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.
Access this article
Subscribe and save
- Get 10 units per month
- Download Article/Chapter or eBook
- 1 Unit = 1 Article or 1 Chapter
- Cancel anytime Subscribe now
Buy Now
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
Instant access to the full article PDF.
Similar content being viewed by others
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
References
- Hille R (1996) Chem Rev 96:2757–2816
Article PubMed CAS Google Scholar - Romão MJ, Knäblein J, Huber R, Moura JJG (1997) Prog Biophys Mol Biol 68:121–144
Article PubMed Google Scholar - Moura JJG, Brondino CD, Trincao J, Romao MJ (2004) J Biol Inorg Chem 9:791–799
Article PubMed CAS Google Scholar - Vorholt JA, Thauer RK (2002) In: Sigel A, Sigel H (eds) Metal ions in biological systems, vol 39. Dekker, New York, pp 571–619
- Berg BL, Li J, Heider J, Stewart V (1991) J Biol Chem 266:22380–22385
PubMed CAS Google Scholar - Abaibou H, Pommier J, Giordano G, Mandrand-Berthelot MA (1995) J Bacteriol 177:7141–7149
PubMed CAS Google Scholar - Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD (1997) Science 275:1305–1308
Article PubMed CAS Google Scholar - Jormakka M, Tornroth S, Byrne B, Iwata S (2002) Science 295:1863–1868
Article PubMed Google Scholar - Raaijmakers H, Teixeira S, Dias JM, Almendra MJ, Brondino CD, Moura I, Moura JJ, Romao MJ (2001) J Biol Inorg Chem 64:398–404
Google Scholar - Raaijmakers H, Macieira S, Dias JM, Teixeira S, Bursakov S, Huber R, Moura JJ, Moura I, Romao MJ (2002) Structure 10:1261–1272
Article PubMed CAS Google Scholar - George GN, Colangelo CM, Dong J, Scott RA, Khangulov SV, Gladyshev VN, Stadtman TC (1998) J Am Chem Soc 120:1267–1273
Article CAS Google Scholar - Gladyshev VN, Boyington JC, Khangulov SV, Grahame DA, Stadtman TC, Sun PD (1996) J Biol Chem 271:8095–8100
Article PubMed CAS Google Scholar - Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Acta Crystallogr Sect A 47:110–119
Article Google Scholar - Murshudov GN, Vagin AA, Dodson EJ (1997) Acta Crystallogr Sect D 53:240–245
Article CAS Google Scholar - Perrakis A, Morris RJ, Lamzin VS (1999) Nat Struct Biol 6:458–463
Article PubMed CAS Google Scholar - Barber M, May H, Ferry JG (1986) Biochemistry 25:8150–8155
Article CAS Google Scholar - Khangulov SV, Gladyshev VN, Dismukes GC, Stadtman TC (1998) Biochemistry 37:3518–3528
Article PubMed CAS Google Scholar - Axley MJ, Bock A, Stadtman TC (1991) Proc Natl Acad Sci USA 88:8450–8454
Article PubMed CAS Google Scholar - Heider J, Böck A (1993) Adv Microb Physiol 35:71–109
Article PubMed CAS Google Scholar - DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos. http://www.pymol.org
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.
Author information
Author notes
- Hans C. A. Raaijmakers
Present address: N.V. Organon, Molenstraat 110, 5342CC, Oss, The Netherlands
Authors and Affiliations
- 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
- Hans C. A. Raaijmakers
You can also search for this author inPubMed Google Scholar - Maria João Romão
You can also search for this author inPubMed Google Scholar
Corresponding author
Correspondence toMaria João Romão.
Rights and permissions
About this article
Cite this article
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
- Received: 16 March 2006
- Accepted: 12 June 2006
- Published: 08 July 2006
- Issue Date: October 2006
- DOI: https://doi.org/10.1007/s00775-006-0129-2