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Structure analysis and characterization of the cytochrome c-554 from thermophilic green sulfur photosynthetic bacterium Chlorobaculum tepidum

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Abstract

The cytochrome (Cyt) c-554 in thermophilic green photosynthetic bacterium Chlorobaculum tepidum serves as an intermediate electron carrier, transferring electrons to the membrane-bound Cyt c z from various enzymes involved in the oxidations of sulfide, thiosulfate, and sulfite compounds. Spectroscopically, this protein exhibits an asymmetric α-absorption band for the reduced form and particularly large paramagnetic 1H NMR shifts for the heme methyl groups with an unusual shift pattern in the oxidized form. The crystal structure of the Cyt c-554 has been determined at high resolution. The overall fold consists of four α-helices and is characterized by a remarkably long and flexible loop between the α3 and α4 helices. The axial ligand methionine has S-chirality at the sulfur atom with its CεH3 group pointing toward the heme pyrrole ring I. This configuration corresponds to an orientation of the lone-pair orbital of the sulfur atom directed at the pyrrole ring II and explains the lowest-field 1H NMR shift arising from the 181 heme methyl protons. Differing from most other class I Cyts c, no hydrogen bond was formed between the methionine sulfur atom and polypeptide chain. Lack of this hydrogen bond may account for the observed large paramagnetic 1H NMR shifts of the heme methyl protons. The surface-exposed heme pyrrole ring II edge is in a relatively hydrophobic environment surrounded by several electronically neutral residues. This portion is considered as an electron transfer gateway. The structure of the Cyt c-554 is compared with those of other Cyts c, and possible interactions of this protein with its electron transport partners are discussed.

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Abbreviations

Cba :

Chlorobaculum

Chl :

Chlorobium

CD:

Circular dichroism

COSY:

Correlation spectroscopy

HMQC:

Heteronuclear multiple-quantum coherence

MALDI-TOF:

Matrix-assisted laser desorption/ionization time-of-flight

MCD:

Magnetic circular dichroism

NOESY:

Nuclear Overhauser effect spectroscopy

RC:

Reaction center

RR:

Resonance Raman

Tch :

Thermochromatium

TOMES:

Thiosulfate oxidizing multi-enzyme system

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Acknowledgments

We thank M. Higuchi for technical assistance. This work was supported by Grants-in-aid for Scientific Research on Priority Areas “Structures of Biological Macromolecular Assemblies” (to Z.-Y.W-O.) and Grants-in-aid for Scientific Research (C) (No. 24570183 to H. O.), from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and partially supported by The Kurata Memorial Hitachi Science and Technology Foundation. The X-ray experiments were performed under the approval of the Photon Factory Program Advisory Committee (Proposal No. 2009G525 and 2011G514), and we thank the beamline staff for their help in data collection.

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Authors and Affiliations

  1. Faculty of Science, Ibaraki University, Bunkyo 2-1-1, Mito, 310-8512, Japan

    Long-Jiang Yu, Kasumi Yanagimoto & Zheng-Yu Wang-Otomo

  2. Frontier Research Center for Applied Atomic Science, Ibaraki University, 162-1 Shirakata, Tokai, Naka, Ibaraki, 319-1106, Japan

    Masaki Unno

  3. Graduate School of Science and Engineering, Ibaraki University, 4-12-1, Nakanarusawa, Hitachi, 316-8511, Japan

    Masaki Unno

  4. Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, 657-8501, Japan

    Yukihiro Kimura

  5. Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan

    Hirozo Oh-oka

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  1. Long-Jiang Yu
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Correspondence to Zheng-Yu Wang-Otomo.

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Long-Jiang Yu and Masaki Unno have contributed equally to this study.

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Yu, LJ., Unno, M., Kimura, Y. et al. Structure analysis and characterization of the cytochrome c-554 from thermophilic green sulfur photosynthetic bacterium Chlorobaculum tepidum . Photosynth Res 118, 249–258 (2013). https://doi.org/10.1007/s11120-013-9922-2

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