5EJX

X-ray Free Electron Laser Structure of Cytochrome C Peroxidase

Summary for 5EJX

• Entry DOI: 10.2210/pdb5ejx/pdb
• Related: 3M23 3M25 3M26 3M27 3M28 3M29 3M2A 3M2B 3M2C 3M2D 3M2E 3M2F 3M2G 3M2H 3M2I 5EJT
• Descriptor: Cytochrome c peroxidase, mitochondrial, PROTOPORPHYRIN IX CONTAINING FE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 34325.79

Authors

Doukov, T.,Soltis, S.M.,Baxter, E.L.,Cohen, A.,Song, J.,McPhillips, S.,Poulos, T.L.,Meharenna, Y.T.,Chreifi, G. (deposition date: 2015-11-02, release date: 2016-01-20, Last modification date: 2023-09-27)

Primary citation

Chreifi, G.,Baxter, E.L.,Doukov, T.,Cohen, A.E.,McPhillips, S.E.,Song, J.,Meharenna, Y.T.,Soltis, S.M.,Poulos, T.L.
Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer.
Proc.Natl.Acad.Sci.USA, 113:1226-1231, 2016

PubMed Abstract: The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray-generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH.

PubMed: 26787871
DOI: 10.1073/pnas.1521664113

Experimental method

X-RAY DIFFRACTION (1.5 Å)