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Yadav U, Abbas Z, Butcher RJ, Patra AK. A luminescent terbium( iii) probe as an efficient ‘Turn-ON’ sensor for dipicolinic acid, a Bacillus Anthracis biomarker. NEW J CHEM 2022. [DOI: 10.1039/d2nj03437a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work drives the potential of lanthanide luminescence in the quantification and detection of the B. Anthracis bacterial spore by targeting dipicolinic acid (DPA), a principal component of anthrax spores.
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Affiliation(s)
- Usha Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Zafar Abbas
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC 20059, USA
| | - Ashis K. Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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Dudka AP. Structural analysis by reduced data: VII. Experimental check of the new method for refining the parameters of the model describing the absorption of radiation by a specimen. CRYSTALLOGR REP+ 2006. [DOI: 10.1134/s1063774506010263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Dudka AP. Structural analysis by reduced data: VI. A new method for refining the parameters of the model describing the absorption of radiation by a single-crystal specimen. CRYSTALLOGR REP+ 2005. [DOI: 10.1134/1.2132419] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Conformational analysis of cationic (R,S)- and (R,R)-(salen)manganese complexes possessing axial chirality as a chiral element based on x-ray crystallography: an explanation of the effect of apical ligand on enantioselection by (salen)manganese catalyst. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00952-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sakurai A, Akita M, Moro-oka Y. Synthesis and Characterization of the Dodecahexaynediyldiiron Complex, Fp*−(C⋮C)6−Fp* [Fp*= Fe(η5-C5Me5)(CO)2], the Longest Structurally Characterized Polyynediyl Complex. Organometallics 1999. [DOI: 10.1021/om990266i] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aizoh Sakurai
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Munetaka Akita
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yoshihiko Moro-oka
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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Ohta K, Hashimoto M, Takahashi Y, Hikichi S, Akita M, Moro-oka Y. Synthesis of a Series of Rhodium Complexes, TpiPrRhIL2 and TpiPrRhIII(X)(Y)(MeCN), with the Hydridotris(3,5-diisopropylpyrazolyl)borato Ligand (TpiPr) from a Versatile Precursor, (κ3-TpiPr)Rh(coe)(MeCN), and Dependence of κ2−κ3 Interconversion Rate of the TpiPr Ligand on the Chelate Ring Size. Organometallics 1999. [DOI: 10.1021/om990104m] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keisuke Ohta
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Mariko Hashimoto
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yoshiaki Takahashi
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Shiro Hikichi
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Munetaka Akita
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yoshihiko Moro-oka
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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Takahashi Y, Akita M, Hikichi S, Moro-oka Y. Two Isomeric Structures of Hydridoruthenium Complexes Supported by Hydrotrispyrazolylborates, TpRRu(H)(1,5-cyclooctadiene): An Octahedral Structure with Additional 3-Center-2-Electron Ru−H−B Interaction Is More Stable than a Square-Pyramidal Structure with a κ2-TpR Ligand. Organometallics 1998. [DOI: 10.1021/om980363w] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshiaki Takahashi
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Munetaka Akita
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Shiro Hikichi
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yoshihiko Moro-oka
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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Jenkins J, Janin J, Rey F, Chiadmi M, van Tilbeurgh H, Lasters I, De Maeyer M, Van Belle D, Wodak SJ, Lauwereys M. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites. Biochemistry 1992; 31:5449-58. [PMID: 1610791 DOI: 10.1021/bi00139a005] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structure and function of the xylose (glucose) isomerase from Actinoplanes missouriensis have been analyzed by X-ray crystallography and site-directed mutagenesis after cloning and overexpression in Escherichia coli. The crystal structure of wild-type enzyme has been refined to an R factor of 15.2% against diffraction data to 2.2-A resolution. The structures of a number of binary and ternary complexes involving wild-type and mutant enzymes, the divalent cations Mg2+, Co2+, or Mn2+, and either the substrate xylose or substrate analogs have also been determined and refined to comparable R factors. Two metal sites are identified. Metal site 1 is four-coordinated and tetrahedral in the absence of substrate and is six-coordinated and octahedral in its presence; the O2 and O4 atoms of linear inhibitors and substrate bind to metal 1. Metal site 2 is octahedral in all cases; its position changes by 0.7 A when it binds O1 of the substrate and by more than 1 A when it also binds O2; these bonds replace bonds to carboxylate ligands from the protein. Side chains involved in metal binding have been substituted by site-directed mutagenesis. The biochemical properties of the mutant enzymes are presented. Together with structural data, they demonstrate that the two metal ions play an essential part in binding substrates, in stabilizing their open form, and in catalyzing hydride transfer between the C1 and C2 positions.
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Affiliation(s)
- J Jenkins
- Laboratoire de Biologie Physicochimique, CNRS UA1131, Université Paris-Sud, Orsay, France
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Rey F, Jenkins J, Janin J, Lasters I, Alard P, Claessens M, Matthyssens G, Wodak S. Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis. Proteins 1988; 4:165-72. [PMID: 3237716 DOI: 10.1002/prot.340040303] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The structure of Xylose isomerase (X.I.) from Actinoplanes missouriensis has been solved to 2.8 Angstroms resolution. Phases were determined from a single Eu3+ derivative and from the noncrystallographic 222 symmetry of the tetrameric molecule. An atomic model was built and subjected to restrained crystallographic refinement. The resulting model is shown to be closely similar to the recently reported X.I.'s structures from three other bacterial sources. Each monomer is found to be composed of an eight-stranded alpha/beta "T.I.M." barrel forming an N-terminal domain of 328 residues followed by a large loop of 66 residues embracing an adjacent subunit. Analysis of intersubunit packing shows that the X.I. tetramer is an assembly of two tight dimers. The beta barrel fits a simple hyperboloid model as other T.I.M. barrels do. The active site, identified as the binding site for the inhibitor xylitol, is located at the carboxyl end of the beta strands in the barrel next to a pair of binding sites for Eu3+ ions, which are assumed to be sites for the divalent ions involved in catalysis. Active sites in the tetramer are oriented towards the interface between dimers. It is suggested that subunit interfaces might stabilize the active site region and this might explain the oligomeric nature of other alpha/beta barrel enzymes.
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Affiliation(s)
- F Rey
- Laboratoire de Biologie Physicochimique, Universite Paris Sud, Orsay, France
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