JBIC Journal of Biological Inorganic Chemistry

, Volume 18, Issue 6, pp 693–700 | Cite as

Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory

  • Toshiko Miyake
  • Maurizio Bruschi
  • Ugo Cosentino
  • Carole Baffert
  • Vincent Fourmond
  • Christophe Léger
  • Giorgio Moro
  • Luca De Gioia
  • Claudio Greco
Original Paper


[FeFe] hydrogenases are H2-evolving enzymes that feature a diiron cluster in their active site (the [2Fe]H cluster). One of the iron atoms has a vacant coordination site that directly interacts with H2, thus favoring its splitting in cooperation with the secondary amine group of a neighboring, flexible azadithiolate ligand. The vacant site is also the primary target of the inhibitor O2. The [2Fe]H cluster can span various redox states. The active-ready form (Hox) attains the FeIIFeI state. States more oxidized than Hox were shown to be inactive and/or resistant to O2. In this work, we used density functional theory to evaluate whether azadithiolate-to-iron coordination is involved in oxidative inhibition and protection against O2, a hypothesis supported by recent results on biomimetic compounds. Our study shows that Fe–N(azadithiolate) bond formation is favored for an FeIIFeII active-site model which disregards explicit treatment of the surrounding protein matrix, in line with the case of the corresponding FeIIFeII synthetic system. However, the study of density functional theory models with explicit inclusion of the amino acid environment around the [2Fe]H cluster indicates that the protein matrix prevents the formation of such a bond. Our results suggest that mechanisms other than the binding of the azadithiolate nitrogen protect the active site from oxygen in the so-called H ox inact state.


Hydrogen Hydrogenases Density functional theory Iron–sulfur cluster 



Financial support of this work from the Cluster of Excellence “Unifying Concepts in Catalysis” (Berlin) is gratefully acknowledged; We acknowledge the CINECA award under the ISCRA initiative, for the availability of high performance computing resources and support. C.L., F.V., and C.B. acknowledge the CNRS, Aix-Marseille Université, and the ANR (ANR-12-BS08-0014) for funding.

Supplementary material

775_2013_1014_MOESM1_ESM.pdf (1.1 mb)
Supplementary material 1 (PDF 1156 kb)


