Dlx5 Homeodomain:DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome

Abstract

SUMMARY The Dlx5 homeodomain is a transcription factor related to the Drosophila Distal-less gene that is associated with breast and lung cancer, lymphoma, Rett syndrome and osteoporosis in humans. Mutations in the DLX5 gene have been linked to deficiencies in craniofacial and limb development in higher eukaryotes, including Split Hand and Foot Malformation-1 (SHFM-1) in humans. Our characterization of a Dlx5 homeodomain–(CGACTAATTAGTCG)2 complex by NMR spectroscopy paved the way for determination of its crystal structure at 1.85 Å resolution that enabled rationalization of the effects of disease-related mutations on the protein function. A remarkably subtle mutation, Q186H, is linked to SHFM-1; this change likely affects affinity of DNA binding by disrupting water-mediated interactions with the DNA major groove. A more subtle effect is implicated for the Q178P mutation, which is not in direct contact with the DNA. Our data indicate that these mutations diminish the ability of the Dlx5 homeodomain to recognize and bind target DNAs, and likely destabilize the formation of functional complexes.

Dinosaurs, Chameleons, Humans, and Evo‐Devo Path: Linking Étienne Geoffroy's Teratology, Waddington's Homeorhesis, Alberch's Logic of “Monsters,” and Goldschmidt Hopeful “Monsters”

“…The human syndrome is classified into six different types with only general chromosomal regions having been mapped for a majority of the cases, the most common nonsyndromic form being SHFM type‐1 associated with variable deletions in chromosome 7q21. The region most commonly affected spans Dlx5 and Dlx6 genes, both expressed in the apical ectodermal ridge (AER) of the growing limb bud, with other genes identified being Wnt10B , Tp63 , Wnt5a , Ror2 , and Dactylin (Duijf et al., ; Conte et al., ; Proudfoot et al., ; Stevenson and Hall, ). Recent work identifying the role of Wnt5a in SHFM has shown the importance of the noncanonical PCP Wnt pathway in establishing basolateral and planar cell polarity to the AER, thus promoting a role in the maintenance of the AER rather than the initial establishment for this source of Fgf8 and Dlx5/6.…”

Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis

“…DLX5 is a member of the DLX family of homeodomain transcription factors, which share sequence similarities with the Drosophila distal-less gene. DLX5 has been shown to stimulate tumor cell proliferation through upregulation of the MYC expression [50, 51]. GRB10 encodes a growth receptor bound protein that plays an important role in multiple key cancer signalling pathways such as the Wnt and Akt pathways [52, 53].…”

Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3

“…The crystal structural study of the HD of distal-less 5 (Dlx5-HD) complexed with a DNA duplex revealed that the α3 helix directly contacts DNA bases through the major groove of the DNA ( Figure 1 C,D) [ 21 ]. The side-chain of N187 (N179 in Dlx3) exhibits two hydrogen-bonding (H-bonding) interactions with the A3 base of the consensus 5′-T1-A2-A3-T4-T5-3′ site ( Figure 1 C) [ 21 ]. Q186 (Q178 in Dlx3) recognizes the T5 base via water-mediated H-bonding interactions ( Figure 1 C) [ 21 ].…”

“…The side-chain of N187 (N179 in Dlx3) exhibits two hydrogen-bonding (H-bonding) interactions with the A3 base of the consensus 5′-T1-A2-A3-T4-T5-3′ site ( Figure 1 C) [ 21 ]. Q186 (Q178 in Dlx3) recognizes the T5 base via water-mediated H-bonding interactions ( Figure 1 C) [ 21 ]. In addition, R141 (R133 in Dlx3) in the L1 loop also shows a H-bonding interaction with the T1 base ( Figure 1 C) [ 21 ].…”