Three-Dimensional Structure of Cytochrome c' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures

Abstract

The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution 1 1Edited by R. Huber

“…Helix directions within the subunit bundles resemble those found in other proteins (e.g. myohemerythrin and hemerythrin, Sheriff et al, 1987;Stenkamp et al, 1985; cytochrome c H , Dobbs et al, 1996). However, the helix connectivities are different, with the two helix pairs A, B and C,D being connected by the long BC loop which joins opposite ends of the bundle to give an up-down-downup arrangement (Figure 1) instead of the classical up-down-up-down in which the positions of helices C and D are reversed.…”

The pH Dependent Protein Structure Transitions and Related Spin-State Transition of Cytochrome c′ from Alcaligenes xylosoxidans NCIMB 11015

“…The imidazole group of the heme ligand (His120) is exposed to solvent, and the N δ H makes a hydrogen bond with water in the structure of AxCyt c¤ and other Cyt c¤ species. 12,31,58 The correlation between the imidazoleH 2 O interaction and Fe(III) heme oxidation states has been reported. 57 The H 2 O molecule forming the hydrogen bond with His120 would become OH ¹ at alkaline pH in AxCyt c¤.…”

“…The protein structure of Cyt c¤ is well known to be a head-to-tail dimer with two identical 14 kDa protomers. 12 The unusual magnetic properties of the Fe(III) heme in Cyt c¤ at neutral pH have been explained as a quantum mechanical admixture of an intermediate-spin (S = 3/2) and a high-spin (S = 5/2) states. 1315 The pH and ionic strength dependences of the Fe(III) spin states of Cyt c¤ have been characterized, 16 but the origin for the pH dependent spin-state transitions have not been identified to date.…”

Conformational control of the binding of diatomic gases to cytochrome c′

“…CYTcps have been classified into two groups based on the nature of their distal heme pockets [6][7][8]. Group 1 CYTcps, including those from Rhodobacter capsulatus (RCCP) and Chromatium vinosum (CVCP), possess an aromatic residue (Phe or Tyr) above the distal heme coordination site.…”