Taxonomic distribution of proteins containing HOX domains

The HOX domain within your query sequence starts at position 297 and ends at position 359, and its E-value is 3.8e-18.

The U box is a modified RING finger - a common domain in ubiquitination.

Aravind L, Koonin EV
Curr Biol. 2000; 10: 1324-1324

Protein interactions of homeodomain proteins.

Vershon AK
Curr Opin Biotechnol. 1996; 7: 392-6

Homeodomain proteins are conserved DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Many homeodomain proteins require additional cofactors to bind with high affinity and specificity to their DNA sites. The recent structural determinations and biochemical analysis of several multimeric complexes have provided a better understanding of how protein interactions influence the DNA-binding activity of homeodomain proteins.

Homeodomain interactions.

Wolberger C
Curr Opin Struct Biol. 1996; 6: 62-8

Homeodomain proteins play key roles in development and gene regulation in eukaryotes. Past structural studies have focused on the binding of monomeric homeodomains to DNA, but two recent structures have revealed how homeodomains bind DNA as multimers. The structures of the Drosophila Paired homodimer and the yeast a1/alpha2 heterodimer bound to DNA, along with a high-resolution study of a Drosophila eve-DNA complex, have deepened our understanding of how homeodomains locate their DNA targets.

Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations.

Xu W, Rould MA, Jun S, Desplan C, Pabo CO
Cell. 1995; 80: 639-50

The 2.5 A resolution structure of a cocrystal containing the paired domain from the Drosophila paired (prd) protein and a 15 bp site shows structurally independent N-terminal and C-terminal subdomains. Each of these domains contains a helical region resembling the homeodomain and the Hin recombinase. The N-terminal domain makes extensive DNA contacts, using a novel beta turn motif that binds in the minor groove and a helix-turn-helix unit with a docking arrangement surprisingly similar to that of the lambda repressor. The C-terminal domain is not essential for prd binding and does not contact the optimized site. All known developmental missense mutations in the paired box of mammalian Pax genes map to the N-terminal subdomain, and most of them are found at the protein-DNA interface.

Homeodomain proteins.

Gehring WJ, Affolter M, Burglin T
Annu Rev Biochem. 1994; 63: 487-526

Homeodomain-DNA recognition.

Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wuthrich K
Cell. 1994; 78: 211-23

Origins of segment periodicity.

Ghysen A
Nature. 1990; 344: 297-8

Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.

Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO
Cell. 1990; 63: 579-90

The crystal structure of a complex containing the engrailed homeodomain and a duplex DNA site has been determined at 2.8 A resolution and refined to a crystallographic R factor of 24.4%. In this complex, two separate regions of the 61 amino acid polypeptide contact a TAAT subsite. An N-terminal arm fits into the minor groove, and the side chains of Arg-3 and Arg-5 make contacts near the 5' end of this "core consensus" binding site. An alpha helix fits into the major groove, and the side chains of IIe-47 and Asn-51 contact base pairs near the 3' end of the TAAT site. This "recognition helix" is part of a structurally conserved helix-turn-helix unit, but these helices are longer than the corresponding helices in the lambda repressor, and the relationship between the helix-turn-helix unit and the DNA is significantly different.

The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins.

Landschulz WH, Johnson PF, McKnight SL
Science. 1988; 240: 1759-64

A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.