Biological Information-, Material - and Energy-Conversion by Iron-Containing Proteins
Iron is a metal element indispensable for life. It usually plays important roles as reaction centers of the iron-containing proteins and enzymes, and is responsible for many physiological actions, e.g., conversion of bio-materials (biosynthesis and metabolism), bio-information (signal trasnduction)...
Saved in:
| Published in | Biomedical Research on Trace Elements Vol. 22; no. 4; pp. 50 - 58 |
|---|---|
| Main Author | |
| Format | Journal Article |
| Language | English Japanese |
| Published |
Osaka
Japan Society for Biomedical Research on Trace Elements
01.10.2011
Japan Science and Technology Agency |
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Iron is a metal element indispensable for life. It usually plays important roles as reaction centers of the iron-containing proteins and enzymes, and is responsible for many physiological actions, e.g., conversion of bio-materials (biosynthesis and metabolism), bio-information (signal trasnduction) and bio-energy, through the ligand binding, acid-base and reductionoxidation reactions. Our group has had much interest in iron-containing proteins and enzymes, especially heme-containing proteins and enzymes (hemoproteins and heme-enzymes). Heme is a iron-porphyrin complexes. We are studying their molecular properties on the basis of their molecular structures, which can be crystallographycally determined using the SPring-8 Beam Lines. In this article, we focus on structure-function relationship of heme-containing oxygenases, oxygensensor proteins and nitric oxide reductases. |
|---|---|
| AbstractList | Iron is a metal element indispensable for life. It usually plays important roles as reaction centers of the iron-containing proteins and enzymes, and is responsible for many physiological actions, e.g., conversion of bio-materials (biosynthesis and metabolism), bio-information (signal trasnduction) and bio-energy, through the ligand binding, acid-base and reductionoxidation reactions. Our group has had much interest in iron-containing proteins and enzymes, especially heme-containing proteins and enzymes (hemoproteins and heme-enzymes). Heme is a iron-porphyrin complexes. We are studying their molecular properties on the basis of their molecular structures, which can be crystallographycally determined using the SPring-8 Beam Lines. In this article, we focus on structure-function relationship of heme-containing oxygenases, oxygensensor proteins and nitric oxide reductases. |
| Author | Shiro, Yoshitsugu |
| Author_xml | – sequence: 1 fullname: Shiro, Yoshitsugu organization: RIKEN SPring-8 Center |
| BookMark | eNo9kE1LAzEQhoNUsK2e_AMLXk3NVzebgwctVQsVPVTwFpLd2TXLNqnZVOi_d0vFy7zw8DDvMBM08sEDQteUzChlSt3ZmGDG2GxOztCYFgXBVBAxQmOiaI4llZ8XaNL3LSFcMinG6OPRhS40rjRdtvJ1iFuTXPD4Nns1CaIbMM6Mr7Klh9gc8CL4H4j9oGT2kK3ioA4oGeedb7L3GBI431-i89p0PVz95RRtnpabxQtevz2vFg9r3BaMYWVMngtiZVHlooS6hEIJAEZtwUvOKZWVOR5aV8ZWQAtLrSCykrK2ipua8ym6Oa3dxfC9hz7pNuyjHxo1FUJxxXLFBuv-ZLV9Mg3oXXRbEw_axOTKDvTxZ5oxLY5jTv55-WWiBs9_AV7OasU |
| ContentType | Journal Article |
| Copyright | 2011 by Japan Society for Biomedical Research on Trace Elements Copyright Japan Science and Technology Agency 2011 |
| Copyright_xml | – notice: 2011 by Japan Society for Biomedical Research on Trace Elements – notice: Copyright Japan Science and Technology Agency 2011 |
| DBID | 7QO 7T5 7TK 7U7 8FD C1K FR3 H94 P64 |
| DOI | 10.11299/brte.22.50 |
