Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins

  • John R. Cort
  • Theresa A. Ramelot
  • Diana Murray
  • Thomas B. Acton
  • Li-Chung Ma
  • Rong Xiao
  • Gaetano T. Montelione
  • Michael A. Kennedy
Article

Abstract

We have determined the solution NMR structure of SACOL2532, a putative GCN5-like N-acetyltransferase (GNAT) from Staphylococcus aureus. SACOL2532 was shown to bind both CoA and acetyl-CoA, and structures with and without bound CoA were determined. Based on analysis of the structure and sequence, a subfamily of small GCN5-related N-acetyltransferase (GNAT)-like proteins can be defined. Proteins from this subfamily, which is largely congruent with COG2388, are characterized by a cysteine residue in the acetyl-CoA binding site near the acetyl group, by their small size in relation to other GNATs, by a lack of obvious substrate binding site, and by a distinct conformation of bound CoA in relation to other GNATs. Subfamily members are found in many bacterial and eukaryotic genomes, and in some archaeal genomes. Whereas other GNATs transfer the acetyl group of acetyl-CoA directly to an aliphatic amine, the presence of the conserved cysteine residue suggests that proteins in the COG2388 GNAT-subfamily transfer an acetyl group from acetyl-CoA to one or more presently unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The apparent absence of a substrate-binding region suggests that the substrate is a macromolecule, such as another protein, or that a second protein subunit providing a substrate-binding region must combine with SACOL2532 to make a fully functional N-acetyl transferase.

Keywords

Acetyl coenzyme A Acetyl enzyme Acyl enzyme GCN5 GNAT N-acetyltransferase 

Abbreviations

1D

One-dimensional

2D

Two-dimensional

BME

β-Mercaptoethanol

CoA

Coenzyme A

DTT

Dithiothreitol

GNAT

GCN5-like N-acetyltransferase

HMQC

Heteronuclear multiple quantum coherence

HSQC

Heteronuclear single quantum coherence

MES

2-(N-morpholino)ethanesulfonic acid

NMR

Nuclear magnetic resonance

NOE(SY)

Nuclear Overhauser effect (spectroscopy)

RMSD

Root mean square deviation

Notes

Acknowledgments

This research was supported by a grant from the Protein Structure Initiative of the National Institutes of Health (U54 GM074958). NMR spectra were acquired in the Environmental Molecular Sciences Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy Office of Biological and Environmental Research) located at Pacific Northwest National Laboratory and operated for DOE by Battelle (contract KP130103). We thank Luciano Mueller for assistance with the doubly-filtered 1H–1H NOESY and TOCSY experiments.

