Journal:MicroPubl Biol:000670
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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<ref name='Aravind'>PMID: 23146749</ref>). | 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<ref name='Aravind'>PMID: 23146749</ref>). | ||
| - | <scene name='94/945522/Cv/14'>The structure was overlaid with the CRE recombinase DBD</scene> (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<ref name='Aravind'>PMID: 23146749</ref>) were highlighted in the structure and these residues cluster around the modeled DNA binding site. <scene name='94/945522/Cv/13'>GhLSH4L-A0A1U8MC48 structure modeled with bound DNA with identified potential DNA binding residues shown in green and Zinc-Ribbon insert shown in blue</scene>. 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. ConSurf analysis of the conservation of residues in <scene name='94/945522/Cv/17'>GhLSH4L-A0A1U8MC48 showed that residues around the proposed DNA binding site are highly conserved</scene>. Amino acids 28-60 were removed for easier viewing. | + | <scene name='94/945522/Cv/14'>The structure was overlaid with the CRE recombinase DBD</scene> (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<ref name='Aravind'>PMID: 23146749</ref>) were highlighted in the structure and these residues cluster around the modeled DNA binding site. <scene name='94/945522/Cv/13'>GhLSH4L-A0A1U8MC48 structure modeled with bound DNA with identified potential DNA binding residues shown in green and Zinc-Ribbon insert shown in blue</scene>. 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. |
| + | [[Image:Consurf_key_small.gif|left]] ConSurf analysis of the conservation of residues in <scene name='94/945522/Cv/17'>GhLSH4L-A0A1U8MC48 showed that residues around the proposed DNA binding site are highly conserved</scene>. Amino acids 28-60 were removed for easier viewing. | ||
{{Clear}} | {{Clear}} | ||
| - | The UCSF ChimeraX electrostatic potential tool showed this <scene name='94/945522/Cv/16'>crevice around the binding site was also highly positive for interaction with the negatively charged DNA backbone</scene> | + | The UCSF ChimeraX electrostatic potential tool showed this <scene name='94/945522/Cv/16'>crevice around the binding site was also highly positive for interaction with the negatively charged DNA backbone</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_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. |
<b>References</b><br> | <b>References</b><br> | ||
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