Backbone NMR resonance assignment of the intrinsically disordered UBact protein from Nitrospira nitrosa
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Barandun J, Damberger FF, Delley CL, Laederach J, Allain FH, Weber-Ban E (2017) Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. BMC Struct Biol 17(1):1. https://doi.org/10.1186/s12900-017-0072-1
Benoist P, Müller A, Diem HG, Schwencke J (1992) High-molecular-mass multicatalytic proteinase complexes produced by the nitrogen-fixing actinomycete Frankia strain BR. J Bacteriol 174(5):1495–1504. https://doi.org/10.1128/jb.174.5.1495-1504.1992
Bode NJ, Darwin KH (2014) The Pup-proteasome system of Mycobacteria. Microbiol Spectr. https://doi.org/10.1128/microbiolspec.MGM2-0008-2013
Dahlmann B, Kopp F, Kuehn L, Niedel B, Pfeifer G, Hegerl R, Baumeister W (1989) The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria. FEBS Lett 251(1–2):125–131
Grzesiek S, Bax A (1993) The importance of not saturating water in protein NMR. Application to sensitivity enhancement and NOE measurements. J Am Chem Soc 115(26):12593–12594
Hall JB, Fushman D (2003) Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G. J Biomol NMR 27(3):261–275. https://doi.org/10.1023/a:1025467918856
Hough R, Pratt G, Rechsteiner M (1987) Purification of two high molecular weight proteases from rabbit reticulocyte lysate. J Biol Chem 262(17):8303–8313
Kjaergaard M, Poulsen FM (2011) Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution. J Biomol NMR 50(2):157–165. https://doi.org/10.1007/s10858-011-9508-2
Kjaergaard M, Brander S, Poulsen FM (2011) Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH. J Biomol NMR 49(2):139–149. https://doi.org/10.1007/s10858-011-9472-x
Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31(8):1325–1327. https://doi.org/10.1093/bioinformatics/btu830
Lehmann G, Udasin RG, Livneh I, Ciechanover A (2017) Identification of UBact, a ubiquitin-like protein, along with other homologous components of a conjugation system and the proteasome in different gram-negative bacteria. Biochem Biophys Res Commun 483(3):946–950. https://doi.org/10.1016/j.bbrc.2017.01.037
Li Y, Maciejewski MW, Martin J, Jin K, Zhang Y, Maupin-Furlow JA, Hao B (2013) Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii. Protein Sci 22(9):1206–1217. https://doi.org/10.1002/pro.2305
Maupin-Furlow JA (2013) Archaeal proteasomes and SAMPylation. Subcell Biochem 66:297–327. https://doi.org/10.1007/978-94-007-5940-4_11
Miranda HV, Nembhard N, Su D, Hepowit N, Krause DJ, Pritz JR, Phillips C, Soll D, Maupin-Furlow JA (2011) E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci USA 108(11):4417–4422. https://doi.org/10.1073/pnas.1018151108
Pickart CM, Fushman D (2004) Polyubiquitin chains: polymeric protein signals. Curr Opin Chem Biol 8(6):610–616. https://doi.org/10.1016/j.cbpa.2004.09.009
Ranjan N, Damberger FF, Sutter M, Allain FH, Weber-Ban E (2011) Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins. J Mol Biol 405(4):1040–1055. https://doi.org/10.1016/j.jmb.2010.11.040
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44(4):213–223. https://doi.org/10.1007/s10858-009-9333-z
Sutter M, Damberger FF, Imkamp F, Allain FH, Weber-Ban E (2010) Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the side chain of its C-terminal glutamate. J Am Chem Soc 132(16):5610–5612. https://doi.org/10.1021/ja910546x
Venyaminov SYu, Baikalov IA, Shen ZM, Wu CS, Yang JT (1993) Circular dichroic analysis of denatured proteins: inclusion of denatured proteins in the reference set. Anal Biochem 214(1):17–24. https://doi.org/10.1006/abio.1993.1450
Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194(3):531–544. https://doi.org/10.1016/0022-2836(87)90679-6
Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Markley J, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59(4):687–696. https://doi.org/10.1002/prot.20449