Structure Gallery



Bacterial ABC Heme transporter BhuUV-T

  • Naoe, Y., Nakamura, N., Doi, A., Sawabe, M., Nakamura, H., Shiro, Y., and Sugimoto, H. "Crystal structure of bacterial haem importer complex in the inward-facing conformation. Nature Commun. 13411 (2016). [doi]


Heme-sensing response regulator ChrA

  • Doi, A., Nakamura, H., Shiro, Y., and Sugimoto, H. "Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae". Acta Crystallogr. F Struct. Biol. Commun. 71, 966-971 (2015).





Diiron site in a bacterial hemerythrin (collaboration with Prof. T. Hayashi)

  • Okamoto, Y., Onoda, A., Sugimoto, H., Takano, Y., Hirota, S., Kurtz, D. M., Shiro, Y., Hayashi, T. "H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin". Chem. Commun. 50, 3421-3423 (2014)
  • Okamoto, Y., Onoda, A., Sugimoto, H., Takano, Y., Hirota, S., Kurtz, D. M., Jr., Shiro, Y., Hayashi, T. "Crystal Structure, Exogenous Ligand Binding, and Redox Properties of an Engineered Diiron Active Site in a Bacterial Hemerythrin". Inorg. Chem. 52, 13014-13020 (2013)


Heme sensor HrtR (collaboration with Prof. S. Aono)

  • Sawai, H., Yamanaka, M., Sugimoto, H., Shiro, Y., Aono, S. "Structural basis for the transcriptional regulation of heme homeostasis in Lactococcus lactis." J. Biol. Chem 287, 30755-30768 (2012) [PubMed]


Quinol-dependent NO reductase (qNOR)

  • Matsumoto, Y., Tosha, T., Pisliakov, A. V., Hino, T., Sugimoto, H., Nagano, S., Sugita, Y., Shiro, Y. "Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus ". Nature Struct. Mol. Biol. 19, 238-245 (2012) [PubMed]


Cytochrome c-dependent NO reductase (cNOR) in denifrification

  • Hino, T., Matsumoto, Y., Nagano, S., Sugimoto, H., Y., F., Murata, T., Iwata, S., Shiro, Y. Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330, 1666-1670 (2010) [PubMed]


Nitrile synthesis by "aldoxime dehydratase OxdRE"

  • Sawai, H., Sugimoto, H., Kato, Y., Asano, Y., Shiro, Y., Aono, S. X-ray crystal structure of the michaelis complex of aldoxime dehydratase. J. Biol. Chem. 284, 32089-96 (2009) [PubMed]


Histidine kinase and response regulator complex

  • Yamada, S., Sugimoto, H., Kobayashi, M., Ohno, A., Nakamura, H., Shiro, Y. Structure of PAS-linked histidine kinase and the response regulator complex. Structure 17, 1333-1344 (2009) [PubMed]
  • Seeing the sencein it all (RIKEN Research Highlights) 25 Dec. 2009


New cyan fluorecent protein

  • Kikuchi, A., Fukumura, E., Karasawa, S., Shiro, Y., Miyawaki, A. Crystal structure of a new cyan fluorescent protein and its hue-shifted variants. Biochemistry 48, 5276-5283 (2009)



CYP105A1 enzyme metabolizing vitamin D3

  • Sugimoto, H., Shinkyo, R., Hayashi, K., Yoneda, S., Yamada, M., Kamakura, M., Ikushiro, S., Shiro, Y., Sakaki, T. Crystal structure of CYP105A1 (P450SU-1) in complex with 1alpha,25-dihydroxyvitamin D3. Biochemistry 47, 4017-4027 (2008)
  • Hayashi, K., Sugimoto, H., Shinkyo, R., Yamada, M., Ikeda, S., Ikushiro, S., Kamakura, M., Shiro, Y., Sakaki, T. Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1. Biochemistry 47, 11964-11972 (2008)


Orange fluorecent protein: Kusabira Orange

  • Kikuchi, A., Fukumura, E., Karasawa, S., Mizuno, H., Miyawaki, A., Shiro, Y. Structural characterization of a thiazoline-containing chromophore in an orange fluorescent protein, monomeric Kusabira Orange. Biochemistry 47, 11573-11580 (2008)


Dronpa: fluorecent protein

  • Mizuno, H., Mal, T. K., Walchli, M., Kikuchi, A., Fukano, T., Ando, R., Jeyakanthan, J., Taka, J., Shiro, Y., Ikura, M., Miyawaki, A. Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. Proc. Natl. Acad. Sci. USA 105, 9227-9232 (2008)



  • Hirano, S., Asamizu, S., Onaka, H., Shiro, Y., Nagano, S. Crystal Structure of VioE, a Key Player in the Construction of the Molecular Skeleton of Violacein. J. Biol. Chem. 283, 6459-6466 (2008)


Myoglobin with one-legged heme

  • Harada, K., Makino, M., Sugimoto, H., Hirota, S., Matsuo, T., Shiro, Y., Hisaeda, Y., Hayashi, T. Structure and ligand binding properties of myoglobins reconstituted with monodepropionated heme: functional role of each heme propionate side chain. Biochemistry 46, 9406-9416 (2007)



P450 StaP: producuction of indolocarbazole skeleton for anti-cancer drug.

