PDBsum entry 1ft6

Electron transport

PDB id: 1ft6

Contents

Protein chain

208 a.a.

Ligands

SO3

PO4

HEC ×4

DTN

Waters ×142

References listed in PDB file

Key reference

Title

High-Resolution structures of the oxidized and reduced states of cytochrome c554 from nitrosomonas europaea.

Authors

T.M.Iverson, D.M.Arciero, A.B.Hooper, D.C.Rees.

Ref.

J Biol Inorg Chem, 2001, 6, 390-397.

PubMed id

11372197

Abstract

Cytochrome c554 (cyt c554) is a tetra-heme cytochrome involved in the oxidation of NH3 by Nitrosomonas europaea. The X-ray crystal structures of both the oxidized and dithionite-reduced states of cyt c554 in a new, rhombohedral crystal form have been solved by molecular replacement, at 1.6 A and 1.8 A resolution, respectively. Upon reduction, the conformation of the polypeptide chain changes between residues 175 and 179, which are adjacent to hemes III and IV. Cyt c554 displays conserved heme-packing motifs that are present in other heme-containing proteins. Comparisons to hydroxylamine oxidoreductase, the electron donor to cyt c554, and cytochrome c nitrite reductase, an enzyme involved in nitrite ammonification, reveal substantial structural similarity in the polypeptide chain surrounding the heme core environment. The structural determinants of these heme-packing motifs extend to the buried water molecules that hydrogen bond to the histidine ligands to the heme iron. In the original structure determination of a tetragonal crystal form, a cis peptide bond between His129 and Phe130 was identified that appeared to be stabilized by crystal contacts. In the rhombohedral crystal form used in the present high-resolution structure determination, this peptide bond adopts the trans conformation, but with disallowed angles of phi and psi.

Secondary reference #1

Title

Heme packing motifs revealed by the crystal structure of the tetra-Heme cytochrome c554 from nitrosomonas europaea.

Authors

T.M.Iverson, D.M.Arciero, B.T.Hsu, M.S.Logan, A.B.Hooper, D.C.Rees.

Ref.

Nat Struct Biol, 1998, 5, 1005-1012. [DOI no: 10.1038/2975]

PubMed id

9808046

Figure 1.
Figure 1. The oxidation of NH[3] to NO[2]^− by Nitrosomonas europaea. Ammonia is first oxidized to hydroxylamine (NH[2]OH) by ammonia monooxygenase (AMO.) The product, NH[2]OH, is oxidized to NO[ 2]^− by HAO. The released electrons are transferred to cyt c554 (a two electron acceptor) and then possibly to cyt c552 (a one electron acceptor), which ultimately passes electrons to terminal oxidases. The electron transfer pathway following the oxidation of NH[2]OH to NO[2]^− is not fully understood and alternative electron transfer routes may exist^30, including the transfer of electrons from cyt c554 directly to a membrane-bound electron transport chain^31.

Figure 3.
Figure 3. Heme configuration and superposition of heme stacking motifs. a, Inter-heme iron distances and overall heme configuration. Hemes are shown in the same view as in Fig. 2a. b, Overlay of hemes I and III from cyt c554 (red) with hemes 1 and 2 from HAO (teal), hemes 3 and 5 from HAO (magenta), hemes 6 and 7 from HAO (green) and hemes 1 and 2 from the split Soret cytochrome (yellow). The pseudo two-fold axis has been calculated for the hemes of cyt c554 and is shown as a black line. c, Overlay of hemes II and IV from cyt c554 (red) with P460 and 6 of HAO (teal). The 5-coordinate hemes II (cyt c554) and P460 (HAO) are on the right. The pseudo two-fold axis calculated for hemes II and IV of cyt c554 is indicated as a black line. d, Overlay of the two central hemes, hemes III and IV, from cyt c554 with hemes 5 and 6 from HAO (teal), hemes 7 and 8 from HAO (green), hemes 69 and 70 from cyt c551.5 (magenta) and hemes 201 and 203 from cyt c[3] (yellow). e, Stereoview of the overlay of all hemes and surrounding structural elements from cyt c554 (red) with hemes 3−6 of HAO (teal).

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd