scale precision

Several enzyme complexes drive cellular movements by coupling free energy-liberating chemical reactions to the production of mechanical work. A key goal in the study of these systems is to characterize at the molecular level mechanical events associated with individual reaction steps in the catalytic cycles of single enzyme molecules. Ideally, one would like to measure movements driven by single (or a few) enzyme molecules with sufficient temporal resolution and spatial precision that these events can be directly observed. Kinesin, a force-generating ATPase involved in microtubule-based intracellular organelle transport, will drive the unidirectional movement of microscopic plastic beads along microtubules in vitro. Under certain conditions, a few (less than or equal to 10) kinesin molecules may be sufficient to drive either bead movement or organelle transport. Here we describe a method for determining precise positional information from light-microscope images. The method is applied to measure kinesin-driven bead movements in vitro with a precision of 1-2 nm. Our measurements reveal basic mechanical features of kinesin-driven movements along the microtubule lattice, and place significant constraints on possible molecular mechanisms of movement.     

苏氨酸分子的构象转变及水分子与羟基自由基的催化机理

采用密度泛函理论的B3LYP方法和微扰论的MP2方法, 研究苏氨酸分子构象转变机制以及水分子与羟基自由基对氢迁移反应的催化作用. 结果表明： S-苏氨酸向R 别苏氨酸的构象转变反应有4个通道, R-别苏氨酸向R-苏氨酸与S-苏氨酸向S-别苏氨酸的构象转变反应各有1个通道; S-苏氨酸向R-别苏氨酸构象转变反应的最高能垒为250.2 kJ/mol; R-别苏氨酸向R-苏氨酸构象转变反应的最高能垒为335.0 kJ/mol; S-苏氨酸向S-别苏氨酸构象转变反应的最高能垒为359.6 kJ/mol; 2个水分子构成的链及水分子/羟基自由基构成的链对质子迁移反应有较好的催化作用, 使S-苏氨酸向R-别苏氨酸构象转变反应的高能垒分别降为128.3 kJ/mol和108.6 kJ/mol.     

A conformational switch controls hepatitis delta virus ribozyme catalysis

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.     

Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide

Peptide bond formation is the principal reaction of protein synthesis. It takes place in the peptidyl transferase centre of the large (50S) ribosomal subunit. In the course of the reaction, the polypeptide is transferred from peptidyl transfer RNA to the alpha-amino group of amino acyl-tRNA. The crystallographic structure of the 50S subunit showed no proteins within 18 A from the active site, revealing peptidyl transferase as an RNA enzyme. Reported unique structural and biochemical features of the universally conserved adenine residue A2451 in 23S ribosomal RNA (Escherichia coli numbering) led to the proposal of a mechanism of rRNA catalysis that implicates this nucleotide as the principal catalytic residue. In vitro genetics allowed us to test the importance of A2451 for the overall rate of peptide bond formation. Here we report that large ribosomal subunits with mutated A2451 showed significant peptidyl transferase activity in several independent assays. Mutations at another nucleotide, G2447, which is essential to render catalytic properties to A2451 (refs 2, 3), also did not dramatically change the transpeptidation activity. As alterations of the putative catalytic residues do not severely affect the rate of peptidyl transfer the ribosome apparently promotes transpeptidation not through chemical catalysis, but by properly positioning the substrates of protein synthesis.     

Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme

The biosynthetic pathway of the clinically important antibiotic fosfomycin uses enzymes that catalyse reactions without precedent in biology. Among these is hydroxypropylphosphonic acid epoxidase, which represents a new subfamily of non-haem mononuclear iron enzymes. Here we present six X-ray structures of this enzyme: the apoenzyme at 2.0 A resolution; a native Fe(II)-bound form at 2.4 A resolution; a tris(hydroxymethyl)aminomethane-Co(II)-enzyme complex structure at 1.8 A resolution; a substrate-Co(II)-enzyme complex structure at 2.5 A resolution; and two substrate-Fe(II)-enzyme complexes at 2.1 and 2.3 A resolution. These structural data lead us to suggest how this enzyme is able to recognize and respond to its substrate with a conformational change that protects the radical-based intermediates formed during catalysis. Comparisons with other family members suggest why substrate binding is able to prime iron for dioxygen binding in the absence of alpha-ketoglutarate (a co-substrate required by many mononuclear iron enzymes), and how the unique epoxidation reaction of hydroxypropylphosphonic acid epoxidase may occur.     

Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase

Fructose-1,6-bisphosphate (FBP) aldolase/phosphatase is a bifunctional, thermostable enzyme that catalyses two subsequent steps in gluconeogenesis in most archaea and in deeply branching bacterial lineages. It mediates the aldol condensation of heat-labile dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) to FBP, as well as the subsequent, irreversible hydrolysis of the product to yield the stable fructose-6-phosphate (F6P) and inorganic phosphate; no reaction intermediates are released. Here we present a series of structural snapshots of the reaction that reveal a substantial remodelling of the active site through the movement of loop regions that create different catalytic functionalities at the same location. We have solved the three-dimensional structures of FBP aldolase/phosphatase from thermophilic Thermoproteus neutrophilus in a ligand-free state as well as in complex with the substrates DHAP and FBP and the product F6P to resolutions up to 1.3??. In conjunction with mutagenesis data, this pinpoints the residues required for the two reaction steps and shows that the sequential binding of additional Mg(2+) cations reversibly facilitates the reaction. FBP aldolase/phosphatase is an ancestral gluconeogenic enzyme optimized for high ambient temperatures, and our work resolves how consecutive structural rearrangements reorganize the catalytic centre of the protein to carry out two canonical reactions in a very non-canonical type of bifunctionality.     

Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B

Protein tyrosine phosphatases regulate signal transduction pathways involving tyrosine phosphorylation and have been implicated in the development of cancer, diabetes, rheumatoid arthritis and hypertension. Increasing evidence suggests that the cellular redox state is involved in regulating tyrosine phosphatase activity through the reversible oxidization of the catalytic cysteine to sulphenic acid (Cys-SOH). But how further oxidation to the irreversible sulphinic (Cys-SO2H) and sulphonic (Cys-SO3H) forms is prevented remains unclear. Here we report the crystal structures of the regulatory sulphenic and irreversible sulphinic and sulphonic acids of protein tyrosine phosphatase 1B (PTP1B), an important enzyme in the negative regulation of the insulin receptor and a therapeutic target in type II diabetes and obesity. We also identify a sulphenyl-amide species that is formed through oxidation of its catalytic cysteine. Formation of the sulphenyl-amide causes large changes in the PTP1B active site, which are reversible by reduction with the cellular reducing agent glutathione. The sulphenyl-amide is a protective intermediate in the oxidative inhibition of PTP1B. In addition, it may facilitate reactivation of PTP1B by biological thiols and signal a unique state of the protein.     

Ta亚烷基化合物与Os氧化物间的亚烷基转移反应机理

使用密度泛函理论B3LYP方法研究了金属Ta亚烷基化合物与Os氧化物间的亚烷基转移反应机理.使用B3LYP方法,金属原子采用LanL2DZ基组和赝势,其他原子采用6-31G（d）基组,优化得到了反应物、产物、中间体和过渡态的几何构型.对所得到的结构使用B3LYP方法,金属原子采用包含f轨道的SDDAll基组和赝势,其他原子采用6-311＋＋G（d,p）基组计算了反应的活化Gibbs自由能.研究结果表明,金属Ta亚烷基化合物与Os氧化物间的亚烷基转移反应经由4个基元反应完成,每一基元反应的过渡态都具有四元环结构并且其活化Gibbs自由能都很小,反应在低温下容易完成.研究结果还表明,总反应是放热反应并且第1个基元反应是决速步骤.     

A covalent adduct between the uracil ring and the active site of an aminoacyl tRNA synthetase

A covalent adduct of an aminoacyl tRNA synthetase and uracil nucleoside has been isolated. The enzyme adduct is catalytically inactive; one nucleoside is bound per catalytic site. The release of uridine restores enzyme activity. The nucleoside attaches to a protein segment required for tRNA interaction. The findings add support to concepts of a covalent component for some protein-nucleic acid complexes.     

Kemp elimination catalysts by computational enzyme design

The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.     

Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism

Insulin-degrading enzyme (IDE), a Zn2+-metalloprotease, is involved in the clearance of insulin and amyloid-beta (refs 1-3). Loss-of-function mutations of IDE in rodents cause glucose intolerance and cerebral accumulation of amyloid-beta, whereas enhanced IDE activity effectively reduces brain amyloid-beta (refs 4-7). Here we report structures of human IDE in complex with four substrates (insulin B chain, amyloid-beta peptide (1-40), amylin and glucagon). The amino- and carboxy-terminal domains of IDE (IDE-N and IDE-C, respectively) form an enclosed cage just large enough to encapsulate insulin. Extensive contacts between IDE-N and IDE-C keep the degradation chamber of IDE inaccessible to substrates. Repositioning of the IDE domains enables substrate access to the catalytic cavity. IDE uses size and charge distribution of the substrate-binding cavity selectively to entrap structurally diverse polypeptides. The enclosed substrate undergoes conformational changes to form beta-sheets with two discrete regions of IDE for its degradation. Consistent with this model, mutations disrupting the contacts between IDE-N and IDE-C increase IDE catalytic activity 40-fold. The molecular basis for substrate recognition and allosteric regulation of IDE could aid in designing IDE-based therapies to control cerebral amyloid-beta and blood sugar concentrations.     

Snapshots of tRNA sulphuration via an adenylated intermediate

Uridine at the first anticodon position (U34) of glutamate, lysine and glutamine transfer RNAs is universally modified by thiouridylase into 2-thiouridine (s2U34), which is crucial for precise translation by restricting codon-anticodon wobble during protein synthesis on the ribosome. However, it remains unclear how the enzyme incorporates reactive sulphur into the correct position of the uridine base. Here we present the crystal structures of the MnmA thiouridylase-tRNA complex in three discrete forms, which provide snapshots of the sequential chemical reactions during RNA sulphuration. On enzyme activation, an alpha-helix overhanging the active site is restructured into an idiosyncratic beta-hairpin-containing loop, which packs the flipped-out U34 deeply into the catalytic pocket and triggers the activation of the catalytic cysteine residues. The adenylated RNA intermediate is trapped. Thus, the active closed-conformation of the complex ensures accurate sulphur incorporation into the activated uridine carbon by forming a catalytic chamber to prevent solvent from accessing the catalytic site. The structures of the complex with glutamate tRNA further reveal how MnmA specifically recognizes its three different tRNA substrates. These findings provide the structural basis for a general mechanism whereby an enzyme incorporates a reactive atom at a precise position in a biological molecule.     