  • Makino, M., Sugimoto, H., Shiro, Y., Asamizu, S., Onaka, H., Nagano, S. Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton. Proc. Natl. Acad. Sci. USA 104, 11591-11596 (2007)
  • Wang, Y., Chen, H., Makino, M., Shiro, Y., Nagano, S., Asamizu, S., Onaka, H., Shaik, S. Theoretical and experimental studies of the conversion of chromopyrrolic acid to an antitumor derivative by cytochrome P450 StaP: the catalytic role of water molecules. J. Am. Chem. Soc. 131, 6748-6762 (2009)
  • Core structures -- RIKEN Research Highlights (14 Sep 2007)
  • Water-powered reactions -- RIKEN Research Highlights (26 Jun 2009)


Myoglobin reconstituted with porphycene

  • Hayashi, T., Murata, D., Makino, M., Sugimoto, H., Matsuo, T., Sato, H., Shiro, Y., Hisaeda, Y. Crystal structure and peroxidase activity of myoglobin reconstituted with iron porphycene. Inorg. Chem. 45, 10530-10536 (2006)


Human indoleamine 2,3-dioxygenase (IDO)

  • Sugimoto, H., Oda, S., Otsuki, T., Hino, T., Yoshida, T., Shiro, Y. Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase. Proc. Natl. Acad. Sci. USA 103, 2611-2616 (2006)
  • Chung, L. W., Li, X., Sugimoto, H., Shiro, Y., Morokuma, K. Density functional theory study on a missing piece in understanding of heme chemistry: the reaction mechanism for indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. J. Am. Chem. Soc. 130, 12299-12309 (2008)
  • Missing piece gets a work over -- RIKEN RESEARCH Highlights 2009-Jan-16


XTAL and SAXS analyais of histidine kinase

  • Yamada, S., Akiyama, S., Sugimoto, H., Kumita, H., Ito, K., Fujisawa, T., Nakamura, H., Shiro, Y. The signaling pathway in histidine kinase and the response regulator complex revealed by X-ray crystallography and solution scattering. J. Mol. Biol. 362, 123-139 (2006)


Fourth globin in human´╝Ücytoglobin

  • Sugimoto, H., Makino, M., Sawai, H., Kawada, N., Yoshizato, K., Shiro, Y. Structural basis of human cytoglobin for ligand binding. J. Mol. Biol. 339, 873-885 (2004)
  • Makino, M., Sugimoto, H., Sawai, H., Kawada, N., Yoshizato, K., Shiro, Y. High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode. Acta Crystallogr. Sect. D Biol. Crystallogr. 62, 671-677 (2006)


FixJ DNA binding domain

  • Kurashima-Ito, K., Kasai, Y., Hosono, K., Tamura, K., Oue, S., Isogai, M., Ito, Y., Nakamura, H., Shiro, Y. Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter. Biochemistry 44, 14835-14844 (2005)


Peroxygenase P450BSbeta

  • Lee, D. S., Yamada, A., Sugimoto, H., Matsunaga, I., Ogura, H., Ichihara, K., Adachi, S., Park, S. Y., Shiro, Y. Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies. J. Biol. Chem. 278, 9761-9767 (2003)
  • Shoji, O., Fujishiro, T., Nakajima, H., Kim, M., Nagano, S., Shiro, Y., Watanabe, Y. Hydrogen peroxide dependent monooxygenations by tricking the substrate recognition of cytochrome P450BSbeta. Angew. Chem. Int. Ed. 46, 3656-3659 (2007)


Snapshot of stuctural change in hemoglobin

  • Adachi, S., Park, S. Y., Tame, J. R., Shiro, Y., Shibayama, N. Direct observation of photolysis-induced tertiary structural changes in hemoglobin. Proc. Natl. Acad. Sci. USA 100, 7039-7044 (2003)


Biliverdin reductase

  • Kikuchi, A., Park, S. Y., Miyatake, H., Sun, D., Sato, M., Yoshida, T., Shiro, Y. Crystal structure of rat biliverdin reductase. Nat. Struct. Biol. 8, 221-225 (2001)


Oxygen sensing PAS domain of FixL

  • Miyatake, H., Mukai, M., Park, S. Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T., Shiro, Y. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J. Mol. Biol. 301, 415-431 (2000)


Hyperthermophilic P450 (CYP1119)

  • Denisov, I. G., Hung, S. C., Weiss, K. E., McLean, M. A., Shiro, Y., Park, S. Y., Champion, P. M., Sligar, S. G. Characterization of the oxygenated intermediate of the thermophilic cytochrome P450 CYP119. J. Inorg. Biochem. 87, 215-226 (2001)


Fungal nitric oxide reductase P450nor

  • Park, S.Y., Shimizu, H., Adachi, S., Nakagawa, A., Tanaka, I., Nakahara, K., Shoun, H., Obayashi, E., Nakamura, H., Iizuka, T., Shiro, Y. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum. Nature truct. Biol. 4, 827-32 (1997)
  • Shimizu, H., Park, S. Y., Shiro, Y., Adachi, S. X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution. Acta Crystallogr. Sect. D Biol. Crystallogr. 58, 81-89 (2002)