Snapshot of a Michaelis complex in a sulfuryl transfer reaction: Crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter substrate

We report the crystal structure of mouse sulfotransferase, mSULT1D1, complexed with donor substrate 3′-phosphoadenosine 5′-phosphosulfate and accepter substrate p-nitrophenol. The structure is the first report of the native Michaelis complex of sulfotransferase. In the structure, three proposed catalytic residues (Lys48, Lys106, and His108) were in proper positions for engaging in the sulfuryl transfer reaction. The data strongly support that the sulfuryl transfer reaction proceeds through an S_N2-like in-line displacement mechanism.     

An enzyme-coupled assay for amidotransferase activity of glucosamine-6-phosphate synthase

An assay for glucosamine-6-phosphate synthase using a yeast glucosamine-6-phosphate N-acetyltransferase 1 (GNA1) as coupling enzyme was developed. GNA1 transfers the acetyl moiety from acetyl-coenzyme A (CoA) to glucosamine-6-phosphate, releasing coenzyme A. The assay measures the production of glucosamine-6-phosphate by either following the consumption of acetyl-CoA spectrophotometrically at 230nm or quantifying the free thiol with 5,5'-dithio-bis(2-nitrobenzoic acid) (Ellman's reagent) in a discontinuous manner. This method is simple to perform and can be adapted to a 96-well microtiter plate format, which will facilitate high-throughput inhibitor screening and mechanistic studies using purified GlmS.     

Acceptor substrate binding revealed by crystal structure of human glucosamine-6-phosphate N-acetyltransferase 1

Glucosamine-6-phosphate (GlcN6P) N-acetyltransferase 1 (GNA1) is a key enzyme in the pathway toward biosynthesis of UDP-N-acetylglucosamine, an important donor substrate for N-linked glycosylation. GNA1 catalyzes the formation of N-acetylglucosamine-6-phosphate (GlcNAc6P) from acetyl-CoA (AcCoA) and the acceptor substrate GlcN6P. Here, we report crystal structures of human GNA1, including apo GNA1, the GNA1-GlcN6P complex and an E156A mutant. Our work showed that GlcN6P binds to GNA1 without the help of AcCoA binding. Structural analyses and mutagenesis studies have shed lights on the charge distribution in the GlcN6P binding pocket, and an important role for Glu156 in the substrate binding. Hence, these findings have broadened our knowledge of structural features required for the substrate affinity of GNA1. STRUCTURED SUMMARY:     

Molecular modeling of formate dehydrogenase: the formation of the Michaelis complex

The formation of the reactive enzyme–substrate complex of formate dehydrogenase has been investigated by molecular dynamics techniques accounting for different conformational states of the enzyme. Simulations revealed that the transport of substrate to the active site through the substrate channel proceeds in the open conformation of enzyme due to the crucial role of the Arg284 residue acting as a vehicle. However, formate binding in the active site of the open conformation leads to the formation of a nonproductive enzyme–substrate complex. The productive Michaelis complex is formed only in the closed enzyme conformation after the substrate and coenzyme have bound, when required rigidity of the binding site and reactive formate orientation due to interactions with Arg284, Asn146, Ile122, and His332 residues is attained. Then, the high occupancy (up to 75%) of the reactive substrate–coenzyme conformation is reached, which was demonstrated by hybrid quantum mechanics/molecular mechanics simulations using various semiempirical Hamiltonians.     

Glucose-6-phosphate dehydrogenase porbandar: A new slow variant with slightly reduced activity in a South African family of Indian descent

A new variant of the red cell enzyme glucose-6-phosphate dehydrogenase has been detected in a South African male of Indian descent and in several of his relatives. The enzyme variant is characterized by slow electrophoretic mobility, low Michaelis constants for the substrates glucose-6-phosphate and NADP, and increased utilization of the substrate analogues 2-deoxyglucose-6-phosphate and deamino-NADP relative to the normal (B⁺) enzyme. There is no evidence that the enzyme variant, for which the name G6PD Porbandar is suggested, is associated with any hematological abnormality.The Atomic Energy Board and the South African Medical Research Council provided support for part of this work.     

