Abstract
Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.
Highlights
Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742, Korea
C-terminal peptide of HP0895, the residue-specific interaction sites of HP0894 were cleared (Figure 4). These results indicate that the HP0894-HP0895 TA system, especially through negative regulation of the HP0894 toxin by the HP0895 antitoxin, may be related to the status of infections of
CopA is a member of the bacterial copper ion ATPase family, and CopP, which is homologous to E. hirae CopZ, is a putative copper binding regulatory protein of 66 amino acids [104,108]
Summary
The methods need to be improved since similarity-free methods still depend to a certain extent on similarity Another approach to identify function is to use 3D structures. This approach often succeeds in cases where sequence-based methods fail. The structural comparison still has the limitation of false positives being reported and needs to be improved to overcome overestimation of statistical significance like sequence-similarity searches [70]. This means that experimental confirmation is still required for exact assignment of function to an unknown protein. We generally conducted four steps: (i) structure determination; (ii) sequence homology search using PSI-BLAST [71]; (iii) structural homology search using the web server DALI [62]; and (iv) experimental confirmation of the function
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