7BI1
XFEL crystal structure of soybean ascorbate peroxidase compound II
Summary for 7BI1
Entry DOI | 10.2210/pdb7bi1/pdb |
Descriptor | Ascorbate peroxidase, PROTOPORPHYRIN IX CONTAINING FE, POTASSIUM ION, ... (4 entities in total) |
Functional Keywords | intermediates, heme protein, oxidoreductase |
Biological source | Glycine max (Soybean) |
Total number of polymer chains | 1 |
Total formula weight | 29017.49 |
Authors | Kwon, H.,Tosha, T.,Sugimoto, H.,Raven, E.L.,Moody, P.C.E. (deposition date: 2021-01-12, release date: 2021-04-21, Last modification date: 2024-01-31) |
Primary citation | Kwon, H.,Basran, J.,Pathak, C.,Hussain, M.,Freeman, S.L.,Fielding, A.J.,Bailey, A.J.,Stefanou, N.,Sparkes, H.A.,Tosha, T.,Yamashita, K.,Hirata, K.,Murakami, H.,Ueno, G.,Ago, H.,Tono, K.,Yamamoto, M.,Sawai, H.,Shiro, Y.,Sugimoto, H.,Raven, E.L.,Moody, P.C.E. XFEL Crystal Structures of Peroxidase Compound II. Angew.Chem.Int.Ed.Engl., 60:14578-14585, 2021 Cited by PubMed Abstract: Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an Fe =O or Fe -OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated Fe =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme. PubMed: 33826799DOI: 10.1002/anie.202103010 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
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