The Histone Database: a comprehensive resource for histones and histone fold-containing proteins

Abstract

The Histone Database is a curated and searchable collection of full-length sequences and structures of histones and nonhistone proteins containing histone-like folds, compiled from major public databases. Several new histone fold-containing proteins have been identified, including the huntingtin-interacting protein HYPM. Additionally, based on the recent crystal structure of the Son of Sevenless protein, an interpretation of the sequence analysis of the histone fold domain is presented. The database contains an updated collection of multiple sequence alignments for the four core histones (H2A, H2B, H3, and H4) and the linker histones (H1/H5) from a total of 975 organisms. The database also contains information on the human histone gene complement and provides links to three-dimensional structures of histone and histone fold-containing proteins. The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold-containing proteins. The database is available at http://research.nhgri.nih.gov/histones/.

Fig. 1

Histone Database data model. The Histone Database stores selected information from the GenBank records, such as the GenBank unique identifier (GI), accession number, definition line, sequence string, and taxonomic identifier. The database front end is written in Perl, the data are stored in the relational database Oracle 9i, and are retrieved via Perl DBI and DBD libraries.

Fig. 2

Structure-based alignment of the first histone fold domain in human Son of Sevenless with yeast histone H2B. Yeast histone H2B (pdb|1ID3, chain D) aligned with the first histone fold domain present in the human ras activator Son of Sevenless (pdb|1Q9C, chain A). Secondary structural elements are represented above the sequence alignment and identical residues are colored in red.

Fig. 3

Multiple sequence alignment of three histone H2A members and the human huntingtin-interacting protein M (HYPM). Human, frog, and chicken histone H2A sequences aligned with the human HYPM protein. Secondary structural elements from the crystal structures of frog (pdb|1AOI, chain C) and chicken (pdb|2HIO, chain A) nucleosomes are represented above the sequence alignments and identical residues are colored in red; conserved residues in HYPM are uppercase.