Journal:MicroPubl Biol:000867
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Sequence analysis of GhCPP1-A0A1U8HKT6 indicated it has a N-terminal chloroplast transit peptide with a cleavage site at amino acid 45 along with four predicted TM regions in the C-terminal half of the protein. A domain architecture was created to visualize these sequence features. Interestingly, Arabidopsis thaliana and Nicotiana benthamiana CPP1 proteins are indicated to contain three, not four, TM regions <ref name="Lee">PMID:24151298</ref>. However, a homolog of Arabidopsis CPP1, At2g20920, has been identified to also contain four TM regions<ref name="Kawai">PMID:24097264</ref> suggesting a potential structural or functional difference between these family members. | Sequence analysis of GhCPP1-A0A1U8HKT6 indicated it has a N-terminal chloroplast transit peptide with a cleavage site at amino acid 45 along with four predicted TM regions in the C-terminal half of the protein. A domain architecture was created to visualize these sequence features. Interestingly, Arabidopsis thaliana and Nicotiana benthamiana CPP1 proteins are indicated to contain three, not four, TM regions <ref name="Lee">PMID:24151298</ref>. However, a homolog of Arabidopsis CPP1, At2g20920, has been identified to also contain four TM regions<ref name="Kawai">PMID:24097264</ref> suggesting a potential structural or functional difference between these family members. | ||
| - | The AlphaFold model structure of GhCPP1-A0A1U8HKT6 depicts two high-confidence modeled domain regions between amino acids 56-119 and 150-254 and a low-confidence modeled region between them from amino acids 119-150. The predicted TM regions are seen as a 4-helix bundle that exhibits expected high hydrophobicity as visualized by the ChimeraX surface calculation tool. The aqueous N-terminal domain is a predicted J-like domain that when overlaid with the J-domain of the human DnaJ family member Tid1 (PDB ID: [[2dn9]]) displays a similar anti-parallel hairpin between the horizontally-displayed alpha helices II and III, although the GhCPP1-A0A1U8HKT6 J-like domain lacks the fourth helix of human Tid1 and has a shorter loop. | + | The <scene name='97/977777/Alphafold_model/1'>AlphaFold model structure of GhCPP1-A0A1U8HKT6</scene> depicts two high-confidence modeled domain regions between amino acids 56-119 and 150-254 and a low-confidence modeled region between them from amino acids 119-150. The predicted TM regions are seen as a 4-helix bundle that exhibits expected high hydrophobicity as visualized by the ChimeraX surface calculation tool. The aqueous N-terminal domain is a predicted J-like domain that when overlaid with the J-domain of the human DnaJ family member Tid1 (PDB ID: [[2dn9]]) displays a similar anti-parallel hairpin between the horizontally-displayed alpha helices II and III, although the GhCPP1-A0A1U8HKT6 J-like domain lacks the fourth helix of human Tid1 and has a shorter loop. |
When DALI <ref name="Holm">PMID:32006276</ref> was used to search for proteins having a similar tertiary structure to the proposed J-like domain of GhCPP1-A0A1U8HKT6, one of the highest similarity hits (Z-score of 7.9 and RMSD score of 1.5) was with the J-like domain of yeast TIM16 that is part of the mitochondrial translocase of the inner membrane protein complex, TIM16/TIM14 (PDB ID: [[2guz]]). The TIM16/TIM14 heterodimer complex serves as a co-chaperone duo, a critical part of the translocase import motor responsible for piloting translocation proteins into the mitochondria<ref name="Mokranjac">PMID:16977310</ref>. As the biosynthesis of chlorophyll in plants requires the light-dependent enzyme POR1 to be post-translationally imported into the chloroplast, it is possible that the J-like domain found in GhCPP1-A0A1U8HKT6 may allow it to partner with an as yet unknown co-chaperone to function similarly to the TIM16/TIM14 complex, chaperoning the translocation of POR1. This is supported by an overlay of the GhCPP1-A0A1U8HKT6 J-like domain (transparent ConSurf colored surface) with the J-like domain of TIM16 (light blue ribbon, PDB [[2guz]]) that shows a conserved surface on GhCPP1-A0A1U8HKT6 at the modeled protein-protein interaction site with the TIM14 protein (dark blue ribbon). | When DALI <ref name="Holm">PMID:32006276</ref> was used to search for proteins having a similar tertiary structure to the proposed J-like domain of GhCPP1-A0A1U8HKT6, one of the highest similarity hits (Z-score of 7.9 and RMSD score of 1.5) was with the J-like domain of yeast TIM16 that is part of the mitochondrial translocase of the inner membrane protein complex, TIM16/TIM14 (PDB ID: [[2guz]]). The TIM16/TIM14 heterodimer complex serves as a co-chaperone duo, a critical part of the translocase import motor responsible for piloting translocation proteins into the mitochondria<ref name="Mokranjac">PMID:16977310</ref>. As the biosynthesis of chlorophyll in plants requires the light-dependent enzyme POR1 to be post-translationally imported into the chloroplast, it is possible that the J-like domain found in GhCPP1-A0A1U8HKT6 may allow it to partner with an as yet unknown co-chaperone to function similarly to the TIM16/TIM14 complex, chaperoning the translocation of POR1. This is supported by an overlay of the GhCPP1-A0A1U8HKT6 J-like domain (transparent ConSurf colored surface) with the J-like domain of TIM16 (light blue ribbon, PDB [[2guz]]) that shows a conserved surface on GhCPP1-A0A1U8HKT6 at the modeled protein-protein interaction site with the TIM14 protein (dark blue ribbon). | ||
Revision as of 14:22, 23 July 2023
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