JBIC Journal of Biological Inorganic Chemistry

, Volume 23, Issue 7, pp 1049–1056 | Cite as

Crystal structure of VnfH, the iron protein component of vanadium nitrogenase

  • Michael Rohde
  • Christian Trncik
  • Daniel Sippel
  • Stefan Gerhardt
  • Oliver EinsleEmail author
Original Paper
Part of the following topical collections:
  1. Alison Butler: Papers in Celebration of Her 2018 ACS Alfred Bader Award in Bioorganic or Bioinorganic Chemistry


Nitrogenases catalyze the biological fixation of inert N2 into bioavailable ammonium. They are bipartite systems consisting of the catalytic dinitrogenase and a complementary reductase, the Fe protein that is also the site where ATP is hydrolyzed to drive the reaction forward. Three different subclasses of dinitrogenases are known, employing either molybdenum, vanadium or only iron at their active site cofactor. Although in all these classes the mode and mechanism of interaction with Fe protein is conserved, each one encodes its own orthologue of the reductase in the corresponding gene cluster. Here we present the 2.2 Å resolution structure of VnfH from Azotobacter vinelandii, the Fe protein of the alternative, vanadium-dependent nitrogenase system, in its ADP-bound state. VnfH adopts the same conformation that was observed for NifH, the Fe protein of molybdenum nitrogenase, in complex with ADP, representing a state of the functional cycle that is ready for reduction and subsequent nucleotide exchange. The overall similarity of NifH and VnfH confirms the experimentally determined cross-reactivity of both ATP-hydrolyzing reductases.


Biological nitrogen fixation Vanadium nitrogenase Fe protein Dinitrogenase reductase X-ray crystallography 



Electron paramagnetic resonance


Molecular replacement



The authors thank the staff at beam line X06DA of the Swiss Light Source, Paul Scherrer Institute, Villigen, CH, for their excellent assistance with diffraction data collection. This work was supported by the Deutsche Forschungsgemeinschaft (RTG 1976 and PP 1927) and the European Research Council (Grant no. 310656).


