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Published online before print March 7, 2006, 10.1110/ps.051993506
Protein Science (2006), 15:921-928. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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PROTEIN STRUCTURE REPORTS

Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae

Dong Hae Shin1, Jeong-Sun Kim2, Hisao Yokota3, Rosalind Kim3 and Sung-Hou kim2,3

1 College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea
2 Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
3 Department of Chemistry, University of California, Berkeley, California 94720-5230, USA

(RECEIVED November 23, 2005; FINAL REVISION December 13, 2005; ACCEPTED December 13, 2005)

We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 Å resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right-handed coiled-coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled-coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled-coils. The first part, containing one stutter, is an unusual phenylalanine-rich region that is not found in any other coiled-coil structures. The second part is a highly conserved glutamine-rich region, frequently found in other trimeric coiled-coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N-terminal sequences. Based on the structural comparison with other coiled-coil structures, a probable molecular function of the DUF16 family is discussed.

Keywords: DUF16; MPN010; hypothetical protein; coiled-coil; stutter


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