  1. 1.
    Lubitz W, Reijerse E, van Gastel M (2007) Chem Rev 107:4331–4365. doi: 10.1021/Cr050186q PubMedCrossRefGoogle Scholar
  2. 2.
    Tard C, Pickett CJ (2009) Chem Rev 109:2245–2274. doi: 10.1021/Cr800542q PubMedCrossRefGoogle Scholar
  3. 3.
    Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC (1999) Structure 7:13–23. doi: 10.1016/S0969-2126(99)80005-7 PubMedCrossRefGoogle Scholar
  4. 4.
    Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC (1998) Science 282:1853–1858PubMedCrossRefGoogle Scholar
  5. 5.
    Pandey AS, Harris TV, Giles LJ, Peters JW, Szilagyi RK (2008) J Am Chem Soc 130:4533–4540. doi: 10.1021/ja711187e PubMedCrossRefGoogle Scholar
  6. 6.
    Bruschi M, Greco C, Kaukonen M, Fantucci P, Ryde U, De Gioia L (2009) Angew Chem Int Ed 48:3503–3506. doi: 10.1002/anie.200900494 CrossRefGoogle Scholar
  7. 7.
    Adamska ASA, Lambertz C, Rüdiger O, Happe T, Reijerse E, Lubitz W (2012) Angew Chem Int Ed 51:11458–11462CrossRefGoogle Scholar
  8. 8.
    Fan HJ, Hall MB (2001) J Am Chem Soc 123:3828–3829. doi: 10.1021/ja004120i PubMedCrossRefGoogle Scholar
  9. 9.
    Greco C, Bruschi M, De Gioia L, Ryde U (2007) Inorg Chem 46:5911–5921. doi: 10.1021/Ic062320a PubMedCrossRefGoogle Scholar
  10. 10.
    Lemon BJ, Peters JW (1999) Biochemistry 38:12969–12973PubMedCrossRefGoogle Scholar
  11. 11.
    Baffert C, Bertini L, Lautier T, Greco C, Sybirna K, Ezanno P, Etienne E, Soucaille P, Bertrand P, Bottin H, Meynial-Salles I, De Gioia L, Leger C (2011) J Am Chem Soc 133:2096–2099. doi: 10.1021/Ja110627b PubMedCrossRefGoogle Scholar
  12. 12.
    Bruska MK, Stiebritz MT, Reiher M (2011) J Am Chem Soc 133:20588–20603. doi: 10.1021/Ja209165r PubMedCrossRefGoogle Scholar
  13. 13.
    Stiebritz MT, Reiher M (2009) Inorg Chem 48:7127–7140. doi: 10.1021/Ic9002127. Erratum in: Stiebritz MT, Reiher M (2010) Inorg Chem 49:8645. doi 10.1021/ic1015737
  14. 14.
    Stripp ST, Goldet G, Brandmayr C, Sanganas O, Vincent KA, Haumann M, Armstrong FA, Happe T (2009) Proc Natl Acad Sci USA 106:17331–17336. doi: 10.1073/pnas.0905343106 PubMedCrossRefGoogle Scholar
  15. 15.
    Baffert C, Demuez M, Cournac L, Burlat B, Guigliarelli B, Bertrand P, Girbal L, Leger C (2008) Angew Chem Int Ed 47:2052–2054. doi: 10.1002/anie.200704313 CrossRefGoogle Scholar
  16. 16.
    Wait AF, Brandmayr C, Stripp ST, Cavazza C, Fontecilla-Camps JC, Happe T, Armstrong FA (2011) J Am Chem Soc 133:1282–1285. doi: 10.1021/Ja110103p PubMedCrossRefGoogle Scholar
  17. 17.
    Foster CE, Kramer T, Wait AF, Parkin A, Jennings DP, Happe T, McGrady JE, Armstrong FA (2012) J Am Chem Soc 134:7553–7557. doi: 10.1021/Ja302096r PubMedCrossRefGoogle Scholar
  18. 18.
    Ryde U, Greco C, De Gioia L (2010) J Am Chem Soc 132:4512. doi: 10.1021/ja909194f Google Scholar
  19. 19.
    Nicolet Y, de Lacey AL, Vernede X, Fernandez VM, Hatchikian EC, Fontecilla-Camps JC (2001) J Am Chem Soc 123:1596–1601. doi: 10.1021/ja0020963 PubMedCrossRefGoogle Scholar
  20. 20.
    Silakov A, Wenk B, Reijerse E, Lubitz W (2009) Phys Chem Chem Phys 11:6592–6599. doi: 10.1039/B905841a PubMedCrossRefGoogle Scholar
  21. 21.
    Erdem OF, Schwartz L, Stein M, Silakov A, Kaur-Ghumaan S, Huang P, Ott S, Reijerse EJ, Lubitz W (2011) Angew Chem Int Ed 50:1439–1443. doi: 10.1002/anie.201006244 CrossRefGoogle Scholar
