PDBsum entry 2c1v

Oxidoreductase

PDB id: 2c1v

Contents

Protein chains

335 a.a.

Ligands

HEC ×4

EDO ×4

Metals

_CA ×2

Waters ×1055

References listed in PDB file

Key reference

• Title: Activation and catalysis of the di-Heme cytochrome c peroxidase from paracoccus pantotrophus.
• Authors: A.Echalier, C.F.Goodhew, G.W.Pettigrew, V.Fülöp.
• Ref.: Structure, 2006, 14, 107-117. [DOI no: 10.1016/j.str.2005.09.011]
• PubMed id: 16407070

Abstract

Bacterial cytochrome c peroxidases contain an electron transferring (E) heme domain and a peroxidatic (P) heme domain. All but one of these enzymes are isolated in an inactive oxidized state and require reduction of the E heme by a small redox donor protein in order to activate the P heme. Here we present the structures of the inactive oxidized and active mixed valence enzyme from Paracoccus pantotrophus. Chain flexibility in the former, as expressed by the crystallographic temperature factors, is strikingly distributed in certain loop regions, and these coincide with the regions of conformational change that occur in forming the active mixed valence enzyme. On the basis of these changes, we postulate a series of events that occur to link the trigger of the electron entering the E heme from either pseudoazurin or cytochrome c(550) and the dissociation of a coordinating histidine at the P heme, which allows substrate access.

Figure 3.
Figure 3. The Domain Interface and Heme Binding Sites of Pap Cytochrome c Peroxidase
(A) Domain interface of the oxidized Pap CCP looking down at the noncrystallographic 2-fold axis. Color code is the same as used in Figure 1 and Figure 2. The hemes, the calcium ion, and some key residues in the Pap structures are in ball-and-stick representation.
(B) Domain interface of the mixed valence form Pap CCP shown as in Figure 3A.
(C) Close view of the peroxidatic heme site and dimer interface of the mixed valence form of Pap CCP. The loop carrying His85 moves away to the interface of the homodimer. This structure is stabilized by p-stacking interaction between the aromatic side chain of Trp87 and the peptide bond of Gly72 of the opposite chain (labeled as G72B). The peroxide binding site is occupied by a water molecule, which is hydrogen bonded to Gln118 and Glu128. The corresponding residues in the oxidized form are shown in red.
(D) Stereoview of the electron-transferring heme of the mixed valence form of Pap CCP. The propionate D group of the heme undergoes a conformational change upon reduction and loses the interaction with the main chain amide of Leu230. The corresponding conformation in the oxidized form is shown in red. The SIGMAA (Read, 1986) weighted 2mF[o] - DF[c] electron density using phases from the final model of the half-reduced form is contoured at 1.5 s level, where s represents the rms electron density for the unit cell. Contours more than 1.4 Å from any of the displayed atoms have been removed for clarity. Thin lines indicate hydrogen bonds.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 107-117) copyright 2006.