scholarly journals Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase

2019 ◽  
Vol 75 (4) ◽  
pp. 212-216 ◽  
Author(s):  
Tzu-Ping Ko ◽  
Xiansha Xiao ◽  
Rey-Ting Guo ◽  
Jian-Wen Huang ◽  
Weidong Liu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Active Site ◽  
Complex Structure ◽  
Binding Mode ◽  
Farnesyl Diphosphate ◽  
The Other ◽  
Isopentenyl Diphosphate ◽  
Promising Direction ◽  
Substrate Analogues ◽  
Resolution Structure

Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.

scholarly journals GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C β-Lactamase

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Jung-Hyun Na ◽  
Young Jun An ◽  
Sun-Shin Cha
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Binding Mode ◽  
Competitive Inhibitor ◽  
Phosphate Group ◽  
The Other ◽  
Extended Spectrum ◽  
Competitive Inhibitors ◽  
Class C

ABSTRACT Nucleotides were effective in inhibiting the class C β-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a Ki value of 16.2 μM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.

scholarly journals Decaprenyl Diphosphate Synthesis in Mycobacterium tuberculosis

2004 ◽  
Vol 186 (22) ◽  
pp. 7564-7570 ◽  
Author(s):  
Devinder Kaur ◽  
Patrick J. Brennan ◽  
Dean C. Crick
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Divalent Cations ◽  
Expression System ◽  
Catalytic Efficiency ◽  
Farnesyl Diphosphate ◽  
Isopentenyl Diphosphate ◽  
Prenyl Diphosphate ◽  
Mycobacterial Cell Wall ◽  
Prenyl Diphosphate Synthase

ABSTRACT Z-prenyl diphosphate synthases catalyze the sequential condensation of isopentenyl diphosphate with allylic diphosphates to synthesize polyprenyl diphosphates. In mycobacteria, these are precursors of decaprenyl phosphate, a molecule which plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan. Recently, it was demonstrated that open reading frame Rv2361c of the Mycobacterium tuberculosis H37Rv genome encodes a unique prenyl diphosphate synthase (M. C. Schulbach, P. J. Brennan, and D. C. Crick, J. Biol. Chem. 275:22876-22881, 2000). We have now purified the enzyme to near homogeneity by using an Escherichia coli expression system and have shown that the product of this enzyme is decaprenyl diphosphate. Rv2361c has an absolute requirement for divalent cations and an optimal pH range of 7.5 to 8.5, and the activity is stimulated by both detergent and dithiothreitol. The enzyme catalyzes the addition of isopentenyl diphosphate to geranyl diphosphate, neryl diphosphate, ω,E,E-farnesyl diphosphate, ω,E,Z-farnesyl diphosphate, or ω,E,E,E-geranylgeranyl diphosphate, with Km values for the allylic substrates of 490, 29, 84, 290, and 40 μM, respectively. The Km value for isopentenyl diphosphate is 89 μM. The catalytic efficiency is greatest when ω,E,Z-farnesyl diphosphate is used as the allylic acceptor, suggesting that this is the natural substrate in vivo, a conclusion that is supported by previous structural studies of decaprenyl phosphoryl mannose isolated from M. tuberculosis. This is the first report of a bacterial Z-prenyl diphosphate synthase that preferentially utilizes an allylic diphosphate primer having the α-isoprene unit in the Z configuration, indicating that Rv1086 (ω,E,Z-farnesyl diphosphate synthase) and Rv2361c act sequentially in the biosynthetic pathway that leads to the formation of decaprenyl phosphate in M. tuberculosis.

scholarly journals Determination of the Substrate Binding Mode to the Active Site Iron of (S)-2-Hydroxypropylphosphonic Acid Epoxidase Using17O-Enriched Substrates and Substrate Analogues†

Biochemistry ◽  
2007 ◽  
Vol 46 (44) ◽  
pp. 12628-12638 ◽  
Author(s):  
Feng Yan ◽  
Sung-Ju Moon ◽  
Pinghua Liu ◽  
Zongbao Zhao ◽  
John D. Lipscomb ◽  
...  
Keyword(s):  
Active Site ◽  
Substrate Binding ◽  
Binding Mode ◽  
Substrate Analogues

scholarly journals Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites

1992 ◽  
Vol 287 (3) ◽  
pp. 797-803 ◽  
Author(s):  
M J Kim ◽  
D Yamamoto ◽  
K Matsumoto ◽  
M Inoue ◽  
T Ishida ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Cysteine Proteinase ◽  
Complex Structure ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Cysteine Proteinase Inhibitor ◽  
Binding Modes ◽  
Replacement Method ◽  
Solvent Molecules

In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.

scholarly journals Relationship between rifampin MICs for and rpoB mutations of Mycobacterium tuberculosis strains isolated in Japan.