Synthesis, crystal structure and esterification of a novel iron(III) 18-metallacrown-6 complex

The trianionic heptadentate ligand, (Z)-3-(5′-chlorosalicylhydrazinocarbonyl) propenoic acid, has been synthesized and reacted with FeCl₃·6H₂O, to produce the complex [Fe^III₆(C₁₂H₈N₂O₅Cl)₆(H₂O)₄(CH₃OH)₂]·8H₂O·4CH₃OH. In the self-assembly process the ligand was esterified and transferred into (Z)-methyl 3-(5′-chlorosalicylhydrazinocarbonyl) propenoate. In the crystal structure, the neutral Fe(III) complex contain a 18-membered metallacrown ring consisting of six Fe(III) and six trianionic ligands. The 18-membered metallacrown ring is formed by the succession of six structural moieties of the type [Fe(III)-N-N]. Due to the meridional coordination of the ligands to the Fe³⁺ ions, the ligands enforce the stereochemistry of the Fe³⁺ ions as a propeller configuration with alternating Λ/Δ forms. The metallacrown can be treated with SnCl₂ or Zn powder to obtain purified ester.     

Crystal Structure of the Michaelis Complex between Tissue-type Plasminogen Activator and Plasminogen Activators Inhibitor-1

Thrombosis is a leading cause of death worldwide. Recombinant tissue-type plasminogen activator (tPA) is the Food and Drug Administration-approved thrombolytic drug. tPA is rapidly inactivated by endogenous plasminogen activator inhibitor-1 (PAI-1). Engineering on tPA to reduce its inhibition by PAI-1 without compromising its thrombolytic effect is a continuous effort. Precise details, with atomic resolution, of the molecular interactions between tPA and PAI-1 remain unknown despite previous extensive studies. Here, we report the crystal structure of the tPA·PAI-1 Michaelis complex, which shows significant differences from the structure of its urokinase-type plasminogen activator analogue, the uPA·PAI-1 Michaelis complex. The PAI-1 reactive center loop adopts a unique kinked conformation. The structure provides detailed interactions between tPA 37- and 60-loops with PAI-1. On the tPA side, the S2 and S1β pockets open up to accommodate PAI-1. This study provides structural basis to understand the specificity of PAI-1 and to design newer generation of thrombolytic agents with reduced PAI-1 inactivation.     

Smilax china root extract as a novel Glucose- 6-phosphate dehydrogenase inhibitor for the treatment of hepatocellular carcinoma

A novel therapeutic strategy for cancer treatment is to target altered tumor metabolism. Glucose- 6-phosphate dehydrogenase (G6PD) has been recently discovered to be implicated in apoptosis and angiogenesis, making it an excellent target in cancer treatment. The current study aimed to screen the plant extracts library to find potent hits against G6PD through enzymatic assay. Protein expression was induced by IPTG and purified using Ni-NTA columns after transformation of the pET-24a-HmG6PD plasmid into E. coli BL21-DE3 strain. An enzymatic assay was established by using purified rG6PD protein, for the screening of G6PD inhibitors. Out of 46 plant extracts screened, the sixteen plant extracts have shown inhibitory activity against the G6PD enzyme. At doses from 1 to 4 µg/ml, this extract demonstrated concentration-dependent inhibition of G6PD with an IC₅₀ value of I.397 µg/ml. Moreover, the anticancer activity evaluation against HepG2 cells determined Smilax china as a potent inhibitor of cancer cells (IC₅₀ value of 16.017 μg/ml). The acute and subacute toxicities were not observed in mice with various concentrations (50, 100, 200 and 2000 mg/kg). Furthermore, to identify the compounds from Smilax china as G6PD inhibitors, a literature-based phytochemical investigation of Smilax china was conducted, and sixty compounds were docked against the NADP+ and G6P binding sites of G6PD. The results of this study showed that three compounds were Scirpusin A, Smilachinin and Daucosterol with MolDock Score of ?156.832, ?148.215, and ?145.733 respectively, against NADP+ binding site of G6PD. Conclusively, Smilax china root extract could be a safer drug candidate for the treatment of hepatocellular carcinoma.     

Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae

The riboflavin biosynthesis pathway has been shown to be essential in many pathogens and is absent in humans. Therefore, enzymes involved in riboflavin synthesis are considered as potential antibacterial drug targets. The enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes one of the two committed steps in the riboflavin pathway and converts d-ribulose 5-phosphate (Ru5P) to l-3,4-dihydroxy-2-butanone 4-phosphate and formate. Moreover, DHBPS is shown to be indispensable for Mycobacterium, Salmonella, and Helicobacter species. Despite the essentiality of this enzyme in bacteria, no inhibitor has been identified hitherto. Here, we describe kinetic and crystal structure characterization of DHBPS from Vibrio cholerae (vDHBPS) with a competitive inhibitor 4-phospho-d-erythronohydroxamic acid (4PEH) at 1.86-Å resolution. In addition, we also report the structural characterization of vDHBPS in its apo form and in complex with its substrate and substrate plus metal ions at 1.96-, 1.59-, and 2.04-Å resolution, respectively. Comparison of these crystal structures suggests that 4PEH inhibits the catalytic activity of DHBPS as it is unable to form a proposed intermediate that is crucial for DHBPS activity. Furthermore, vDHBPS structures complexed with substrate and metal ions reveal that, unlike Candida albicans, binding of substrate to vDHBPS induces a conformational change from an open to closed conformation. Interestingly, the position of second metal ion, which is different from that of Methanococcus jannaschii, strongly supports an active role in the catalytic mechanism. Thus, the kinetic and structural characterization of vDHBPS reveals the molecular mechanism of inhibition shown by 4PEH and that it can be explored further for designing novel antibiotics.     