  1. 1.
    Rees DC (1993) Curr Opin Struct Biol 3:921–928CrossRefGoogle Scholar
  2. 2.
    Leigh GJ (2004) The world’s greatest fix: A history of nitrogen in agriculture. Oxford University Press, OxfordGoogle Scholar
  3. 3.
    Smil V (2002) Ambio 31:126–131CrossRefGoogle Scholar
  4. 4.
    Rees DC, Tezcan FA, Haynes CA, Walton MY, Andrade S, Einsle O, Howard JB (2005) Philos Trans R Soc Lond A 363:971–984CrossRefGoogle Scholar
  5. 5.
    Howard JB, Rees DC (1996) Chem Rev 96:2965–2982CrossRefGoogle Scholar
  6. 6.
    Georgiadis MM, Komiya H, Chakrabarti P, Woo D, Kornuc JJ, Rees DC (1992) Science 257:1653–1659CrossRefGoogle Scholar
  7. 7.
    Burgess BK, Lowe DJ (1996) Chem Rev 96:2983–3011CrossRefGoogle Scholar
  8. 8.
    Grossmann JG, Hasnain SS, Yousafzai FK, Smith BE, Eady RR, Schindelin H, Kisker C, Howard JB, Tsuruta H, Muller J, Rees DC (1999) Acta Crystallogr D 55:727–728CrossRefGoogle Scholar
  9. 9.
    Peters JW, Fisher K, Newton WE, Dean DR (1995) J Biol Chem 270:27007–27013CrossRefGoogle Scholar
  10. 10.
    Angove HC, Yoo SJ, Münck E, Burgess BK (1999) J Inorg Biochem 74:65Google Scholar
  11. 11.
    Danyal K, Dean DR, Hoffman BM, Seefeldt LC (2011) Biochemistry 50:9255–9263CrossRefGoogle Scholar
  12. 12.
    Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC (2014) Chem Rev 114:4041–4062CrossRefGoogle Scholar
  13. 13.
    Howard JB, Kechris KJ, Rees DC, Glazer AN (2013) Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships. Plos One 8:e72751CrossRefGoogle Scholar
  14. 14.
    Einsle O (2014) J Biol Inorg Chem 19:737–745CrossRefGoogle Scholar
  15. 15.
    Spatzal T, Aksoyoğlu M, Zhang LM, Andrade SLA, Schleicher E, Weber S, Rees DC, Einsle O (2011) Science 334:940CrossRefGoogle Scholar
  16. 16.
    Lancaster KM, Roemelt M, Ettenhuber P, Hu YL, Ribbe MW, Neese F, Bergmann U, DeBeer S (2011) Science 334:974–977CrossRefGoogle Scholar
  17. 17.
    Sippel D, Einsle O (2017) Nat Chem Biol 13:956–960CrossRefGoogle Scholar
  18. 18.
    Lee CC, Hu YL, Ribbe MW (2010) Science 329:642CrossRefGoogle Scholar
  19. 19.
    Sippel D, Rohde M, Netzer J, Trncik C, Gies J, Grunau K, Djurdjevic I, Decamps L, Andrade SLA, Einsle O (2018) Science 359:1484–1489CrossRefGoogle Scholar
  20. 20.
    Zheng Y, Harris DF, Yu Z, Fu Y, Poudel S, Ledbetter RN, Fixen KR, Yang ZY, Boyd ES, Lidstrom ME, Seefedt LC, Harwood CS (2018) Nat Microbiol 3:281–286CrossRefGoogle Scholar
  21. 21.
    Setubal JC, dos Santos P, Goldman BS, Ertesvag H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, Curatti L, Du ZJ, Godsy E, Goodner B, Hellner-Burris K, Hernandez JA, Houmiel K, Imperial J, Kennedy C, Larson TJ, Latreille P, Ligon LS, Lu J, Maerk M, Miller NM, Norton S, O’Carroll IP, Paulsen I, Raulfs EC, Roemer R, Rosser J, Segura D, Slater S, Stricklin SL, Studholme DJ, Sun J, Viana CJ, Wallin E, Wang BM, Wheeler C, Zhu HJ, Dean DR, Dixon R, Wood D (2009) J Bacteriol 191:4534–4545CrossRefGoogle Scholar
  22. 22.
    Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R (2012) Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genom 13:162–174CrossRefGoogle Scholar
  23. 23.
    Owens CP, Katz FEH, Carter CH, Oswald VF, Tezcan FA (2016) J Am Chem Soc 138:10124–10127CrossRefGoogle Scholar
  24. 24.
    Hales BJ, Langosch DJ, Case EE (1986) J Biol Chem 261:5301–5306Google Scholar
  25. 25.
    Schlesier J, Rohde M, Gerhardt S, Einsle O (2016) J Am Chem Soc 138:239–247CrossRefGoogle Scholar
  26. 26.
    Lipman JG (1903) Rep N J Agric Exp Stn 24:217–285Google Scholar
  27. 27.
    Burk D, Lineweaver H (1930) J Bacteriol 19:389–414PubMedPubMedCentralGoogle Scholar
  28. 28.
    Sippel D, Schlesier J, Rohde M, Trncik C, Decamps L, Djurdjevic I, Spatzal T, Andrade SLA, Einsle O (2017) J Biol Inorg Chem 22:161–168CrossRefGoogle Scholar
  29. 29.
    Kabsch W (2010) Acta Crystallogr D 66:125–132CrossRefGoogle Scholar
  30. 30.
    Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Acta Crystallogr D 67:235–242CrossRefGoogle Scholar
  31. 31.
    McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) J Appl Crystallogr 40:658–674CrossRefGoogle Scholar
  32. 32.
    Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Acta Crystallogr D 66:486–501CrossRefGoogle Scholar
  33. 33.
    Blanc E, Roversi P, Vonrhein C, Flensburg C, Lea SM, Bricogne G (2004) Acta Crystallogr D 60:2210–2221CrossRefGoogle Scholar
  34. 34.
    Schrödinger LLC (2010) The PyMOL molecular graphics systemGoogle Scholar
  35. 35.
    Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen JH, Liles K, Chun MJ, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng WH, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA (2018) Protein Sci 27:112–128CrossRefGoogle Scholar
  36. 36.
    Schindelin H, Kisker C, Sehlessman JL, Howard JB, Rees DC (1997) Nature 387:370–376CrossRefGoogle Scholar
  37. 37.
    Tezcan FA, Kaiser JT, Mustafi D, Walton MY, Howard JB, Rees DC (2005) Science 309:1377–1380CrossRefGoogle Scholar
  38. 38.
    Owens CP, Katz FE, Carter CH, Luca MA, Tezcan FA (2015) J Am Chem Soc 137:12704–12712CrossRefGoogle Scholar
  39. 39.
    Danyal K, Shaw S, Page TR, Duval S, Horitani M, Marts AR, Lukoyanov D, Dean DR, Raugei S, Hoffman BM, Seefeldt LC, Antony E (2016) Proc Natl Acad Sci USA 113:E5783–E5791CrossRefGoogle Scholar
  40. 40.
    Kaiser JT, Hu YL, Wiig JA, Rees DC, Ribbe MW (2011) Science 331:91–94CrossRefGoogle Scholar
  41. 41.
    Hu Y, Ribbe MW (2011) Coord Chem Rev 255:1218–1224CrossRefGoogle Scholar
  42. 42.
    Hu YL, Fay AW, Lee CC, Wiig JA, Ribbe MW (2010) Dalton T 39:2964–2971CrossRefGoogle Scholar
  43. 43.
    Weiss M, Hilgenfeld R (1997) J Appl Crystallogr 30:203–205CrossRefGoogle Scholar
  44. 44.
    Karplus PA, Diederichs K (2012) Science 336:1030–1033CrossRefGoogle Scholar
  45. 45.
    Cruickshank DWJ (1999) Acta Crystallogr D 55:583–601CrossRefGoogle Scholar
  46. 46.
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283–291CrossRefGoogle Scholar

Copyright information

© SBIC 2018

Authors and Affiliations

  • Michael Rohde
    • 1
  • Christian Trncik
    • 1
  • Daniel Sippel
    • 1
  • Stefan Gerhardt
    • 1
  • Oliver Einsle
    • 1
    • 2
    Email author
  1. 1.Institute for BiochemistryAlbert-Ludwigs-University FreiburgFreiburgGermany
  2. 2.BIOSS Centre for Biological Signalling StudiesFreiburgGermany

Personalised recommendations