| DatabaseName | Biotechnology Research Abstracts Immunology Abstracts Neurosciences Abstracts Toxicology Abstracts Technology Research Database Environmental Sciences and Pollution Management Engineering Research Database AIDS and Cancer Research Abstracts Biotechnology and BioEngineering Abstracts |
| DatabaseTitle | Biotechnology Research Abstracts Technology Research Database Toxicology Abstracts AIDS and Cancer Research Abstracts Immunology Abstracts Engineering Research Database Neurosciences Abstracts Biotechnology and BioEngineering Abstracts Environmental Sciences and Pollution Management |
| DatabaseTitleList | Biotechnology Research Abstracts |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology |
| EISSN | 1880-1404 |
| EndPage | 58 |
| ExternalDocumentID | 3121566071 article_brte_22_4_22_50_article_char_en |
| GroupedDBID | 2WC 53G ACIWK ACPRK ADBBV AFRAH ALMA_UNASSIGNED_HOLDINGS BAWUL DIK JMI JSF JSH KQ8 MOJWN OK1 RJT RZJ TKC 7QO 7T5 7TK 7U7 8FD C1K FR3 H94 P64 |
| ID | FETCH-LOGICAL-j822-9aa6640b78d64cefce894ee21b83c33117da0037fdabde18b1b407d77fb93af33 |
| ISSN | 0916-717X |
| IngestDate | Mon Jun 30 10:15:48 EDT 2025 Wed Apr 05 06:55:07 EDT 2023 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | false |
| IsScholarly | true |
| Issue | 4 |
| Language | English Japanese |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-j822-9aa6640b78d64cefce894ee21b83c33117da0037fdabde18b1b407d77fb93af33 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 |
| OpenAccessLink | https://www.jstage.jst.go.jp/article/brte/22/4/22_50/_article/-char/en |
| PQID | 1449392692 |
| PQPubID | 1966362 |
| PageCount | 9 |
| ParticipantIDs | proquest_journals_1449392692 jstage_primary_article_brte_22_4_22_50_article_char_en |
| PublicationCentury | 2000 |
| PublicationDate | 20111001 |
| PublicationDateYYYYMMDD | 2011-10-01 |
| PublicationDate_xml | – month: 10 year: 2011 text: 20111001 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | Osaka |
| PublicationPlace_xml | – name: Osaka |
| PublicationTitle | Biomedical Research on Trace Elements |
| PublicationTitleAlternate | Biomed. Res. Trace Elements |
| PublicationYear | 2011 |
| Publisher | Japan Society for Biomedical Research on Trace Elements Japan Science and Technology Agency |
| Publisher_xml | – name: Japan Society for Biomedical Research on Trace Elements – name: Japan Science and Technology Agency |
| References | [12] W. Gong, B. Hao, M. K. Chan: "New Mechanism Insights from Structural Studies of the Oxygen-sensing Domain of Bradyrhizobium japonicum FixL" Biochemistry 39, 3955-3962 (2000) [21] H. N. Chapman, et al.: "Femtosecond X-ray Protein Nanocrystallography" Nature 470, 73-78 (2011) [16] Y. Shiro, M. Fujii, T. Iizuka, S. Adachi, K. Tsukamoto, K. Nakahara, H. Shoun: "Spectroscopic and Kinetic Studies on Reaction of Cytochrome P450nor with Nitric Oxide: Implication for Its NO Reduction Mechanism" J. Biol. Chem. 270, 1617-1623, (1995) [10] W. Gong, B. Hao, S. S. Mansy, G. Gonzalez, M. A. Gilles-Gonzalez, M. K. Chan: "Structure of a Biological Oxygen Sensor: A new Mechanism for Heme-driven Signal Transduction" Proc. Natl. Acad. Sci. USA 95, 15177-15182 (1998) [7] S. Yanagisawa, K. Yotsuya, Y. Hashiwaki, M. Horitani, H. Sugimoto, Y. Shiro, E. H. Appelman, T. Ogura: "Identification of the Fe-O2 and the Fe=O Heme Species for Indoleamine 2,3-Dioxygenase during Catalytic Turnover" Chem. Lett. 39, 36-37 (2009) [14] A. R. Ravishankara, J. S. Daniel, R. W. Portmann: "Nitrous Oxide (N2O): The Dominant Ozone-Depleting Substance Emitted in the 21st Century" Science 326, 123-125 (2009) [19] H. Kumita, K. Matsuura, T. Hino, S. Takahashi, H. Hori, Y. Fukumori, I. Morishima, Y. Shiro: "NO Reduction by Nitric Oxide Reductase from Denitrifying Bacterium Pseudomonas aeruginosa : Characterization of Reaction Intermediates That Appear in the Single-Turnover Cycle" J. Biol. Chem. 279, 55247-55254 (2004) [18] Y. Matsumoto, T. Tosha, A. V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, Y. Shiro: "Crystal Structure of Ouinol-dependent Nitric Oxide Reductase from Geobacillus stearothermophilus" Nat. Strl. Mol. Biol. (2011) in press [3] 3.D.-S. Lee, A. Yamada, H. Sugimoto, I. Matsunaga, H. Ogura, K. Ichihara, S. Adachi, S.-Y. Park, Y. Shiro: "Substrate Recognition and Molecular Mechanism of Fatty Acid Hydroxylation by Cytchrome P450 from Bacillus subtilis : Crystallographic, Spectroscopic and Mutational Studies" J. Biol. Chem. 278, 9761-9767 (2003) [15] S.-Y. Park, H. Shimizu, S. Adachi, A. Nakagawa, I. Tanaka, K. Nakahara, H. Shoun, E. Obayashi, H. Nakamura, T. Iizuka, Y. Shiro: "Crystal Structure of Nitric Oxide Reductase from Denitrifying Fungus Fusarium oxysporum" Nature Strl. Biol. 4, 827-832 (1997) [13] S. Yamada, H. Sugimoto, M. Kobayashi, A. Ohno, H. Nakamura, Y. Shiro: "Structure of PAS-linked Histidine Kinase and the Response Regulator Complex" Structure 17, 1333-1344 (2009) [17] T. Hino, Y. Matsumoto, S. Nagano, H. Sugimoto, Y. Fukumori, T. Murata, S. Iwata, Y. Shiro: "Structural Basis of Biological N2O Generation by Bacterial Nitric Oxide Reductase" Science 330, 1666-1670 (2010) [8] L. W. Chung, X. Li, H. Sugimoto, Y. Shiro, K. Morokuma: "ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants" J. Am. Chem. Soc. 132, 11993-12005 (2010) [1] T. L. Poulos, B. C. Finzel, I. C. Gunsalus, G. C. Wagner, J. Kraut: "The 2.6 Å Crystal Structure of Pseudomonas putida Cytochrome P450" J. Biol. Chem. 260, 16122-16130 (1985) [11] H. Miyatake, M. Mukai, S.-Y. Park, S. Adachi, K. Tamura, H. Nakamura, K. Nakamura, T. Tsuchiya, T. Iizuka, Y. Shiro: "Sensory Mechanism of Oxygen Sensor FixL from Rhizobium meliloti : Crystallographic, Mutagenesis and Resonance Raman Spectroscopic Studies" J. Mol. Biol. 301, 415-431, (2000) [2] 杉本宏、永野真吾、城宜嗣：2.2 P450の分子構造：X線結晶構造解析を中心に．大村恒雄、石村巽、藤井義明 編：P450の分子生物学 第２版．講談社、東京、2009、35-45 [4] O. Shoji, T. Fujishiro, S. Nagano, S. Tanaka, T. Hirose, Y. Shiro, Y. Watanabe: "Understanding Substrate Misrecognition of Hydrogen Peroxide-Dependent Cytochrome P450 from Bacillus subtilis" J. Biol. Inorg. Chem. 15, 1331-1339 (2010) [6] H. Sugimoto, S. Oda, T. Otsuki, T. Hino, T. Yoshida, Y. Shiro: "Crystal Structure of Human Indoleamine 2,3-dioxygenase: Insight into the Catalytic Mechanism of O2 In corporation by a Heme-containing Dioxygenase" Proc. Natl. Acad. Sci. USA 103, 2611-2616 (2006) [5] O. Shoji, T. Fujishiro, H. Nakajima, M. Kim, S. Nagano, Y. Shiro, Y. Watanabe: "Hydrogen Peroxide Dependent Monooxygenations by Tricking the Substrate Recognition of Cytochrome P450BSβ" Angw. Chem. Int. Ed. 46, 3656-3659 (2007) [9] H. C. Brastianos, E. Vottero, B. O. Patrick, R. Van Soest, T. Matainaho, A. G. Mauk, R. J. Andersen: "Exiguamine A, An Indoleamine-2,3-dioxygenase (IDO) Inhibitor Isolated from the Marine Sponge Neopetrosia exigua" J. Am. Chem. Soc. 128, 16046-16047 (226) [20] S. Buschmann, E. Warkentin, H. Xie, J. D. Langer, U. Ermler, H. Michel: "The Structure of cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping" Science 329, 327-330 (2010) |