References

  1. 1.
    Acton TB, Gunsalus KC, Xiao R, Ma L-C, Aramini JM, Baran MC et al (2005) Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. Methods Enzymol 394:210. doi:10.1016/S0076-6879(05)94008-1 PubMedCrossRefGoogle Scholar
  2. 2.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389 PubMedCrossRefGoogle Scholar
  3. 3.
    Andres HH, Klem AJ, Schopfer LM, Harrison JK, Weber WW (1988) On the active-site of liver acetyl-CoA-arylamine N-acetyltransferase from rapid acetylator rabbits (III/J). J Biol Chem 263:7521–7527PubMedGoogle Scholar
  4. 4.
    Berndsen CE, Albaugh BN, Tan S, Denu JM (2007) Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry 46:623–629. doi:10.1021/bi602513x PubMedCrossRefGoogle Scholar
  5. 5.
    Bhattacharya A, Tejero R, Mondtelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66:778–795. doi:10.1002/prot.21165 PubMedCrossRefGoogle Scholar
  6. 6.
    Bischoff M, Dunman P, Kormanec J, Macapagal D, Murphy E, Mounts W et al (2004) Microarray-based analysis of the Staphylococcus aureus σB regulon. J Bacteriol 186:4085–4099. doi:10.1128/JB.186.13.4085-4099.2004 PubMedCrossRefGoogle Scholar
  7. 7.
    Cavanagh J, Fairbrother WJ, Palmer AGIII, Skelton NJ (1996) Protein NMR spectroscopy, principles and practice. Academic Press, San Diego, CAGoogle Scholar
  8. 8.
    DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
  9. 9.
    Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: a protein protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737. doi:10.1021/ja026939x PubMedCrossRefGoogle Scholar
  10. 10.
    Dutnall RN, Tafrov ST, Sternglanz R, Ramakrishnan V (1998) Structure of the histone acetyltransferase Hat1: a paradigm for the GCN5-related N-acetyl transferase superfamily. Cell 94:427–438. doi:10.1016/S0092-8674(00)81584-6 PubMedCrossRefGoogle Scholar
  11. 11.
    Dyda F, Klein DC, Burgess-Hickman A (2000) GCN5-related N-acetyltransferases: a structural overview. Annu Rev Biophys Biomol Struct 29:81–103. doi:10.1146/annurev.biophys.29.1.81 PubMedCrossRefGoogle Scholar
  12. 12.
    Ferentz AE, Wagner G (2000) NMR spectroscopy: a multifaceted approach to macromolecular structure. Q Rev Biophys 33:29–65. doi:10.1017/S0033583500003589 PubMedCrossRefGoogle Scholar
  13. 13.
    Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J et al (2005) Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producting methicillin-resistant Staphylococcus epidermis strain. J Bacteriol 187:2426–2438. doi:10.1128/JB.187.7.2426-2438.2005 PubMedCrossRefGoogle Scholar
  14. 14.
    Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E et al (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19:163–164. doi:10.1093/bioinformatics/19.1.163 PubMedCrossRefGoogle Scholar
  15. 15.
    Hegde SS, Javid-Majd F, Blanchard JS (2001) Overexpression and mechanistic analysis of chromosomally encoded aminoglycoside 2′-N-acetyltransferase (AAC(2′)-Ic) from Mycobacterium tuberculosis. J Biol Chem 276:45876–45881. doi:10.1074/jbc.M108810200 PubMedCrossRefGoogle Scholar
  16. 16.
    Holm L, Sander C (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26:316–319. doi:10.1093/nar/26.1.316 PubMedCrossRefGoogle Scholar
  17. 17.
    Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665–1674. doi:10.1021/ja047109h PubMedCrossRefGoogle Scholar
  18. 18.
    Huang YJ, Tejero R, Powers R, Montelione GT (2006) AutoStructure: a topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62:587–603. doi:10.1002/prot.20820 PubMedCrossRefGoogle Scholar
  19. 19.
    Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486. doi:10.1007/BF00228148 PubMedCrossRefGoogle Scholar
  20. 20.
    Lin Y, Fletcher CM, Zhou J, Allis CD, Wagner G (1999) Solution structure of the catalytic domain of GCN5 histone acetyltransferase bound to coenzyme A. Nature 400:86–89. doi:10.1038/21922 PubMedCrossRefGoogle Scholar
  21. 21.
    Linge JP, Nilges M (1999) Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation. J Biomol NMR 13:51–59. doi:10.1023/A:1008365802830 PubMedCrossRefGoogle Scholar
  22. 22.
