1ZBY

High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP)

Summary for 1ZBY

• Entry DOI: 10.2210/pdb1zby/pdb
• Related: 1KOK 1Z53 1ZBZ 2CYP
• Descriptor: Cytochrome c peroxidase, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: ccp, heme peroxidase, resting state, trp-cation radical, high-spin heme, oxidoreductase
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Mitochondrion matrix: P00431
• Total number of polymer chains: 1
• Total formula weight: 34187.72

Authors

Bonagura, C.A.,Bhaskar, B.,Shimizu, H.,Li, H.,Sundaramoorthy, M.,McRee, D.E.,Goodin, D.B.,Poulos, T.L. (deposition date: 2005-04-09, release date: 2005-05-03, Last modification date: 2023-10-25)

Primary citation

Bonagura, C.A.,Bhaskar, B.,Shimizu, H.,Li, H.,Sundaramoorthy, M.,McRee, D.E.,Goodin, D.B.,Poulos, T.L.
High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase
Biochemistry, 42:5600-5608, 2003

PubMed Abstract: Cytochrome c peroxidase (CCP) is a 32.5 kDa mitochondrial intermembrane space heme peroxidase from Saccharomyces cerevisiae that reduces H(2)O(2) to 2H(2)O by oxidizing two molecules of cytochrome c (cyt c). Here we compare the 1.2 A native structure (CCP) with the 1.3 A structure of its stable oxidized reaction intermediate, Compound I (CCP1). In addition, crystals were analyzed by UV-vis absorption and electron paramagnetic resonance spectroscopies before and after data collection to determine the state of the Fe(IV) center and the cationic Trp191 radical formed in Compound I. The results show that X-ray exposure does not lead to reduction of Fe(IV) and only partial reduction of the Trp radical. A comparison of the two structures reveals subtle but important conformational changes that aid in the stabilization of the Trp191 cationic radical in Compound I. The higher-resolution data also enable a more accurate determination of changes in heme parameters. Most importantly, when one goes from resting state Fe(III) to Compound I, the His-Fe bond distance increases, the iron moves into the porphyrin plane leading to shorter pyrrole N-Fe bonds, and the Fe(IV)-O bond distance is 1.87 A, suggesting a single Fe(IV)-O bond and not the generally accepted double bond.

PubMed: 12741816
DOI: 10.1021/bi034058c

Experimental method

X-RAY DIFFRACTION (1.2 Å)