Journal:MicroPubl Biol:000669
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| - | <StructureSection load='' size='450' side='right' scene=' | + | <StructureSection load='' size='450' side='right' scene='94/945522/Cv/1' caption=''> |
| - | ===Gossypium hirsutum gene Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site=== | + | ===''Gossypium hirsutum'' gene Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site=== |
| - | <big> | + | <big>Emma R. Smith, Lauryn R. Caulley, Amanda M. Hulse-Kemp, Amanda R Storm, Angela K. Stoeckman</big> <ref>doi: 10.17912/micropub.biology.000669</ref> |
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<b>Molecular Tour</b><br> | <b>Molecular Tour</b><br> | ||
| + | Based on our analyses, the uncharacterized ''Gossypium hirsutum'' protein (UniProt A0A1U8N485; NCBI XP_016732659) here referred to as GhVAB-A0A1U8N485, identified as a gene of unknown function in cotton species (Chen ''et al''., 2020<ref name='Chen'>PMID: 32313247</ref>), contains two domains: a VAN3-binding protein-like, auxin canalisation domain (domain of unknown function, DUF828) and a pleckstrin homology (PH) domain. The specific function of these domains is unknown but they are often found together in proteins of the VAN3-binding (VAB) protein family, also known as the FORKED-like (FL) family. It is proposed that members of this plant-specific family in Arabidopsis are involved in aiding asymmetrical localization of PIN1 (PINFORMED) an auxin transport protein responsible for establishing vein patterns and numbers in leaves (Hou ''et al''., 2010<ref name='Hou'>PMID: 20626652</ref>). GhVAB-A0A1U8N485 is most similar in sequence to the Group 3 FL proteins in Arabidopsis, FL5-7, which appear to be localized to the Golgi apparatus and decrease leaf size when mutated. | ||
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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. | ||
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| + | 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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