  22. 22.
    Greco C, Bruschi M, Heimdal J, Fantucci P, De Gioia L, Ryde U (2007) Inorg Chem 46:7256–7258. doi: 10.1021/Ic701051h PubMedCrossRefGoogle Scholar
  23. 23.
    Greco C, Bruschi M, Fantucci P, Ryde U, De Gioia L (2011) Chem Eur J 17:1954–1965. doi: 10.1002/chem.201001493 PubMedCrossRefGoogle Scholar
  24. 24.
    Knorzer P, Silakov A, Foster CE, Armstrong FA, Lubitz W, Happe T (2012) J Biol Chem 287:1489–1499. doi: 10.1074/jbc.M111.305797 PubMedCrossRefGoogle Scholar
  25. 25.
    Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y (2007) Chem Rev 107:4273–4303. doi: 10.1021/cr050195z PubMedCrossRefGoogle Scholar
  26. 26.
    Roseboom W, De Lacey AL, Fernandez VM, Hatchikian EC, Albracht SPJ (2006) J Biol Inorg Chem 11:102–118. doi: 10.1007/s00775-005-0040-2 PubMedCrossRefGoogle Scholar
  27. 27.
    Albracht SPJ, Roseboom W, Hatchikian EC (2006) J Biol Inorg Chem 11:88–101. doi: 10.1007/s00775-005-0039-8 PubMedCrossRefGoogle Scholar
  28. 28.
    Vanderwesten HM, Mayhew SG, Veeger C (1978) FEBS Lett 86:122–126. doi: 10.1016/0014-5793(78)80112-4 CrossRefGoogle Scholar
  29. 29.
    Pereira AS, Tavares P, Moura I, Moura JJG, Huynh BH (2001) J Am Chem Soc 123:2771–2782. doi: 10.1021/Ja003176+ PubMedCrossRefGoogle Scholar
  30. 30.
    Huynh BH, Czechowski MH, Kruger HJ, Dervartanian DV, Peck HD, Legall J (1984) Proc Natl Acad Sci USA 81:3728–3732. doi: 10.1073/pnas.81.12.3728 PubMedCrossRefGoogle Scholar
  31. 31.
    Liu ZP, Hu P (2002) J Am Chem Soc 124:5175–5182. doi: 10.1021/Ja0118690 PubMedCrossRefGoogle Scholar
  32. 32.
    Cao ZX, Hall MB (2001) J Am Chem Soc 123:3734–3742. doi: 10.1021/Ja000116v PubMedCrossRefGoogle Scholar
  33. 33.
    Vincent KA, Parkin A, Lenz O, Albracht SPJ, Fontecilla-Camps JC, Cammack R, Friedrich B, Armstrong FA (2005) J Am Chem Soc 127:18179–18189. doi: 10.1021/Ja055160v PubMedCrossRefGoogle Scholar
  34. 34.
    Vandijk C, Vanberkelarts A, Veeger C (1983) FEBS Lett 156:340–344CrossRefGoogle Scholar
  35. 35.
    Silakov A, Kamp C, Reijerse E, Happe T, Lubitz W (2009) Biochemistry 48:7780–7786. doi: 10.1021/Bi9009105 PubMedCrossRefGoogle Scholar
  36. 36.
    Stiebritz MT, Reiher M (2012) Chem Sci 3:1739–1751. doi: 10.1039/c2sc01112c CrossRefGoogle Scholar
  37. 37.
    Olsen MT, Rauchfuss TB, Wilson SR (2010) J Am Chem Soc 132:17733–17740. doi: 10.1021/Ja103998v PubMedCrossRefGoogle Scholar
  38. 38.
    Vincent KA, Parkin A, Armstrong FA (2007) Chem Rev 107:4366–4413. doi: 10.1021/Cr050191u PubMedCrossRefGoogle Scholar
  39. 39.
    Moro G, Bonati L, Bruschi M, Cosentino U, De Gioia L, Fantucci P, Pandini A, Papaleo E, Pitea D, Saracino GAA, Zampella G (2007) Theor Chem Acc 117:723–741. doi: 10.1007/s00214-006-0203-4 PubMedCrossRefGoogle Scholar
  40. 40.
    Cosentino U, Pitea D, Moro G, Saracino GAA, Villa A (2009) Phys Chem Chem Phys 11:3943–3950. doi: 10.1039/B902049g PubMedCrossRefGoogle Scholar
  41. 41.
    Cosentino U, Moro G, Pitea D, Villa A, Fantucci PC, Maiocchi A, Uggeri F (1998) J Phys Chem A 102:4606–4614. doi: 10.1021/Jp973271d CrossRefGoogle Scholar
  42. 42.
