Advertisement

Antonie van Leeuwenhoek

, Volume 90, Issue 3, pp 281–290 | Cite as

Sequential and structural analysis of [NiFe]-hydrogenase-maturation proteins from Desulfovibrio vulgaris Miyazaki F

  • Aruna Goenka Agrawal
  • Gerrit Voordouw
  • Wolfgang GärtnerEmail author
Article

Abstract

The complete primary structure of the hyn-region in the genome of Desulfovibrio vulgaris Miyazaki F (DvMF), encoding the [NiFe]-hydrogenase and two maturation proteins has been identified. Besides the formerly reported genes for the large and small subunits, this region comprises genes encoding an endopeptidase (HynC) and a putative chaperone (HynD). The complete genomic region covers 4086 nucleotides including the previously published upstream located promoter region and the sequences of the structural genes. A phylogenetic tree for both maturation proteins shows strongest sequential relationship to the orthologous proteins of Desulfovibrio vulgaris Hildenborough (DvH). Secondary structure prediction for HynC (168 aa, corresponding to a molecular weight of 17.9 kDa) revealed a practically identical arrangement of α-helical and β-strand elements between the orthologous protein HybD from E. coli and allowed a three-dimensional modelling of HynC on the basis of the formerly published structure of HybD. The putative chaperone HynD consists of 83 aa (molecular weight of 9 kDa) and shows 76% homology to DvH HynD. Preliminary experiments demonstrate that the operon is expressed under the control of its own promoter in Escherichia coli, although no further processing could be observed, providing evidence that additional proteins have to be involved in the maturation process. Accession numbers: DQ072852, HynC protein ID AAY90127, HynD protein ID AAY90128.

Keywords

Endopeptidase [NiFe]-hydrogenase Operon structure Protein maturation process Three dimensional structure 

Abbreviations

DvH

Desulfovibrio vulgaris Hildenborough

DvMF

Desulfovibrio vulgaris Miyazaki F

LSU

large subunit

SSU

small subunit

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgements

The support of Ulrich Krauss, U. Düsseldorf/FZ Jülich, in the structure-modelling of HynC is greatly acknowledged. We wish to thank also Dr. Reiner Hedderich from the Max-Planck-Institute for Terrestrial Microbiology, Marburg, for valuable suggestions during the experimental work. This work was supported by the Max-Planck-Society.