| References_xml | – reference: [3] 3.D.-S. Lee, A. Yamada, H. Sugimoto, I. Matsunaga, H. Ogura, K. Ichihara, S. Adachi, S.-Y. Park, Y. Shiro: "Substrate Recognition and Molecular Mechanism of Fatty Acid Hydroxylation by Cytchrome P450 from Bacillus subtilis : Crystallographic, Spectroscopic and Mutational Studies" J. Biol. Chem. 278, 9761-9767 (2003) – reference: [12] W. Gong, B. Hao, M. K. Chan: "New Mechanism Insights from Structural Studies of the Oxygen-sensing Domain of Bradyrhizobium japonicum FixL" Biochemistry 39, 3955-3962 (2000) – reference: [19] H. Kumita, K. Matsuura, T. Hino, S. Takahashi, H. Hori, Y. Fukumori, I. Morishima, Y. Shiro: "NO Reduction by Nitric Oxide Reductase from Denitrifying Bacterium Pseudomonas aeruginosa : Characterization of Reaction Intermediates That Appear in the Single-Turnover Cycle" J. Biol. Chem. 279, 55247-55254 (2004) – reference: [14] A. R. Ravishankara, J. S. Daniel, R. W. Portmann: "Nitrous Oxide (N2O): The Dominant Ozone-Depleting Substance Emitted in the 21st Century" Science 326, 123-125 (2009) – reference: [21] H. N. Chapman, et al.: "Femtosecond X-ray Protein Nanocrystallography" Nature 470, 73-78 (2011) – reference: [10] W. Gong, B. Hao, S. S. Mansy, G. Gonzalez, M. A. Gilles-Gonzalez, M. K. Chan: "Structure of a Biological Oxygen Sensor: A new Mechanism for Heme-driven Signal Transduction" Proc. Natl. Acad. Sci. USA 95, 15177-15182 (1998) – reference: [20] S. Buschmann, E. Warkentin, H. Xie, J. D. Langer, U. Ermler, H. Michel: "The Structure of cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping" Science 329, 327-330 (2010) – reference: [1] T. L. Poulos, B. C. Finzel, I. C. Gunsalus, G. C. Wagner, J. Kraut: "The 2.6 Å Crystal Structure of Pseudomonas putida Cytochrome P450" J. Biol. Chem. 260, 16122-16130 (1985) – reference: [13] S. Yamada, H. Sugimoto, M. Kobayashi, A. Ohno, H. Nakamura, Y. Shiro: "Structure of PAS-linked Histidine Kinase and the Response Regulator Complex" Structure 17, 1333-1344 (2009) – reference: [15] S.-Y. Park, H. Shimizu, S. Adachi, A. Nakagawa, I. Tanaka, K. Nakahara, H. Shoun, E. Obayashi, H. Nakamura, T. Iizuka, Y. Shiro: "Crystal Structure of Nitric Oxide Reductase from Denitrifying Fungus Fusarium oxysporum" Nature Strl. Biol. 4, 827-832 (1997) – reference: [17] T. Hino, Y. Matsumoto, S. Nagano, H. Sugimoto, Y. Fukumori, T. Murata, S. Iwata, Y. Shiro: "Structural Basis of Biological N2O Generation by Bacterial Nitric Oxide Reductase" Science 330, 1666-1670 (2010) – reference: [5] O. Shoji, T. Fujishiro, H. Nakajima, M. Kim, S. Nagano, Y. Shiro, Y. Watanabe: "Hydrogen Peroxide Dependent Monooxygenations by Tricking the Substrate Recognition of Cytochrome P450BSβ" Angw. Chem. Int. Ed. 46, 3656-3659 (2007) – reference: [16] Y. Shiro, M. Fujii, T. Iizuka, S. Adachi, K. Tsukamoto, K. Nakahara, H. Shoun: "Spectroscopic and Kinetic Studies on Reaction of Cytochrome P450nor with Nitric Oxide: Implication for Its NO Reduction Mechanism" J. Biol. Chem. 270, 1617-1623, (1995) – reference: [4] O. Shoji, T. Fujishiro, S. Nagano, S. Tanaka, T. Hirose, Y. Shiro, Y. Watanabe: "Understanding Substrate Misrecognition of Hydrogen Peroxide-Dependent Cytochrome P450 from Bacillus subtilis" J. Biol. Inorg. Chem. 15, 1331-1339 (2010) – reference: [2] 杉本宏、永野真吾、城宜嗣：2.2 P450の分子構造：X線結晶構造解析を中心に．大村恒雄、石村巽、藤井義明 編：P450の分子生物学 第２版．講談社、東京、2009、35-45 – reference: [9] H. C. Brastianos, E. Vottero, B. O. Patrick, R. Van Soest, T. Matainaho, A. G. Mauk, R. J. Andersen: "Exiguamine A, An Indoleamine-2,3-dioxygenase (IDO) Inhibitor Isolated from the Marine Sponge Neopetrosia exigua" J. Am. Chem. Soc. 128, 16046-16047 (226) – reference: [11] H. Miyatake, M. Mukai, S.