Journal of Biomolecular NMR

, Volume 61, Issue 1, pp 83–87 | Cite as

NMR structure determination of the protein NP_344798.1 as the first representative of Pfam PF06042

  • Biswaranjan Mohanty
  • Pedro Serrano
  • Michael Geralt
  • Kurt WüthrichEmail author
NMR structure note

Biological context

The protein NP_344798.1 from Streptococcuspneumoniae (TIGR4) belongs to the Pfam protein family PF06042, which currently contains 786 sequences from 739 species ( Based on sequence analyses, NP_344798.1 has been identified as a member of the nucleotidyltransfererase (NTase)-fold superfamily and annotated as a protein domain of unknown function, DUF925 (Kuchta et al. 2009). The bioinformatics data further suggest that all PF06042 members contain a single domain and are active NTases, as they contain the characteristic functional catalytic residues (Kuchta et al. 2009). Nonetheless, due to scarcity of experimental data, no specific biological role of these enzymes could as yet be ascertained. The NMR core of the Joint Center for Structural Genomics (JCSG) targeted NP_344798.1 to obtain a first structure for the PF06042 family, and the J-UNIO protocol for automated NMR structure determination (Serrano et al. 2012) was applied to...


Complex Point Backbone Assignment Polypeptide Segment Erroneous Assignment Torsion Angle Dynamic 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was funded by the Joint Center for Structural Genomics (JCSG) through the NIH Protein Structure Initiative (PSI) Grant Number U54 GM094586 from the National Institute of General Medical Sciences ( BM received support from the Skaggs Institute of Chemical Biology. Kurt Wüthrich is the Cecil H. and Ida M. Green Professor of Structural Biology at TSRI. BM thanks Dr. Reto Horst for assistance in optimizing the setup of NMR experiments.


  1. DeMarco A, Wüthrich K (1976) Digital filtering with a sinusoidal window function: an alternative technique for resolution enhancement in FT NMR. J Magn Reson 24:201–204ADSGoogle Scholar
  2. Fiorito F, Herrmann T, Damberger FF, Wüthrich K (2008) Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY. J Biomol NMR 42:23–33CrossRefGoogle Scholar
  3. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298CrossRefGoogle Scholar
  4. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189CrossRefGoogle Scholar
  5. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227CrossRefGoogle Scholar
  6. Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876–10881ADSCrossRefGoogle Scholar
  7. Hiller S, Wider G, Wüthrich K (2008) APSY-NMR with proteins: practical aspects and backbone assignment. J Biomol NMR 42:179–195CrossRefGoogle Scholar
  8. Holm L, Rosenstrom P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–W549CrossRefGoogle Scholar
  9. Keller R (2004) CARA: computer aided resonance assignment.
  10. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51–55CrossRefGoogle Scholar
  11. Koradi R, Billeter M, Güntert P (2000) Point-centered domain decomposition for parallel molecular dynamics simulation. Comput Phys Commun 124:139–147ADSCrossRefzbMATHGoogle Scholar
  12. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K (2009) Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. Nucleic Acids Res 37:7701–7714CrossRefGoogle Scholar
  13. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  14. Lloyd NR, Wuttke DS (2014) Less is more: structures of difficult targets with minimal constrains. Structure 22:1223–1224CrossRefGoogle Scholar
  15. Luginbühl P, Güntert P, Billeter M, Wüthrich K (1996) The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8:136–146CrossRefGoogle Scholar
  16. Pedrini B, Serrano P, Mohanty B, Geralt M, Wüthrich K (2013) NMR-Profiles of protein solutions. Biopolymers 99:825–831CrossRefGoogle Scholar
  17. Serrano P, Pedrini B, Mohanty B, Geralt M, Herrmann T, Wüthrich K (2012) The J-UNIO protocol for automated protein structure determination by NMR in solution. J Biomol NMR 53:341–354CrossRefGoogle Scholar
  18. Sgourakis NG, Natajaran K, Ying J, Vögeli B, Boyd LF, Margulies DH, Bax A (2014) The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02–m06 viral immune modulator family. Structure 22:1263–1273CrossRefGoogle Scholar
  19. Toh Y, Takeshita D, Numata T, Fukai S, Nureki O, Tomita K (2009) Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme. EMBO J 28:3353–3365CrossRefGoogle Scholar
  20. Volk J, Herrmann T, Wüthrich K (2008) Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR 41:127–138CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Biswaranjan Mohanty
    • 1
    • 2
    • 3
    • 4
  • Pedro Serrano
    • 1
    • 2
  • Michael Geralt
    • 1
    • 2
  • Kurt Wüthrich
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaUSA
  2. 2.Joint Center for Structural GenomicsLa JollaUSA
  3. 3.Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA
  4. 4.Medicinal Chemistry, Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleAustralia

Personalised recommendations