    Siegbahn PEM, Tye JW, Hall MB (2007) Chem Rev 107:4414–4435. doi: 10.1021/Cr050185y PubMedCrossRefGoogle Scholar
  43. 43.
    Vastine BA, Hall MB (2009) Coord Chem Rev 253:1202–1218. doi: 10.1016/j.ccr.2008.07.015 CrossRefGoogle Scholar
  44. 44.
    Reiher M (2009) Chimia 63:140–145. doi: 10.2533/chimia.2009.140 CrossRefGoogle Scholar
  45. 45.
    Ahlrichs R, Bar M, Haser M, Horn H, Kolmel C (1989) Chem Phys Lett 162:165–169. doi: 10.1016/0009-2614(89)85118-8 CrossRefGoogle Scholar
  46. 46.
    Becke AD (1988) Phys Rev A 38:3098–3100. doi: 10.1103/PhysRevA.38.3098 PubMedCrossRefGoogle Scholar
  47. 47.
    Perdew JP (1986) Phys Rev B 33:8822–8824. doi: 10.1103/PhysRevB.33.8822 CrossRefGoogle Scholar
  48. 48.
    Schafer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829–5835CrossRefGoogle Scholar
  49. 49.
    Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297–3305. doi: 10.1039/B508541a PubMedCrossRefGoogle Scholar
  50. 50.
    Eichkorn K, Treutler O, Ohm H, Haser M, Ahlrichs R (1995) Chem Phys Lett 240:283–289. doi: 10.1016/0009-2614(95)00621-A CrossRefGoogle Scholar
  51. 51.
    Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119–124. doi: 10.1007/s002140050244 CrossRefGoogle Scholar
  52. 52.
    Klamt A (1995) J Phys Chem 99:2224–2235. doi: 10.1021/J100007a062 CrossRefGoogle Scholar
  53. 53.
    Noodleman L, Norman JG (1979) J Chem Phys 70:4903–4906. doi: 10.1063/1.437369 CrossRefGoogle Scholar
  54. 54.
    Noodleman L (1981) J Chem Phys 74:5737–5743. doi: 10.1063/1.440939 CrossRefGoogle Scholar
  55. 55.
    Greco C, Fantucci P, Ryde U, de Gioia L (2011) Int J Quantum Chem 111:3949–3960. doi: 10.1002/Qua.22849 Google Scholar
  56. 56.
    Yu L, Greco C, Bruschi M, Ryde U, De Gioia L, Reiher M (2011) Inorg Chem 50:3888–3900. doi: 10.1021/Ic102039z PubMedCrossRefGoogle Scholar
  57. 57.
    Becke AD (1993) J Chem Phys 98:1372–1377. doi: 10.1063/1.464304 CrossRefGoogle Scholar
  58. 58.
    Lee CT, Yang WT, Parr RG (1988) Phys Rev B 37:785–789. doi: 10.1103/PhysRevB.37.785 CrossRefGoogle Scholar
  59. 59.
    Greco C, De Gioia L (2011) Inorg Chem 50:6987–6995. doi: 10.1021/Ic200297d PubMedCrossRefGoogle Scholar
  60. 60.
    Matito E, Sola M (2009) Coord Chem Rev 253:647–665. doi: 10.1016/j.ccr.2008.10.003 CrossRefGoogle Scholar
  61. 61.
    Francuski BM, Novakovic SB, Bogdanovic GA (2011) CrystEngComm 13:3580–3591. doi: 10.1039/C0ce00760a CrossRefGoogle Scholar
  62. 62.
    Greco C, Silakov A, Bruschi M, Ryde U, De Gioia L, Lubitz W (2011) Eur J Inorg Chem 2011:1043–1049. doi: 10.1002/ejic.201001058

Copyright information

© SBIC 2013

Authors and Affiliations

  • Toshiko Miyake
    • 1
  • Maurizio Bruschi
    • 2
  • Ugo Cosentino
    • 2
  • Carole Baffert
    • 3
  • Vincent Fourmond
    • 3
  • Christophe Léger
    • 3
  • Giorgio Moro
    • 4
  • Luca De Gioia
    • 4
  • Claudio Greco
    • 2
  1. 1.Begegnungszentren der IGAFA, IBZ Berlin-AdlershofBerlinGermany
  2. 2.Department of Environmental and Earth SciencesUniversità degli Studi di Milano BicoccaMilanItaly
  3. 3.BIP UMR 7281, IMM FR 3479, CNRSAix-Marseille UniversitéMarseille Cedex 20France
  4. 4.Department of Biotechnology and BiosciencesUniversità degli Studi di Milano BicoccaMilanItaly

Personalised recommendations