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Watanabe M, Kanai Y, Nakamura S, Nishimura R, Shibata T, Momotake A, Yanagisawa S, Ogura T, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Synergistic Effect of Distal Polar Interactions in Myoglobin and Their Structural Consequences. Inorg Chem 2018; 57:14269-14279. [DOI: 10.1021/acs.inorgchem.8b02302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Kanai Y, Nishimura R, Nishiyama K, Shibata T, Yanagisawa S, Ogura T, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Effects of Heme Electronic Structure and Distal Polar Interaction on Functional and Vibrational Properties of Myoglobin. Inorg Chem 2016; 55:1613-22. [DOI: 10.1021/acs.inorgchem.5b02520] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuki Kanai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kotaro Nishiyama
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Sachiko Yanagisawa
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Department of Life
Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Matsuo
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of
Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Nishimura R, Shibata T, Tai H, Ishigami I, Ogura T, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between the Electron Density of the Heme Fe Atom and the Vibrational Frequencies of the Fe-Bound Carbon Monoxide in Myoglobin. Inorg Chem 2013; 52:3349-55. [DOI: 10.1021/ic3028447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience,
Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Khare G, Gupta V, Nangpal P, Gupta RK, Sauter NK, Tyagi AK. Ferritin structure from Mycobacterium tuberculosis: comparative study with homologues identifies extended C-terminus involved in ferroxidase activity. PLoS One 2011; 6:e18570. [PMID: 21494619 PMCID: PMC3072985 DOI: 10.1371/journal.pone.0018570] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/04/2011] [Indexed: 11/19/2022] Open
Abstract
Ferritins are recognized as key players in the iron storage and detoxification processes. Iron acquisition in the case of pathogenic bacteria has long been established as an important virulence mechanism. Here, we report a 3.0 Å crystal structure of a ferritin, annotated as Bacterioferritin B (BfrB), from Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis that continues to be one of the world's deadliest diseases. Similar to the other members of ferritin family, the Mtb BfrB subunit exhibits the characteristic fold of a four-helical bundle that possesses the ferroxidase catalytic centre. We compare the structure of Mtb BfrB with representatives of the ferritin family belonging to the archaea, eubacteria and eukarya. Unlike most other ferritins, Mtb BfrB has an extended C-terminus. To dissect the role of this extended C-terminus, truncated Mtb BfrB was purified and biochemical studies implicate this region in ferroxidase activity and iron release in addition to providing stability to the protein. Functionally important regions in a protein of known 3D-structure can be determined by estimating the degree of conservation of the amino-acid sites with its close homologues. Based on the comparative studies, we identify the slowly evolving conserved sites as well as the rapidly evolving variable sites and analyze their role in relation to structure and function of Mtb BfrB. Further, electrostatic computations demonstrate that although the electrostatic environment of catalytic residues is preserved within the family, extensive variability is exhibited by residues defining the channels and pores, in all likelihood keeping up with the diverse functions executed by these ferritins in varied environments.
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Affiliation(s)
- Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Prachi Nangpal
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Rakesh K. Gupta
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- Ram Lal Anand College, University of Delhi, New Delhi, India
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
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