Review: Borders, patterns, and distinctive families of homeodomains

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Abstract
Homeotic proteins function as transcription factors in early embryogenesis of many organisms. To date, hundreds of distinctive homeoproteins have been identified, including 84 human homeodomains. However further progress in understanding functional relationships between particular homeoproteins and other embryonic regulators requires a comprehensive structural classification of these proteins. The most probable borders and conservative amino acid positions inside the homeodomain region have been established using a statistical analysis of variabilities of amino acid occurrences at various positions outside and inside the domain. A new format for a homeodomain sequence presentation and regular amino acid patterns which are strongly representative of distinctive homeodomain groups are proposed. Using the established patterns, 33 families of closely related homeodomains have been distinguished and classified. The total list of 297 homeodomain amino acid sequences is presented in the Appendix. The structural classification of homeodomains has been proposed. It can be useful for both the identification (or prediction) of new homeotic genes/proteins and the recognition of possible PCR-induced sequence errors. This systematics will also have an impact on understanding functional relationships among homeotic proteins and other genetic regulators of developmental processes.