Journal:MicroPubl Biol:000670
From Proteopedia
Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulationJonathan Zirkel, Amanda M. Hulse-Kemp, Amanda R. Storm [1] Molecular Tour The ALOG family is largely found in flowering plants with over 80% belonging to dicots (Iyer and Aravind, 2012[3]). Members of the ALOG family appear to be involved in tissue and organ development in plants with evidence that some function as transcription factors, regulating the expression of particular sets of genes. The 125-residue ALOG domain may be derived from the N-terminal DNA-binding domain (DBD) of viral recombinases and integrases, proteins that rearrange DNA segments (Iyer and Aravind, 2012[3]). One of these proteins, CRE recombinase, has been crystalized bound to DNA (PDB 1crx, Guo et al., 1997[4]) through a core four helix-bundle where three helices interact with DNA through the major groove with a fourth helix located near the C-terminal. Biological assembly of 1crx. ALOG domains in plants also have a four helix bundle but are set apart by a Zinc-Ribbon region inserted between helices 2 and 3 that is proposed to chelate a Zinc ion. An AlphaFold model of GhLSH4L-A0A1U8MC48 predicted a high level of confidence in the ALOG domain region from amino acid 55 to 193, which consists of a bundle of four alpha helices characteristic of ALOG proteins (Iyer and Aravind, 2012[3]). The structure was overlaid with the CRE recombinase DBD (PDB 1crx, red), showing very similar helical arrangement and this overlay allowed DNA (shown in white and grey) to be modeled onto the structure of GhLSH4L-A0A1U8MC48 (pink). Helices 1 and 3 are positioned to form contacts deep in the DNA major groove. The position of DNA binding residues in structural analogs (Iyer and Aravind, 2012[3]) were highlighted in the structure and these residues cluster around the modeled DNA binding site. GhLSH4L-A0A1U8MC48 structure modeled with bound DNA with identified potential DNA binding residues shown in green and Zinc-Ribbon insert shown in blue. Although there is almost no conservation in sequence with CRE recombinase, all these predicted DNA binding residues were highly conserved between the plant orthologs suggesting that they have a distinct DNA recognition site.  The UCSF ChimeraX electrostatic potential tool showed this crevice around the binding site was also highly positive for interaction with the negatively charged DNA backbone (Anionic (-) / Cationic (+)). The conservation of predicted DNA binding residues, electrostatic surface potentials, structural similarity to recombinase DBDs, along with a predicted nuclear localization, support GhLSH4L-A0A1U8MC48 functioning as a transcription factor or a recruiter of chromatin remodeling that binds to DNA and alters gene expression, likely as an important step in early plant development. References
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