1996 ◽  
Vol 40 (4) ◽  
pp. 1053-1056 ◽  
Author(s):  
H Ohno ◽  
H Koga ◽  
S Kohno ◽  
T Tashiro ◽  
K Hara
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Point Mutation ◽  
Rpob Gene ◽  
The Other ◽  
Clinical Isolates ◽  
Sequencing Analysis ◽  
The Relationship

We analyzed the relationship between rifampin MICs and rpoB mutations of 40 clinical isolates of Mycobacterium tuberculosis. A point mutation in either codon 516, 526, or 531 was found in 13 strains requiring MICs of > or = 64 micrograms/ml, while 21 strains requiring MICs of < or = 1 microgram/ml showed no alteration in these codons. However, 3 of these 21 strains contained a point mutation in either codon 515 or 533. Of the other six strains requiring MICs between 2 and 32 micrograms/ml, three contained a point mutation in codon 516 or 526, while no alteration was detected in the other three. Our results indicate that the sequencing analysis of a 69-bp fragment in the rpoB gene is useful in predicting rifampin-resistant phenotypes.

scholarly journals Flower-Shaped C-Dots/Co3O4{111} Constructed with Dual-Reaction Centers for Enhancement of Fenton-Like Reaction Activity and Peroxymonosulfate Conversion to Sulfate Radical

Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 135
Author(s):  
Zhibin Wen ◽  
Qianqian Zhu ◽  
Jiali Zhou ◽  
Shudi Zhao ◽  
Jinnan Wang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
High Surface ◽  
High Surface Area ◽  
Reaction Centers ◽  
Organic Radicals ◽  
The Other ◽  
High Catalytic Activity ◽  
High Adsorption ◽  
High Turnover

Novel flower-shaped C-dots/Co3O4{111} with dual-reaction centers were constructed to improve the Fenton-like reaction activity and peroxymonosulfate (PMS) conversion to sulfate radicals. Due to the exposure of a high surface area and Co3O4{111} facets, flower-shaped C-dots/Co3O4{111} could provide more Co(II) for PMS activation than traditional spherical Co3O4{110}. Meanwhile, PMS was preferred for adsorption on Co3O4{111} facets because of a high adsorption energy and thereby facilitated the electron transfer from Co(II) to PMS. More importantly, the Co–O–C linkage between C-dots and Co3O4{111} induced the formation of the dual-reaction center, which promoted the production of reactive organic radicals (R•). PMS could be directly reduced to SO4−• by R• over C-dots. On the other hand, electron transferred from R• to Co via Co–O–C linkage could accelerate the redox of Co(II)/(III), avoiding the invalid decomposition of PMS. Thus, C-dots doped on Co3O4{111} improved the PMS conversion rate to SO4−• over the single active site, resulting in high turnover numbers (TONs). In addition, TPR analysis indicated that the optimal content of C-dots doped on Co3O4{111} is 2.5%. More than 99% of antibiotics and dyes were degraded over C-dots/Co3O4{111} within 10 min. Even after six cycles, C-dots/Co3O4{111} still remained a high catalytic activity.

scholarly journals Probing the ionization state of substrate α-d-glucopyranosyl phosphate bound to glycogen phosphorylase b

1995 ◽  
Vol 308 (3) ◽  
pp. 1017-1023 ◽  
Author(s):  
I P Street ◽  
S G Withers
Keyword(s):  
Active Site ◽  
Glycogen Phosphorylase ◽  
Ph Dependence ◽  
Substrate Inhibition ◽  
19F Nmr ◽  
Ionization State ◽  
Nmr Studies ◽  
Substrate Analogues ◽  
Glycogen Phosphorylase B ◽  
Pka Value

