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Published online before print January 4, 2005, 10.1110/ps.041096705
Protein Science (2005), 14:424-430. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog

Deok Cheon Yeh, Lisa M. Parsons, James F. Parsons, Fang Liu, Edward Eisenstein and John Orban

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA

(RECEIVED September 2, 2004; FINAL REVISION November 3, 2004; ACCEPTED November 4, 2004)

The solution structure of the 154-residue conserved hypothetical protein HI0004 has been determined using multidimensional heteronuclear NMR spectroscopy. HI0004 has sequence homologs in many organisms ranging from bacteria to humans and is believed to be essential in Haemophilus influenzae, although an exact function has yet to be defined. It has a {alpha}–{beta}–{alpha} sandwich architecture consisting of a central four-stranded {beta}-sheet with the {alpha}2-helix packed against one side of the {beta}-sheet and four {alpha}-helices ({alpha}1, {alpha}3, {alpha}4, {alpha}5) on the other side. There is structural homology with the eukaryotic matrix metalloproteases (MMPs), but little sequence similarity except for a conserved region containing three histidines that appears in both the MMPs and throughout the HI0004 family of proteins. The solution structure of HI0004 is compared with the X-ray structure of an Aquifex aeolicus homolog, AQ_1354, which has 36% sequence identity over 148 residues. Despite this level of sequence homology, significant differences exist between the two structures. These differences are described along with possible functional implications of the structures.

Keywords: Haemophilus influenzae; NMR; structural genomics; MMP; hydrolase

Abbreviations: NMR, nuclear magnetic resonance • NOE, nuclear Over-hauser effect • NOESY, NOE spectroscopy • EDTA, ethylenediaminetetra-acetic acid • HSQC, heteronuclear single quantum coherence • RMSD, root mean square deviation

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041096705.

Reprint requests to: John Orban, Center for Advanced Research in Bio-technology, University of Maryland Biotechnology Institute, 9600 Gudel-sky Drive, Rockville, MD 20850, USA; e-mail: orban{at}umbi.umd.edu; fax: (301) 738-6255.


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