Journal:MicroPubl Biol:000669
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The AlphaFold structure model for GhVAB-A0A1U8N485 predicted <scene name='94/945522/Cv/3'>two distinct folding regions with high confidence from Gly111-Arg224 and Gln259-Val366</scene>. The first region (colored in blue), from residues 111-224, consists primarily of four alpha helices and contains most of the DUF828 domain. The second region (in green) contains the PH domain residues 259-366 and consists of a single alpha helix and seven anti-parallel beta sheets. Although VAB proteins are only found in plants, the PH domain structure is found in proteins across kingdoms of life. PH domains often localize to membranes, contain a conserved set of secondary structures and commonly bind phosphatidylinositol phosphates involved in signaling pathways (Le Huray ''et al''., 2022<ref name='Huray'>PMID: 35857458</ref>). From published structures of other PH domains (''Saccharomyces cerevisiae'' Avo1, PDB [[3ulb]] and human protein kinase B/Akt, PDB [[1h10]]), the core of the PH domain is shown to be a seven-stranded anti-parallel beta-sandwich closed at its C-terminus by an alpha-helix. At the N-terminus of this beta-sandwich are three variable loops containing positively charged residues forming a pocket of basic residues that bind negatively-charged phosphoinositides. | The AlphaFold structure model for GhVAB-A0A1U8N485 predicted <scene name='94/945522/Cv/3'>two distinct folding regions with high confidence from Gly111-Arg224 and Gln259-Val366</scene>. The first region (colored in blue), from residues 111-224, consists primarily of four alpha helices and contains most of the DUF828 domain. The second region (in green) contains the PH domain residues 259-366 and consists of a single alpha helix and seven anti-parallel beta sheets. Although VAB proteins are only found in plants, the PH domain structure is found in proteins across kingdoms of life. PH domains often localize to membranes, contain a conserved set of secondary structures and commonly bind phosphatidylinositol phosphates involved in signaling pathways (Le Huray ''et al''., 2022<ref name='Huray'>PMID: 35857458</ref>). From published structures of other PH domains (''Saccharomyces cerevisiae'' Avo1, PDB [[3ulb]] and human protein kinase B/Akt, PDB [[1h10]]), the core of the PH domain is shown to be a seven-stranded anti-parallel beta-sandwich closed at its C-terminus by an alpha-helix. At the N-terminus of this beta-sandwich are three variable loops containing positively charged residues forming a pocket of basic residues that bind negatively-charged phosphoinositides. | ||
| - | When the <scene name='94/945523/Cv/7'>PH domain of human protein kinase B/Akt (in pink) containing a bound phosphatidylinositol trisphosphate ligand (shown in ball-in-sticks; PDB [[1h10]]) was overlaid with the GhVAB-A0A1U8N485 PH domain (in orange)</scene>, a deep binding pocket accommodating the phosphoinositide ligand was observed in the structure. Indeed, <scene name='94/945523/Cv/9'>this GhVAB-A0A1U8N485 binding pocket is lined with positively-charged amino acids that could interact with the negatively-charge phosphate groups</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) and <scene name='94/945523/Cv/14'>residues within this pocket are highly-conserved based on ConSurf analysis</scene>.[[Image:Consurf_key_small.gif| | + | When the <scene name='94/945523/Cv/7'>PH domain of human protein kinase B/Akt (in pink) containing a bound phosphatidylinositol trisphosphate ligand (shown in ball-in-sticks; PDB [[1h10]]) was overlaid with the GhVAB-A0A1U8N485 PH domain (in orange)</scene>, a deep binding pocket accommodating the phosphoinositide ligand was observed in the structure. Indeed, <scene name='94/945523/Cv/9'>this GhVAB-A0A1U8N485 binding pocket is lined with positively-charged amino acids that could interact with the negatively-charge phosphate groups</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) and <scene name='94/945523/Cv/14'>residues within this pocket are highly-conserved based on ConSurf analysis</scene>. |
| + | [[Image:Consurf_key_small.gif|left]] | ||
| + | {{Clear}} | ||
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| + | A structure-based alignment between GhVAB-A0A1U8N485 and human protein kinase B/Akt indicated that two of the five ligand-binding residues in B/Akt are completely conserved in GhVAB-A0A1U8N485, with two others being conservative substitutions (Thomas ''et al''., 2002<ref name='Thomas'>PMID: 12176338</ref>). Evidence from sequence and structure features support that GhVAB-A0A1U8N485 is part of the VAN3-binding protein family. Furthermore, based on functional reports of other VAN3-binding proteins as well as structural analysis of our protein, GhVAB-A0A1U8N485 might be involved in regulating leaf size or vein development in cotton plants by binding phosphoinositides as part of an auxin signaling pathway. | ||
<b>References</b><br> | <b>References</b><br> | ||
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