7BJK

Crystal structure of the chloroplastic Fe superoxide dismutase PAP9 from Arabidopsis thaliana.

Summary for 7BJK

• Entry DOI: 10.2210/pdb7bjk/pdb
• Descriptor: Superoxide dismutase [Fe] 2, chloroplastic, ZINC ION (3 entities in total)
• Functional Keywords: iron superoxide dismutase, chloroplast, oxidoreductase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 5
• Total formula weight: 154742.70

Authors

Cobessi, D.,Blanvillain, R.,Pfannschmidt, T. (deposition date: 2021-01-14, release date: 2021-07-07, Last modification date: 2024-01-31)

Primary citation

Favier, A.,Gans, P.,Boeri Erba, E.,Signor, L.,Muthukumar, S.S.,Pfannschmidt, T.,Blanvillain, R.,Cobessi, D.
The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features.
Front Plant Sci, 12:668897-668897, 2021

PubMed Abstract: In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal- geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.

PubMed: 34276730
DOI: 10.3389/fpls.2021.668897

Experimental method

X-RAY DIFFRACTION (2.25 Å)