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/ | + | <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. | ||
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| - | 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. 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. | + | 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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