References

  1. Blokesch M, Böck A (2002) Maturation of [NiFe]-hydrogenases in Escherichia coli: the HypC cycle. J Mol Biol 324:287–296PubMedCrossRefGoogle Scholar
  2. Blokesch M, Magalon A, Böck A (2001) Interplay between the specific chaperonelike proteins HybG and HypC in maturation of hydrogenases 1, 2, and 3 from Escherichia coli. J Bacteriol 183:2817–2822PubMedCrossRefGoogle Scholar
  3. Brecht M, van Gastel M, Buhrke T, Friedrich B, Lubitz W (2003) Direct detection of a hydrogen ligand in the [NiFe] center of the regulatory H2-sensing hydrogenase from Ralstonia eutropha in its reduced state by HYSCORE and ENDOR spectroscopy. J Am Chem Soc 125:13075–13083PubMedCrossRefGoogle Scholar
  4. Casalot L, Rousset M (2001) Maturation of the [NiFe] hydrogenases. Trends Microbiol 9:228–237PubMedCrossRefGoogle Scholar
  5. Deckers HM, Wilson FR, Voordouw G (1990) Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F. J Gen Microbiol 136:2021–2028PubMedGoogle Scholar
  6. Fan CL, Teixeira M, Moura J, Moura I, Huynh BH, Legall J, Peck HD, Hoffman BM (1991) Detection and characterization of exchangeable protons bound to the hydrogen-activation nickel site of Desulfovibrio gigas hydrogenase—a H-1 and H-2 Q-band endor study. J Am Chem Soc 113:20–24CrossRefGoogle Scholar
  7. Foerster S, Stein M, Brecht M, Ogata H, Higuchi Y, Lubitz W (2003) Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfiovibrio vulgaris Miyazaki F. J Am Chem Soc 125:83–93PubMedCrossRefGoogle Scholar
  8. Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SCE (2005) The SSEA server for protein secondary structure alignment. Bioinformatics 21:393–395PubMedCrossRefGoogle Scholar
  9. Fritsche E, Paschos A, Beisel HG, Böck A, Huber R (1999) Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli. J␣Mol Biol 288:989–998PubMedCrossRefGoogle Scholar
  10. Gerber PR (1998) Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB. J Computer-Aided Molec Design 12:37–51CrossRefGoogle Scholar
  11. Gerber PR, Muller K (1995) Mab, a generally applicable molecular-force field for structure modeling in medicinal chemistry. J Computer-Aided Molec Design 9:251–268CrossRefGoogle Scholar
  12. Gessner C, Trofanchuk O, Kawagoe K, Higuchi Y, Yasuoka N, Lubitz W (1996) Single crystal EPR study of the Ni center of [NiFe] hydrogenase. Chem Phys Lett 256:518–524CrossRefGoogle Scholar
  13. Goenka A, Voordouw JK, Lubitz W, Gärtner W, Voordouw G (2005) Construction of a [NiFe]-hydrogenase deletion mutant of Desulfovibrio vulgaris Hildenborough. Biochem Soc Trans 33:59–60PubMedCrossRefGoogle Scholar
  14. Guex N, Peitsch MC (1997) SWISS-Model and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714–2723PubMedCrossRefGoogle Scholar
  15. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou LW, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (2004) The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol 22:554–559PubMedCrossRefGoogle Scholar
  16. Higuchi Y, Yagi T, Yasuoka N (1997) Unusual ligand structure in Ni–Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis. Structure 5:1671–1680PubMedCrossRefGoogle Scholar
  17. Hube M, Blokesch M, Böck A (2002) Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF. J Bacteriol 184:3879–3885PubMedCrossRefGoogle Scholar
  18. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202PubMedCrossRefGoogle Scholar
  19. Maier T, Jacobi A, Sauter M, Böck A (1993) The product of the Hypb gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein. J Bacteriol 175:630–635PubMedGoogle Scholar
  20. Menon NK, Chatelus CY, Dervartanian M, Wendt JC, Shanmugam KT, Peck HD Jr, Przybyla AE (1994) Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2. J Bacteriol 176:4416–4423PubMedGoogle Scholar
  21. Nicolet Y, De Lacey AL, Vernede X, Fernandez VM, Hatchikian EC, Fontecilla-Camps JC (2001) Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans. J Am Chem Soc 123:1596–1601PubMedCrossRefGoogle Scholar
  22. Roseboom W, Blokesch M, Böck A, Albracht SP (2005) The biosynthetic routes for carbon monoxide and cyanide in the Ni–Fe active site of hydrogenases are different. FEBS Lett 579:469–472PubMedCrossRefGoogle Scholar
  23. Rousset M, Dermoun Z, Wall JD, Belaich JP (1993) Analysis of the Periplasmic [Nife] Hydrogenase Transcription Unit from Desulfovibrio fructosovorans. J Bacteriol 175:3388–3393PubMedGoogle Scholar
  24. Theodoratou E, Huber R, Böck A (2005) [NiFe]-Hydrogenase maturation endopeptidase: structure and function. Biochem Soc Trans 33:108–111PubMedCrossRefGoogle Scholar
  25. Turner JA (2004) Sustainable hydrogen production. Science 305:972–974PubMedCrossRefGoogle Scholar
  26. Vanderzwaan JW, Coremans JMCC, Bouwens ECM, Albracht SPJ (1990) Effect of O-17(2) and (Co)-C-13 on EPR-spectra of nickel in hydrogenase from Chromatium vinosum. Biochim Biophys Acta 1041:101–110Google Scholar
  27. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC (1995) Crystal-structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature 373:580–587PubMedCrossRefGoogle Scholar
  28. Wu LF, Chanal A, Rodrigue A (2000) Membrane targeting and translocation of bacterial hydrogenases. Arch Microbiol 173:319–324PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Aruna Goenka Agrawal
    • 1
  • Gerrit Voordouw
    • 2
  • Wolfgang Gärtner
    • 1
    Email author
  1. 1.Max-Planck-Institut für Bioanorganische ChemieMülheimGermany
  2. 2.Department of Biological SciencesThe University of CalgaryCalgaryCanada

Personalised recommendations