Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues.

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TitleNovel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues.
Publication TypeJournal Article
Year of Publication2004
AuthorsLim, K, Sarikaya, E, Galkin, A, Krajewski, W, Pullalarevu, S, Shin, J-H, Kelman, Z, Howard, A, Herzberg, O
JournalProteins
Volume56
Issue3
Pagination564-71
Date Published2004 Aug 15
ISSN1097-0134
KeywordsAmino Acid Sequence, Bacterial Proteins, Base Sequence, Binding Sites, Crystallization, Crystallography, X-Ray, DNA-Binding Proteins, Electrophoretic Mobility Shift Assay, Haemophilus influenzae, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Protein Structure, Secondary, RNA-Binding Proteins, Selenomethionine, Sequence Homology, Amino Acid
Abstract

The crystal structure of the Haemophilus influenzae protein HI1480 was determined at 2.1-A resolution. The amino acid sequence of HI1480 is unique, having no homology with other known protein sequences. The protein adopts a novel alpha+beta fold, and associates into a dimer of tightly associated dimers. The tight dimers are formed by intermolecular interactions that are mediated by an antiparallel beta-barrel involving both monomers. Helical regions of two dimers mediate the tetramer formation. The helical region contains a four-helix bundle that has been seen only in the anticodon binding domains of class I tRNA synthetases. A cluster of four residues, Tyr18, Arg134, Glu26, and Lys12 is located in a depression formed at the four-helix bundle/ beta-barrel interface. The arrangement is suggestive of an active center, possibly a catalytic site. The HI1480 gene is located within the Mu-like prophage region of H. influenzae, has no homology to bacteriophage genes, and is flanked by transposases. Hence, this is an example of horizontal transfer from an unknown organism. Gel mobility shift assays revealed that HI1480 binds DNA and RNA molecules. Double-stranded DNA is favored over single-stranded DNA, and longer DNA molecules are bound better than shorter ones.

DOI10.1002/prot.20148
Alternate JournalProteins
PubMed ID15229888
Grant ListP01 GM57890 / GM / NIGMS NIH HHS / United States