Co-crystallization between a thymine and a metal complex connected by triple hydrogen bonds

The synthesis and crystal structure of co-crystal between bis(dithiobiureto)platinum(II) ([Pt(dtb)₂]) with thymine is reported. The crystalline structure of [Pt(dtb)₂](thymine)₂ shows two-dimensional arrays created by hydrogen-bonding interactions. One mononuclear complex and two thymine molecules form a building unit connected by triple hydrogen bond employing ADA-DAD arrangements (A, hydrogen bond acceptor; D, hydrogen bond donor). The building unit is linked to adjacent units via additional hydrogen bonds to form planar sheet.     

Synthesis, crystal structure and electroluminescent properties of a Schiff base zinc complex

A new complex of zinc with a Schiff base, zinc(N,N′-bis(salicylidene)-3, 6-dioxa-1, 8-diaminooctane monohydrate) (ZnBSO · H₂O), was synthesized and characterized by means of elemental analyses, IR spectra and DTA-TG. Its structure was determined by X-ray single crystal analysis. It was demonstrated that the zinc atom is coordinated by the two oxygen atoms in phenolate and two nitrogen atoms in imine of the ligand in a slightly distorted tetrahedral geometry, while the two oxygen atoms from the oxa-alkyl chain are not coordinated to Zn(II) atom. The energy levels of the HOMO, LUMO and the electrochemical band gap were determined by cyclic voltammeter. The electroluminescent devices with the complex as the emitter showed bright blue emission with a peak at 450 nm, which is same as the fluorescence of the complex in both solution and solid states.     

The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action

The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) x-ray structure of a complex formed between trypsin and a canonical inhibitor acting through a substrate-like mechanism. The electron density indicates the protonation state of all catalytic residues where the catalytic histidine is, as expected, in its neutral state prior to the acylation step by the catalytic serine. The carboxyl group of the catalytic aspartate displays an asymmetric electron density so that the O_δ2–C_γ bond appears to be a double bond, with O_δ2 involved in a hydrogen bond to His-57 and Ser-214. Only when Asp-102 is protonated on O_δ1 atom could a density functional theory simulation reproduce the observed electron density. The presence of a putative hydrogen atom is also confirmed by a residual mF_obs − DF_calc density above 2.5 σ next to O_δ1. As a possible functional role for the neutral aspartate in the active site, we propose that in the substrate-bound form, the neutral aspartate residue helps to keep the pK_a of the histidine sufficiently low, in the active neutral form. When the histidine receives a proton during the catalytic cycle, the aspartate becomes simultaneously negatively charged, providing additional stabilization for the protonated histidine and indirectly to the tetrahedral intermediate. This novel proposal unifies the seemingly conflicting experimental observations, which were previously seen as either supporting the charge relay mechanism or the neutral pK_a histidine theory.     

Actinide coordination chemistry - a unique example of a homoleptic complex of nine-coordinate thorium(IV)

The dimethylsulfoxide (dmso) solvate of Th(IV) perchlorate is readily obtained from acidic aqueous Th(IV) solutions and has a formulation established from a single crystal structure determination of [Th(dmso-O)₉](ClO₄)₄ · 4dmso; triclinic, , a=12.4811(8) Å, b=12.4879(8) Å, c=23.969(2) Å, α=94.684(1)°, β=95.823(1)°, γ=119.347(1)°. The primary coordination sphere of the Th is of tricapped trigonal prismatic form, with the symmetry of the [Th(dmso-O)₉] entity being close to C_3h.     

