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1 The Northeast Structural Genomics Consortium
2 Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, USA
3 Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10021, USA
4 Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
5 Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
(RECEIVED December 28, 2004; FINAL REVISION March 20, 2005; ACCEPTED March 24, 2005)
The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE–SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.
Keywords: YgdK; SufE; IscU; Fe-S cluster; NMR; homology modeling
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041322705.
Reprint requests to: Thomas Szyperski, Department of Chemistry, University of Buffalo, The State University of New York, 816 Natural Sciences Complex, Buffalo, NY 14260, USA; e-mail: szypersk{at}chem.buffalo.edu; fax: (716) 645-7338.
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