3AJH
Crystal structure of PcyA V225D-biliverdin XIII alpha complex
Summary for 3AJH
| Entry DOI | 10.2210/pdb3ajh/pdb |
| Related | 3AJG |
| Descriptor | Phycocyanobilin:ferredoxin oxidoreductase, 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy l]-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid (3 entities in total) |
| Functional Keywords | alpha/beta/alpha sandwich, oxidoreductase |
| Biological source | Synechocystis |
| Total number of polymer chains | 2 |
| Total formula weight | 57509.52 |
| Authors | Wada, K.,Hagiwara, Y.,Fukuyama, K. (deposition date: 2010-06-05, release date: 2011-03-16, Last modification date: 2024-03-13) |
| Primary citation | Wada, K.,Hagiwara, Y.,Yutani, Y.,Fukuyama, K. One residue substitution in PcyA leads to unexpected changes in tetrapyrrole substrate binding. Biochem.Biophys.Res.Commun., 402:373-377, 2010 Cited by PubMed Abstract: Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the sequential reduction of the vinyl group of the D-ring and A-ring of biliverdin IXα (BV), using reducing equivalents provided by ferredoxin. This reaction produces phycocyanobilin, a pigment used for light-harvesting and light-sensing in red algae and cyanobacteria. The crystal structure of PcyA-BV reveals that BV is specifically bound in the PcyA active pocket through extensive hydrophobic and hydrophilic interactions. During the course of a mutational study of PcyA, we observed that mutation of the V225 position, apart from the processing sites, conferred an unusual property on PcyA; V225D mutant protein could bind BV and its analog BV13, but these complexes showed a distinct UV-vis absorption spectrum from that of the wild-type PcyA-BV complex. The crystal structures of BV- and BV13-bound forms of V225D protein revealed that gross structural changes occurred near the substrate-binding pocket, and that the BV/BV13 binding manner in the pocket was dramatically altered. Protein folding in V225D-BV/BV13 was more similar to that of substrate-free PcyA than that in PcyA-BV; the "induced-fit" did not occur when BV/BV13 was bound to the V225D protein. The unexpected structural change presented here provides a cautionary note about interpreting functional data derived from a mutated protein in the absence of its exact structure. PubMed: 20946883DOI: 10.1016/j.bbrc.2010.10.037 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.25 Å) |
Structure validation
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