Nucleic Acids Research, 1995, Vol. 23, No. 9 1604-1613
© 1995
COMPUTATIONAL BIOLOGY |
The HMG-1 box protein family: classification and functional relationships
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, Room 8N-805, Bethesda, MD 20894, USA
* To whom correspondence should be addressed
Received November 30, 1994. Revised February 27, 1995. Accepted February 27, 1995.
The abundant and highly-conserved nucleoprotelns comprising the high mobility group–1/–2 (HMG–1/–2) family contains two homologous basic domains of about 75 amino acids. These basic domains, termed HMG-1 boxes, are highly structured and facilitate HMG-DNA interactions. Many proteins that regulate various cellular functions involving DNA binding and whose target DNA sequences share common structural characteristics have been identified as having an HMG-1 box; these proteins include the RNA polymer-ase I transcription factor UBF, the mammalian testis-determlning factor SRY and the mitochondrlal transcription factors ABF2 and mtTF1, among others. The sequences of 121 HMG-1 boxes have been compiled and aligned in accordance with thermody-namic results from homology model building (threading) experiments, basing the alignment on structure rather than by using traditional sequence homology methods. The classification of a representative subset of these proteins was then determined using standard least-squares distance methods. The proteins segregate into two groups, the first consisting of HMG–1/–2 proteins and the second consisting of proteins containing the HMG-1 box but which are not canonical HMG proteins. The proteins in the second group further segregate based on their function, their ability to bind specific sequences of DNA, or their ability to recognize discrete non-B-DNA structures. The HMG-1 box provides an excellent example of how a specific protein motif, with slight alteration, can be used to recognize DNA in a variety of functional contexts.
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