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Heteronuclear NMR methods have been used to elucidate the secondary structure and the general tertiary fold of the protein NodF from Rhizobium leguminosarum. A similarity to acyl carrier proteins of the fatty acid synthase system had been suggested by the presence of a phosphopantetheine prosthetic group and a short stretch of sequence homology near the prosthetic group attachment site. NMR results suggest that the structural homology extends well beyond this region. Both proteins have three well-formed helices which fold in a parallel-antiparallel fashion and a prosthetic group attachment site near the beginning of the second helix.

A review is given of the mathematical foundations of average Liouvillian theory and examples are provided of average Liouvillian expressions derived for sequences in nuclear magnetic resonance which possess temporal symmetry or antisymmetry. The utility of this approach is demonstrated in the design of pulse sequences to measure the effect of cross-correlation between chemical shift anisotropy and dipolar couplings on relaxation rates in biomolecules. Experimental verification of the theory is carried out on a 15N labelled sample of ubiquitin.

The ATP-dependent DNA ligase D (LigD) performs a major role in non-homologous end-joining (NHEJ) pathway. Pseudomonas aeruginosa LigD (PaeLigD) contains a N-terminal phosphoesterase domain (PE) domain followed by a ligase domain and a C-terminal polymerase domain. The PE domain (187 residues) possesses manganese dependent phosphodiesterase and phosphomonoesterase activities as it sequentially removes the 3′-ribonucleoside from the primer strand of the RNA primer-DNA template duplex and subsequently hydrolyzes the 3′-PO4 to a 3′-OH group (1).PaeLigD-PE belongs to a class of unique 3′- end-processing enzymes as it cleaves the primer strand to a point at which a single ligatable ribonucleotide remains (2).Extensive mutagenesis studies have identified critical residues required for ribonuclease and 3′-phosphatase activities (1). Multiple active sites present in the enzyme lead to the belief that this enzyme possesses some unique motifs. However, in the absence of atomic level structural information clear structure/function correlations are lacking. We are currently working towards obtaining a high-resolution structure of PaeLigD-PE using solution NMR methods.Reference:1) Zhu, H., and Shuman, S. (2006) J. Biol. Chem. 281, 13873-13881.2) Zhu, H., and Shuman, S. (2008) J. Biol. Chem. 283, 8331-8339.