Publications by authors named "Kyosuke Nakajima"

3 Publications

  • Page 1 of 1

Three p-xylene-solvated pseudopolymorphs of bis[1,3-bis(pentafluorophenyl)propane-1,3-dionato]copper(II).

Acta Crystallogr C Struct Chem 2014 Oct 28;70(Pt 10):960-4. Epub 2014 Sep 28.

School of Science, Kitasato University, Kitasato 1-15-1, Sagamihara, Kanagawa 228-8555, Japan.

The Cu(2+) ions in the title compounds, namely bis[1,3-bis(pentafluorophenyl)propane-1,3-dionato-κ(2)O,O']copper(II) p-xylene n-solvate, [Cu(C15HF10O2)2]·nC8H10, with n = 1, (I), n = 2, (II), and n = 4, (III), are coordinated by two 1,3-bis(pentafluorophenyl)propane-1,3-dionate ligands. The coordination complexes of (I) and (II) have crystallographic inversion symmetry at the Cu atom and the p-xylene molecule in (I) also lies across an inversion centre. The p-xylene molecules in (I) and (II) interact with the pentafluorophenyl groups of the complex via arene-perfluoroarene interactions. In the crystal of (III), two of the p-xylene molecules interact with the pentafluorophenyl groups via arene-perfluoroarene interactions. The other two p-xylene molecules are located on the CuO4 coordination plane, forming a uniform cavity produced by metal···π interactions.
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http://dx.doi.org/10.1107/S2053229614020294DOI Listing
October 2014

Leu65 in the heme distal side is critical for the stability of the Fe(II)-O2 complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase.

J Inorg Biochem 2012 Mar 17;108:163-70. Epub 2011 Sep 17.

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai, Japan.

YddV is a globin-coupled oxygen sensor enzyme in that O(2) binding to the Fe(II) heme in the sensor domain substantially enhances its diguanylate cyclase activity. The Fe(III) heme-bound enzyme is also the active form. Amino acid sequence comparisons indicate that Leu65 is well conserved in globin-coupled oxygen sensor enzymes. Absorption spectra of the Fe(III) heme complexes of L65G, L65M, L65Q and L65T mutants of the isolated heme domain of YddV (YddV-heme) were substantially different from that of the wild-type protein. Specifically, Soret bands of the 6-coordinated high-spin Fe(III) complexes of mutant proteins (with H(2)O and His98 as axial ligands) were located at around 403-406 nm, distinct from that (391 nm) of the 5-coordinated high-spin Fe(III) complex of wild-type protein with His98 as the axial ligand. The autooxidation rate constant (>0.10 min(-1)) of the Fe(II)-O(2) complex of L65G was substantially higher than that (0.011 min(-1)) of the wild-type protein. Affinities of O(2) for the Fe(II) complexes of L65G and L65T were markedly higher than that for the wild-type protein. Thus, we suggest that the well-conserved Leu65 located in the heme distal side is critical for restricting water access to the heme distal side to avoid rapid autooxidation of YddV, which needs a stable Fe(II)-O(2) complex with a low autooxidation rate.
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http://dx.doi.org/10.1016/j.jinorgbio.2011.09.019DOI Listing
March 2012

Important roles of Tyr43 at the putative heme distal side in the oxygen recognition and stability of the Fe(II)-O2 complex of YddV, a globin-coupled heme-based oxygen sensor diguanylate cyclase.

Biochemistry 2010 Dec 19;49(49):10381-93. Epub 2010 Nov 19.

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan.

YddV from Escherichia coli (Ec) is a novel globin-coupled heme-based oxygen sensor protein displaying diguanylate cyclase activity in response to oxygen availability. In this study, we quantified the turnover numbers of the active [Fe(III), 0.066 min(-1); Fe(II)-O(2) and Fe(II)-CO, 0.022 min(-1)] [Fe(III), Fe(III)-protoporphyrin IX complex; Fe(II), Fe(II)-protoporphyrin IX complex] and inactive forms [Fe(II) and Fe(II)-NO, <0.01 min(-1)] of YddV for the first time. Our data indicate that the YddV reaction is the rate-determining step for two consecutive reactions coupled with phosphodiesterase Ec DOS activity on cyclic di-GMP (c-di-GMP) [turnover number of Ec DOS-Fe(II)-O(2), 61 min(-1)]. Thus, O(2) binding and the heme redox switch of YddV appear to be critical factors in the regulation of c-di-GMP homeostasis. The redox potential and autoxidation rate of heme of the isolated heme domain of YddV (YddV-heme) were determined to be -17 mV versus the standard hydrogen electrode and 0.0076 min(-1), respectively. The Fe(II) complexes of Y43A and Y43L mutant proteins (residues at the heme distal side of the isolated heme-bound globin domain of YddV) exhibited very low O(2) affinities, and thus, their Fe(II)-O(2) complexes were not detected on the spectra. The O(2) dissociation rate constant of the Y43W protein was >150 s(-1), which is significantly larger than that of the wild-type protein (22 s(-1)). The autoxidation rate constants of the Y43F and Y43W mutant proteins were 0.069 and 0.12 min(-1), respectively, which are also markedly higher than that of the wild-type protein. The resonance Raman frequencies representing ν(Fe-O(2)) (559 cm(-1)) of the Fe(II)-O(2) complex and ν(Fe-CO) (505 cm(-1)) of the Fe(II)-CO complex of Y43F differed from those (ν(Fe-O(2)), 565 cm(-1); ν(Fe-CO), 495 cm(-1)) of the wild-type protein, suggesting that Tyr43 forms hydrogen bonds with both O(2) and CO molecules. On the basis of the results, we suggest that Tyr43 located at the heme distal side is important for the O(2) recognition and stability of the Fe(II)-O(2) complex, because the hydroxyl group of the residue appears to interact electrostatically with the O(2) molecule bound to the Fe(II) complex in YddV. Our findings clearly support a role of Tyr in oxygen sensing, and thus modulation of overall conversion from GTP to pGpG via c-di-GMP catalyzed by YddV and Ec DOS, which may be applicable to other globin-coupled oxygen sensor enzymes.
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http://dx.doi.org/10.1021/bi100733qDOI Listing
December 2010
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