Formate-reduced E. coli formate dehydrogenase H: the reinterpretation of the crystal structure suggests a new reaction mechanism (original) (raw)

Abstract

Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305–1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.

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Abbreviations

EPR:

Electron paramagnetic resonance

EXAFS:

Extented X-ray absorption fine structure

Fdh:

Formate dehydrogenase

Fdh-H:

Formate dehydrogenase component of the formate-hydrogen lyase complex of E. coli

Fdh-N:

Formate dehydrogenase expressed in E. coli when growing on nitrate

Fdh-O:

Formate dehydrogenase expressed in E. coli for oxygen metabolism

MGD:

Molybdopterin guanine dinucleotide

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Acknowledgements

This work was supported by EC-TMR/FMRX-CT980204 and POCTI/QUI/57641/2004. We thank Jeff Boyington for providing the structure factors corresponding to the deposited coordinates (pdb codes 1aa6 and 1fdo), and A. Boeck for helpful discussions.

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Author notes

  1. Hans C. A. Raaijmakers
    Present address: N.V. Organon, Molenstraat 110, 5342CC, Oss, The Netherlands

Authors and Affiliations

  1. REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Monte de Caparica, Portugal
    Hans C. A. Raaijmakers & Maria João Romão

Authors

  1. Hans C. A. Raaijmakers
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  2. Maria João Romão
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Correspondence toMaria João Romão.

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Raaijmakers, H.C.A., Romão, M.J. Formate-reduced E. coli formate dehydrogenase H: the reinterpretation of the crystal structure suggests a new reaction mechanism.J Biol Inorg Chem 11, 849–854 (2006). https://doi.org/10.1007/s00775-006-0129-2

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