-Y. Park, S. Adachi, K. Tamura, H. Nakamura, K. Nakamura, T. Tsuchiya, T. Iizuka, Y. Shiro: "Sensory Mechanism of Oxygen Sensor FixL from Rhizobium meliloti : Crystallographic, Mutagenesis and Resonance Raman Spectroscopic Studies" J. Mol. Biol. 301, 415-431, (2000) – reference: [8] L. W. Chung, X. Li, H. Sugimoto, Y. Shiro, K. Morokuma: "ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants" J. Am. Chem. Soc. 132, 11993-12005 (2010) – reference: [7] S. Yanagisawa, K. Yotsuya, Y. Hashiwaki, M. Horitani, H. Sugimoto, Y. Shiro, E. H. Appelman, T. Ogura: "Identification of the Fe-O2 and the Fe=O Heme Species for Indoleamine 2,3-Dioxygenase during Catalytic Turnover" Chem. Lett. 39, 36-37 (2009) – reference: [6] H. Sugimoto, S. Oda, T. Otsuki, T. Hino, T. Yoshida, Y. Shiro: "Crystal Structure of Human Indoleamine 2,3-dioxygenase: Insight into the Catalytic Mechanism of O2 In corporation by a Heme-containing Dioxygenase" Proc. Natl. Acad. Sci. USA 103, 2611-2616 (2006) – reference: [18] Y. Matsumoto, T. Tosha, A. V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita, Y. Shiro: "Crystal Structure of Ouinol-dependent Nitric Oxide Reductase from Geobacillus stearothermophilus" Nat. Strl. Mol. Biol. (2011) in press |
| SSID | ssj0037274 |
| Score | 1.7775356 |
| Snippet | Iron is a metal element indispensable for life. It usually plays important roles as reaction centers of the iron-containing proteins and enzymes, and is... |
| SourceID | proquest jstage |
| SourceType | Aggregation Database Publisher |
| StartPage | 50 |
| SubjectTerms | Biosynthesis Crystallography Heme Hemoprotein Iron Molecular mechanism Nitric oxide Proteins |
| Title | Biological Information-, Material - and Energy-Conversion by Iron-Containing Proteins |
| URI | https://www.jstage.jst.go.jp/article/brte/22/4/22_50/_article/-char/en https://www.proquest.com/docview/1449392692 |
| Volume | 22 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| ispartofPNX | Biomedical Research on Trace Elements, 2011, Vol.22(4), pp.50-58 |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LT-MwELZ4XLigBRYtj0U-IC6s2cZ2neRYoSLeaEUqdU-RnbgUJFrUpgf21--MnTbpFqGFQ6zIiTrpzHhmbM83JuQwtFFDSNNkVmaawRUyHYeC8SyHAEKDGnAEON_cqvOOvOw2u1W6rUOXFOYk-_MmruQzUoU-kCuiZD8g2dmPQgfcg3yhBQlD-18y9gdJOjaXsCKkxTwGp3BfcMzc9kDbQfzYKeaYuwUyDDsvRvAylqfyp0QgaADPvhzPbfQ6eL4jUdYF6rv9hZEGg2B97vksLL_vP3rYzO_huP9YjCcPk_qqQpnWVq0qXIKnrswLfme10n_ccqjQ-lJioBhMC7vep3hDCnaBYemeuqXlvKZRsmY2fe3ZRWsOvhJkYEZY0JSf-Lfma2bf3qVnnevrNGl3k_mn3kdj8QyFNfSWySqHmQSawqtfs40mAeGbqzA2_QslhBMp_6zoQnjyBMH6w6LHdmFI8oWsl_MH2vLKsEGW7GCTbLUGuhg-v9Ij6jJ6HQO3SKfSD1rXjx90qh2UUeA6XdAOal7pP9pBp9rxlSRn7eT0nJXHaLAniP5YrLVSsmHCKFcys73MRrG0lgcmEpkQQRDmGhnRy7XJbRCZwMAkPw_DnomF7gmxTVYGw4H9RmhT6MwYGVlpAqljpU2mteVCcCARW7lDlGdT-uJLpaTl0EiRlSnnqcSm2Zj1I7QQRvIO2Z-yNS3H1xgmpTKG6F3FfPf9x3tkrVLhfbJSjCb2O4SKhTlwwv4LR8VwXQ |
| linkProvider | Colorado Alliance of Research Libraries |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Biological+Information-%2C+Material+-+and+Energy-Conversion+by+Iron-Containing+Proteins&rft.jtitle=Biomedical+research+on+trace+elements&rft.au=Shiro%2C+Yoshitsugu&rft.date=2011-10-01&rft.pub=Japan+Science+and+Technology+Agency&rft.issn=0916-717X&rft.eissn=1880-1404&rft.volume=22&rft.issue=4&rft.spage=50&rft_id=info:doi/10.11299%2Fbrte.22.50&rft.externalDBID=NO_FULL_TEXT&rft.externalDocID=3121566071 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0916-717X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0916-717X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0916-717X&client=summon |