葡萄糖-6-磷酸异构酶早期诊断类风湿关节炎的临床意义

目的：探讨血清葡萄糖6-磷酸异构酶（GPI）早期诊断类风湿关节炎（RA）的临床意义。方法：用ELISA法检测105例RA组、51例风湿病组、42例非风湿病组及40例健康对照组的血清GPI浓度,其中RA组分为早期组和中晚期组。同时收集RA患者类风湿因子（RF）、血沉（EsR）、免疫球蛋白、C-反应蛋白（CRP）、补体（C3、C4）、关节炎部位数等相关临床指标。结果：GPI对早期RA和中晚期RA诊断的敏感性分别为70．03％,和79．41％;特异性分别为89．89％和90．91％;二者敏感性、特异性比较均无显著差异;在RA患者中,GPI结果与RF、CRP、ESR、IgA、IgG、关节炎部位数均有相关性（P〈0．05）,与c3、C4、IgM无相关性;RF诊断RA的敏感性80．95％,特异性为78．19％,与GPI比较,二者敏感性无显著差异,特异性有差异（P〈0．05）,二者同时检测诊断RA的敏感性为69．52％,特异性达93．99％。结论：GPI诊断早期RA具有较好的敏感性和特异性,与RF联合检测对RA诊断具有很高的特异性,且可能成为判断RA病情活动的指标之一。     

One trinuclear copper(II) complex derived from a new Schiff base ligand based on the dianion of 4-chloro-6-(hydroxymethyl)-2-((3-aminopropylimino)methyl)-phenol: Synthesis, structure, spectroscopic and magnetic properties

A linear trinuclear copper(II) complex (1), prepared from a new Schiff base ligand, namely the dianion of 4-chloro-6-(hydroxymethyl)-2-((3-aminopropylimino)methyl)-phenol, was synthesized and characterized in this paper. The X-ray structural study reveals that the geometry of the central Cu2 ion is elongated octahedral and that of the two side Cu(II) ions is distorted square pyramidal. The magnetic susceptibility measurements from 2 to 300 K reveal medium antiferromagnetic interactions between the Cu(II) ions with a J value of −64.6(1) cm⁻¹.     

Glucose-1-phosphate as a selective substrate for enumeration of Bacteroides species in the rumen.

When glucose-1-phosphate was used as the only added energy source in a selective roll tube medium, colony counts for rumen contents ranged from 17.8 to 84.8% of the total culturable count. Percentages were highest in rumen contents from sheep fed high-concentrate rations. From a total of 73 cultures isolated from glucose-1-phosphate roll rubes, only 15.1% were presumptively identified as Bacteroides species. Strains presumptively identified as Butyrivibrio, Selenomonas, Treponema, Streptococcus bovis, and Lachnospira also fermented glucose-1-phosphate. Thus, glucose-1-phosphate would not be useful as a selective substrate for isolation or enumeration of Bacteroides species from the rumen.     

Synthesis, structure and characterization of a new tetrameric tungsten-oxo complex [WO2Cl2(THF)]4

WOCl₄ reacts with (Me₃Si)₂O and excess THF to give [WO₂Cl₂(THF)]₄ (1), a new tetrameric tungsten(VI)-oxo complex, which was characterized and crystal structure was determined by X-ray crystallography. Complex 1 has a roughly square planar tetranuclear structure bridged by μ-oxo ligands. Each tungsten atom is coordinated by two bridging oxygens, one terminal oxygen, two “axial” chlorine atoms and one “equatorial” O-bonded THF ligand. One of the two μ-oxo ligands is similar to the terminal oxygen atom and the other one is similar to the coordinated oxygen atom of the THF ligand, respectively, which confirmed a previous proposal. Four WO₃Cl₂(THF) octahedral are associated by sharing corners. Complex 1 is different from three known tetrameric tungsten analogues in its structural arrangement and properties.     

Optical properties of a novel neodymium pentafluoropropionate binuclear complex

A novel neodymium pentafluoropropionate binuclear complex, Nd(C₂F₅COO)₃Dipy (Dipy: 2,2′-dipyridyl), was synthesized and characterized by single-crystal X-ray diffraction. At a concentration of 0.2 M in DMSO-d₆, the Judd-Ofelt parameters (Ω₂, Ω₄, Ω₆) were calculated from the UV-Vis spectrum. According to the small value of Ω₂ and the zero splitting energy of ⁴F/_3/2 level, a symmetric ligand field of the complex was confirmed in DMSO-d₆. Strong emission of the complex in DMSO-d₆ at 1057 nm with a decay time about 1.3 μs were detected when excited at 800 nm pumped by a laser diode. The stimulated emission cross-section of ⁴F_3/2 → ⁴I_11/2 fluorescence transition was 2.36 × 10⁻²⁰ cm² and comparable with some laser glasses, which indicated good radiative properties of this neodymium pentafluoropropionate binuclear complex in liquid matrix.