8JD8
Crystal structure of Citrus limon Cu-Zn superoxide dismutase
Summary for 8JD8
| Entry DOI | 10.2210/pdb8jd8/pdb |
| Descriptor | Superoxide dismutase [Cu-Zn], ZINC ION, COPPER (II) ION, ... (4 entities in total) |
| Functional Keywords | superoxide dismutase, citrus limon, oxidoreductase |
| Biological source | Citrus limon |
| Total number of polymer chains | 4 |
| Total formula weight | 68067.08 |
| Authors | Utami, R.A.,Yoshida, H.,Retnoningrum, D.S.,Ismaya, W.T. (deposition date: 2023-05-12, release date: 2023-12-27, Last modification date: 2024-10-30) |
| Primary citation | Utami, R.A.,Yoshida, H.,Kartadinata, L.H.,Abdillah, V.A.,Faratilla, C.R.,Retnoningrum, D.S.,Ismaya, W.T. Direct relationship between dimeric form and activity in the acidic copper-zinc superoxide dismutase from lemon. Acta Crystallogr.,Sect.F, 79:301-307, 2023 Cited by PubMed Abstract: The copper-zinc superoxide dismutase (CuZnSOD) from lemon (SOD_CL) is active in an acidic environment and resists proteolytic degradation. The enzyme occurs as a dimer, which has an indirect effect on the enzyme activity as the monomer retains only ∼35% of the activity. Here, the crystal structure of SOD_CL at 1.86 Å resolution is reported that may explain this peculiarity. The crystal belonged to space group P2, with unit-cell parameters a = 61.11, b = 74.55, c = 61.69 Å, β = 106.86°, and contained four molecules in the asymmetric unit. The overall structure of SOD_CL resembles that of CuZnSOD from plants. The structure of SOD_CL shows a unique arrangement of surface loop IV that connects the dimer interface and the active site, which is located away from the dimer-interface region. This arrangement allows direct interaction between the residues residing in the dimer interface and those in the active site. The arrangement also includes Leu62 and Gln164, which are conserved in cytoplasmic CuZnSOD. This supports the classification of SOD_CL as a cytoplasmic CuZnSOD despite sharing the highest amino-acid sequence homology with CuZnSODs from spinach and tomato, which are chloroplastic. PubMed: 38108885DOI: 10.1107/S2053230X23010646 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.86 Å) |
Structure validation
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