    Liu J, Hegyi H, Acton TB, Montelione GT, Rost B (2004) Automatic target selection for structural genomics on eukaryotes. Proteins 56:188–200. doi:10.1002/prot.20012 PubMedCrossRefGoogle Scholar
  23. 23.
    Lovell SC, Davis IW, Arendall WBIII, de Bakker PIW, Word JM, Prisant MG et al (2003) Structure validation by Cα geometry: φ, ψ, and Cβ deviation. Proteins 50:437–450. doi:10.1002/prot.10286 PubMedCrossRefGoogle Scholar
  24. 24.
    Neri D, Szyperski T, Otting G, Senn H, Wütrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28:7510–7516. doi:10.1021/bi00445a003 PubMedCrossRefGoogle Scholar
  25. 25.
    Neuwald AF, Landsman D (1997) GCN5-related histone acetyl transferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem Sci 22:154–155. doi:10.1016/S0968-0004(97)01034-7 PubMedCrossRefGoogle Scholar
  26. 26.
    Petros AM, Kawai M, Luly JR, Fesik SW (1992) Conformation of two non-immunosuppressive FK506 analogs when bound to FKBP by isotope-filtered NMR. FEBS Lett 308:309–314. doi:10.1016/0014-5793(92)81300-B PubMedCrossRefGoogle Scholar
  27. 27.
    Schuettelkopf AW, van Aalten DMF (2004) PRODRG—a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr D Biol Crystallogr 60:1355–1363. doi:10.1107/S0907444904011679 CrossRefGoogle Scholar
  28. 28.
    Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73. doi:10.1016/S1090-7807(02)00014-9 PubMedCrossRefGoogle Scholar
  29. 29.
    Sinclair JC, Sandy J, Delgoda R, Sim E, Noble MEM (2000) Structure of arylamine N-acetyltransferase reveals a catalytic triad. Nat Struct Biol 7:560–564. doi:10.1038/76783 PubMedCrossRefGoogle Scholar
  30. 30.
    Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435–459. doi:10.1128/MMBR.64.2.435-459.2000 PubMedCrossRefGoogle Scholar
  31. 31.
    Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS et al (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28. doi:10.1093/nar/29.1.22 PubMedCrossRefGoogle Scholar
  32. 32.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. doi:10.1093/nar/22.22.4673 PubMedCrossRefGoogle Scholar
  33. 33.
    Tyler RC, Bitto E, Berndsen CE, Bingman CA, Singh S, Lee MS et al (2006) Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry 45:14325–14336. doi:10.1021/bi0612059 PubMedCrossRefGoogle Scholar
  34. 34.
    Vetting MW, de Carvalho LPS, Yu M, Hegde SS, Magnet S, Roderick SL et al (2005) Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys 433:212–226. doi:10.1016/j.abb.2004.09.003 PubMedCrossRefGoogle Scholar
  35. 35.
    Vuister GW, Bax A (1993) Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNHα) coupling constatnts in 15N-enriched proteins. J Am Chem Soc 115:7772–7777. doi:10.1021/ja00070a024 CrossRefGoogle Scholar
  36. 36.
    Yan Y, Harper S, Speicher DW, Marmorstein R (2002) The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. Nat Struct Biol 9:862–869. doi:10.1038/nsb0902-638 PubMedCrossRefGoogle Scholar
  37. 37.
    Zwahlen C, Legault P, Vincent SJF, Greenblatt J, Konrat R, Kay LE (1997) Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage λ N-peptide/boxB RNA complex. J Am Chem Soc 119:6711–6721. doi:10.1021/ja970224q CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • John R. Cort
    • 1
    • 2
    • 3
  • Theresa A. Ramelot
    • 3
    • 4
  • Diana Murray
    • 3
    • 5
  • Thomas B. Acton
    • 3
    • 6
  • Li-Chung Ma
    • 3
    • 6
  • Rong Xiao
    • 3
    • 6
  • Gaetano T. Montelione
    • 3
    • 6
    • 7
  • Michael A. Kennedy
    • 3
    • 4
  1. 1.Washington State University Tri-CitiesRichlandUSA
  2. 2.Biological Sciences DivisionPacific Northwest National LaboratoryRichlandUSA
  3. 3.Northeast Structural Genomics Consortium (NESG)
  4. 4.Department of Chemistry and BiochemistryMiami UniversityOxfordUSA
  5. 5.Department of PharmacologyColumbia UniversityNew York CityUSA
  6. 6.Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayUSA
  7. 7.Department of Biochemistry, Robert Wood Johnson Medical SchoolUniversity of Medicine and Dentistry of New JerseyPiscatawayUSA

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