The ionization state of the substrate alpha-D-glucopyranosyl phosphate bound at the active site of glycogen phosphorylase has been probed by a number of techniques. Values of Ki determined for a series of substrate analogue inhibitors in which the phosphate moiety bears differing charges suggest that the enzyme will bind both the monoanionic and dianionic substrates with approximately equal affinity. These results are strongly supported by 31P- and 19F-NMR studies of the bound substrate analogues alpha-D-glucopyranosyl 1-methylenephosphonate and 2-deoxy-2-fluoro-alpha-D-glucopyranosyl phosphate, which also suggest that the substrate can be bound in either ionization state. The pH-dependences of the inhibition constants K1 for these two analogues, which have substantially different phosphate pK2 values (7.3 and 5.9 respectively), are found to be essentially identical with the pH-dependence of K(m) values for the substrate, inhibition decreasing according to an apparent pKa value of 7.2. This again indicates that there is no specificity for monoanion or dianion binding and also reveals that binding is associated with the uptake of a proton. As the bound substrate is not protonated, this proton must be taken up by the proton.

scholarly journals A Study of the Effects of Rain, Snow and Hail on the Atmospheric Electric Field near Ground

Atmosphere ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 996
Author(s):  
Athanasios Karagioras ◽  
Konstantinos Kourtidis
Keyword(s):  
Frequency Distribution ◽  
Complex Structure ◽  
Potential Gradient ◽  
Weather Conditions ◽  
The Other ◽  
Fair Weather ◽  
Northern Greece ◽  
Rain Events ◽  
The Impact ◽  
Bounce Back

The purpose of the present study is to investigate the impact of rain, snow and hail on potential gradient (PG), as observed in a period of ten years in Xanthi, northern Greece. An anticorrelation between PG and rainfall was observed for rain events that lasted several hours. When the precipitation rate was up to 2 mm/h, the decrease in PG was between 200 and 1300 V/m, in most cases being around 500 V/m. An event with rainfall rates up to 11 mm/h produced the largest drop in PG, of 2 kV/m. Shortly after rain, PG appeared to bounce back to somewhat higher values than the ones of fair-weather conditions. A decrease in mean hourly PG was observed, which was around 2–4 kV/m during the hail events which occurred concurrently with rain and from 0 to 3.5 kV/m for hail events with no rain. In the case of no drop, no concurrent drop in temperature was observed, while, for the other cases, it appeared that, for each degree drop in temperature, the drop in hourly mean PG was 1000 V/m; hence, we assume that the intensity of the hail event regulates the drop in PG. The frequency distribution of 1-minute PG exhibits a complex structure during hail events and extend from −18 to 11 kV/m, with most of the values in the negative range. During snow events, 1-minute PG exhibited rapid fluctuations between high positive and high negative values, its frequency distribution extending from −10 to 18 kV/m, with peaks at −10 and 3 kV/m.

scholarly journals Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein

2016 ◽  
Vol 72 (8) ◽  
pp. 609-618 ◽  
Author(s):  
Martin P. Horvath ◽  
Evan W. George ◽  
Quang T. Tran ◽  
Kody Baumgardner ◽  
Gabe Zharov ◽  
...  
Keyword(s):  
Lipid Transfer Protein ◽  
Transport Proteins ◽  
Binding Domain ◽  
Regions Of Interest ◽  
The Other ◽  
Lipid Transfer ◽  
Transfer Protein ◽  
Biochemical Function ◽  
Rigid Body Docking ◽  
Resolution Structure

A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74 Å resolution. A previous structure of the same protein determined to 2.2 Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s.d. of 0.25 Å), especially in terms of the helix-grip fold constructed around a solvent-filled cavity. Regions of interest were defined with alternate conformations in the current higher-resolution structure, including Arg351 found within the cavity and Ω1, a loop of four residues found just outside the cavity entrance. Models of the complex with lutein generated by rigid-body docking indicate that one of the ionone rings must protrude outside the cavity, and this insight has implications for molecular interactions with transport proteins and enzymes that act on lutein. Interestingly, models with the ∊-ionone ring characteristic of lutein pointing towards the bottom of the cavity were associated with fewer steric clashes, suggesting that steric complementarity and ligand asymmetry may play a role in discriminating lutein from the other ocular carotenoids zeaxanthin andmeso-zeaxanthin, which only have β-ionone rings.

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