Journal:MicroPubl Biol:000574
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Genomic sequencing of five ''Gossypium'' allopolyploid species, included the two agricultural species of upland (''G. hirsutum'') and Pima (''G. barbadense'') cotton <ref>PMID 32313247</ref>, revealed thousands of encoded uncharacterized proteins that were shared across all five species. Functional characterization of these proteins will contribute to a richer annotation of the cotton genomes and could identify proteins of interest for important agricultural traits. A protein of unknown function (UniProt: A0A1U8MGX4) encoded by gene Gohir.A02G044702.1 in ''Gossypium hirsutum'', was studied using sequence and structure bioinformatic tools leading to a proposed function as a nuclear, DNA-binding B3 transcription factor of the REM subfamily. | Genomic sequencing of five ''Gossypium'' allopolyploid species, included the two agricultural species of upland (''G. hirsutum'') and Pima (''G. barbadense'') cotton <ref>PMID 32313247</ref>, revealed thousands of encoded uncharacterized proteins that were shared across all five species. Functional characterization of these proteins will contribute to a richer annotation of the cotton genomes and could identify proteins of interest for important agricultural traits. A protein of unknown function (UniProt: A0A1U8MGX4) encoded by gene Gohir.A02G044702.1 in ''Gossypium hirsutum'', was studied using sequence and structure bioinformatic tools leading to a proposed function as a nuclear, DNA-binding B3 transcription factor of the REM subfamily. | ||
| - | + | {{Quote box | |
| + | | quote =pLDDT coloring scheme | ||
*Very low (pLDDT < 50) <span class="bg-orange">orange</span> | *Very low (pLDDT < 50) <span class="bg-orange">orange</span> | ||
*Low (70 > pLDDT > 50) <span class="bg-yellow">yellow</span> | *Low (70 > pLDDT > 50) <span class="bg-yellow">yellow</span> | ||
*Confident (90 > pLDDT > 70) <span class="bg-lightcyan">cyan</span> | *Confident (90 > pLDDT > 70) <span class="bg-lightcyan">cyan</span> | ||
*Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | *Very high (pLDDT > 90) <span class="text-blue">'''blue'''</span> | ||
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| + | }}<scene name='91/919077/Cv/3'>An AlphaFold model of the protein predicted a high confidence structure for the DUF313 domain region</scene> of the protein. The region of highest confidence is between residue 111-241 which includes the entire predicted DUF 313. | ||
| - | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone | + | The model structure was used to search for proteins with similar structures using DALI and to visualize surface features such as electrostatic potential and conserved surface-exposed residues that could indicate the location and properties of potential binding sites. <scene name='91/919077/Cv/5'>A structural overlay</scene> of GhB3-A0A1U8MGX4 model (beige ribbon) with an identified structural analog bound to DNA, LEC2 a known DNA-binding B3 transcription factor (violet ribbon and space-filling DNA, PDB [[6j9c]]), showed similar 3D arrangements of secondary structures including the location of N- and C-arm DNA-interacting loops. The overlay also indicated the location of a potential DNA-binding site and this was supported by the surface features within this region. Electrostatic potential on the surface indicated <scene name='91/919077/Cv/6'>positively charged residues surrounding the DNA-binding site</scene> ({{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}) that could interact with the negatively charged DNA backbone. |
| + | [[Image:Consurf_key_small.gif|right]]Mapping of the level of conservation for each residue showed that <scene name='91/919077/Cv/10'>the residues within this site were all highly conserved</scene> among homologs of this protein, as determined by the ConSurf program. | ||
| - | < | + | <span class="bg-yellow"><span class="far fa-hand-point-right"></span> Remember to drag the structures with the mouse to rotate them.</span><br> |
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| + | <b>References</b> | ||
<references/> | <references/> | ||
</StructureSection> | </StructureSection> | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
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