Effect of Urea on Activity and Conformation of a Glycoprotein

Introduction In some enzymes, inactivation occurs before noticeable conformational change can be detected during denaturation by guanidinium chloride or urea[1-6]. Tsou[7] suggested that enzyme active sites are formed by relatively weak molecular interact…     

PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome.

The assembly of the spliceosome is an ATP-dependent process. The splicing factor PRP16 contains variations of several motifs that define the eIF-4A-like ATP-dependent RNA helicase family. The protein has now been purified and shown to exhibit RNA-dependent ATPase activity. PRP16 is required specifically for the second catalytic step of the splicing reaction in vitro. This function requires ATP binding and/or hydrolysis, which appears to be concomitant with release of the protein from the spliceosome. PRP16 may be the prototype for a set of splicing factors which use ATP to drive a cycle of conformational changes.     

A mutant T4 lysozyme displays five different crystal conformations

Phage T4 lysozyme consists of two domains between which is formed the active-site cleft of the enzyme. The crystallographically determined thermal displacement parameters for the protein suggested that the amino terminal of the two domains undergoes 'hinge-bending' motion about an axis passing through the waist of the molecule. Such conformational mobility may be important in allowing access of substrates to the active site of the enzyme. We report here a crystallographic study of a mutant T4 lysozyme which demonstrates further the conformational flexibility of the protein. A mutant form of the enzyme with a methionine residue (Met 6) replaced by isoleucine crystallizes with four independent molecules in the crystal lattice. These four molecules have distinctly different conformations. The mutant protein can also crystallize in standard form with a structure very similar to the wild-type protein. Thus the mutant protein can adopt five different crystal conformations. The isoleucine for methionine substitution at the intersection of the two domains of T4 lysozyme apparently enhances the hinge-bending motion presumed to occur in the wild-type protein, without significantly affecting the catalytic activity or thermal stability of the protein.     

新型水溶性手性钌催化剂的制备及应用

利用发烟硫酸磺化手性双胺双膦配体[（R．R）-C6P2（NH）2]．合成了PNNP-型水溶性手性双胺双膦配体[（R．R）-C6P2（NH）2（SO3Na）4]，并分别与简单的钌、铑络合物反应，制备水溶性手性钌络合物催化剂[（R，R）-C6P2（NH）2（SO3Na）4RuCl2]和铑络合物催化剂[（R，R）-C6P2（NH）2（SO3Na）4RhCl]．经元素分析、红外光谱和核磁共振等对手性配体及手性Ru络合物进行了结构表征．进而用这些水溶性的钌，铑络合物催化剂或水溶性手性配体与铱络合物[IrHCl2（COD）]2组成的混合催化体系研究了多种芳香酮的不对称转移氢化。结果表明．在以异丙醇作为氢源时．对芳香酮的不对称转移氢化都具有较好的催化活性．与铑，铱催化体系相比，水溶性手性钌络合物催化体系具有更高的活性和对映选择性．对于苯乙酮的氢化．其转化率和对映选择性分别达到91.6％和93．0％e．e．．此外，进一步考察了反应温度和KOH用量对水溶性手性钌络合物催化苯乙酮不对称转移氢化性能的影响，并将水溶性手性钌络合物催化体系应用于多种芳香酮的不对称转移氢化，获得了高的收率和对映选择性，分别可达92．0％和96．4％e．e．．研究结果表明，水溶性手性钌络合物[CR．R）-G6P2（NH）2（SO3Na）4RuCl2]是芳香酮不对称氢转移催化氢化的优良催化剂.     

初始裂解产物对FOX-7裂解通道影响的理论研究

为研究裂解过程中生成的自由基(·H、·OH和·NO)对尚未裂解的1,1-二氨基-2,2-二硝基乙烯(FOX-7)各裂解通道的影响,采用密度泛函理论PW6B95-D3方法,结合def2-TZVP基组和def2-TZVP/J辅助基组在ORCA程序中优化出了·H、·OH、·NO分别与FOX-7的复合体。为判断自由基与FOX-7的复合方式,采用AIM理论计算了各复合体电荷密度的拉普拉斯值(Laplacian)。在相同水平下,计算了各复合体不同裂解通道的活化能;并基于键长、键级、成键方式等电子结构参数的变化,分析了活化能变化的本质。结果表明,自由基的存在使C—NO_2键的离解能(除NO_01外)降低4.1~138 kJ·mol~(-1);但对硝基异构的活化能影响不大。自由基的生成引发了FOX-7的自加速裂解反应。     

Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase

Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.