Journal of Biomolecular NMR

, Volume 7, Issue 3, pp 225–235 | Cite as

1H and 15N NMR resonance assignments and solution secondary structure of oxidized Desulfovibrio desulfuricans flavodoxin

  • John R. Pollock
  • Richard P. Swenson
  • Brian J. Stockman
Research Papers

Summary

Sequence-specific 1H and 15N resonance assignments have been made for 137 of the 146 nonprolyl residues in oxidized Desulfovibrio desulfuricans [Essex 6] flavodoxin. Assignments were obtained by a concerted analysis of the heteronuclear three-dimensional 1H-15N NOESY-HMQC and TOCSY-HMQC data sets, recorded on uniformly 15N-enriched protein at 300 K. Numerous side-chain resonances have been partially or fully assigned. Residues with overlapping 1HN chemical shifts were resolved by a three-dimensional 1H-15N HMQC-NOESY-HMQC spectrum. Medium-and long-range NOEs, 3JNHα coupling constants, and 1HN exchange data indicate a secondary structure consisting of five parallel β-strands and four α-helices with a topology similar to that of Desulfovibrio vulgaris [Hidenborough] flavodoxin. Prolines at positions 106 and 134, which are not conserved in D. vulgaris flavodoxin, contort the two C-terminal α-helices.

Keywords

Chemical shift index Flavodoxin Isotopic enrichment Nitrogen-15 Protein Secondary structure 3D NMR 

Abbreviations

CSI

chemical shift index

DQF-COSY

double-quantum-filtered correlation spectroscopy

DIPSI

decoupling in the presence of scalar interactions

FMN

flavin mononucleotide

GARP

globally optimized alternating phase rectangular pulse

HMQC

heteronuclear multiple-quantum coherence

HSQC

heteronuclear single-quantum coherence

NOE

nuclear Overhauser effect

NOESY

nuclear Overhauser enhancement spectroscopy

TOCSY

total correlation spectroscopy

TPPI

time-proportional phase increments

TSP

3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodium salt

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References

  1. BodenhausenG. and RubenD.L. (1980) Chem. Phys. Lett. 69, 185–188.Google Scholar
  2. CaldeiraJ., PalmaP.N., RegallaM., LampreiaJ., CalveteJ., SchäferW., LeGallJ., MouraI. and MouraJ.J.G. (1994) Eur. J. Biochem., 220, 987–995.Google Scholar
  3. ClubbR.T., ThanabalV., OsborneC. and WagnerG. (1991) Biochemistry, 30, 7718–7730.Google Scholar
  4. DevereuxR., HeS.-H., DoyleC.L., OrklandS., StahlD.A., LeGallJ. and WhitmanW.B. (1990) J. Bacteriol., 172, 3609–3619.Google Scholar
  5. DraperR.D. and IngrahamL.L. (1968) Arch. Biochem. Biophys., 125, 802–808.Google Scholar
  6. FrenkielT., BauerC., CarrM.D., BirdsallB. and FeeneyJ. (1990) J. Magn. Reson., 90, 420–425.Google Scholar
  7. HelmsL.R., KreyG.D. and SwensonR.P. (1990) Biochem. Biophys. Res. Commun., 168, 809–817.Google Scholar
  8. HelmsL.R. and SwensonR.P. (1991) Biochim. Biophys. Acta, 1089, 417–419.Google Scholar
  9. Helms, L.R. (1992) Ph.D. Thesis, The Ohio State University, Columbus, OH.Google Scholar
  10. HelmsL.R. and SwensonR.P. (1992) Biochim. Biophys. Acta, 1131, 325–328.Google Scholar
  11. KayL.E. and BaxA. (1990) J. Magn. Reson., 86, 110–126.Google Scholar
  12. KnaufM.A., LöhrF., CurleyG.P., O'FarrellP., MayhewS.G., MüllerF. and RüterjansH. (1993) Eur. J. Biochem., 213, 167–184.Google Scholar
  13. KumarA., ErnstR.R. and WüthrichK. (1980) Biochem. Biophys. Res. Commun., 95, 1–6.Google Scholar
  14. LudwigM.L. and LuschinskyC.L. (1992) In Chemistry and Biochemistry of Flavoenzymes, Vol. 3 (Ed., MüllerF.), CRC Press, Boca Raton, FL, pp. 427–466.Google Scholar
  15. MarionD. and WüthrichK. (1983) Biochem. Biophys. Res. Commun., 113, 967–974.Google Scholar
  16. MarionD., DriscollP.C., KayL.E., WingfieldP.T., BaxA., GronenbornA.M. and CloreG.M. (1989) Biochemistry, 28, 6150–6156.Google Scholar
  17. MayhewS.G. and LudwigM.L. (1975) In The Enzymes, Vol. 12 (Ed., BoyerP.), Academic Press, New York, NY, pp. 57–117.Google Scholar
  18. PaulsenK.E., StankovichM.T., StockmanB.J. and MarkleyJ.L. (1990) Arch. Biochem. Biophys., 280, 68–73.Google Scholar
  19. PiantiniU., SørensenO.W. and ErnstR.R. (1982) J. Am. Chem. Soc., 104, 6800–6801.Google Scholar
  20. RichardsonJ.S. (1981) Adv. Protein Chem., 34, 167–339.Google Scholar
  21. ShakaA.J., BarkerP.B. and FreemanR. (1985) J. Magn. Reson., 64, 547–552.Google Scholar
  22. ShakaA.J., LeeC.J. and PinesA. (1988) J. Magn. Reson., 77, 274–293.Google Scholar
  23. StatesD.J., HaberkornR.A. and RubenD.J. (1982) J. Magn. Reson., 48, 286–292.Google Scholar
  24. StockmanB.J., EuvrardA., KloostermanD.A., ScahillT.A. and SwensonR.P. (1993) J. Biomol. NMR, 3, 133–149.Google Scholar
  25. StockmanB.J., RichardsonT.E. and SwensonR.P. (1994) Biochemistry, 33, 15298–15308.Google Scholar
  26. SwensonR.P. and KreyG.D. (1994) Biochemistry, 33, 8505–8514.Google Scholar
  27. WagnerG., NeuhausD., WörgötterE., VasákM., KägiJ.H.R. and WüthrichK. (1986) J. Mol. Biol., 187, 131–135.Google Scholar
  28. WagnerG. (1990) Prog. NMR Spectrosc., 22, 101–139.Google Scholar
  29. WattW., TulinskyA., SwensonR.P. and WatenpaughK.D. (1991) J. Mol. Biol., 218, 195–208.Google Scholar
  30. WishartD.S., SykesB.D. and RichardsF.M. (1992) Biochemistry, 31, 1647–1651.Google Scholar
  31. WüthrichK. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.Google Scholar
  32. ZhouZ. and SwensonR.P. (1995) Biochemistry, 34, 3183–3192.Google Scholar
  33. ZuiderwegE.R.P. and FesikS.W. (1989) Biochemistry, 28, 2387–2391.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • John R. Pollock
    • 1
  • Richard P. Swenson
    • 2
  • Brian J. Stockman
    • 1
  1. 1.Pharmacia and Upjohn, Inc.KalamazooU.S.A.
  2. 2.Department of BiochemistryThe Ohio State UniversityColumbusU.S.A.

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