An unusual conformation of the methionine haem ligand in cytochrome cL established by two-dimensional 1H-NMR

Heme axial methionine fluxion in Pseudomonas aeruginosa Asn64Gln cytochrome c551

Heme axial methionine ligands in ferricytochromes c552 from Hydrogenobacter thermophilus (HT) and Nitrosomonas europaea, both members of the cyt c8 family, display fluxional behavior. The ligand motion, proposed to be inversion at sulfur, results in an unusually small range of hyperfine shifts for heme substituents in these proteins. Herein, heme axial Met fluxion is induced in a structurally homologous cytochrome c551 from Pseudomonas aeruginosa (PA) by substituting heme pocket residue Asn64 with Gln. The mutant, PA-N64Q, displays a highly compressed range of heme substituent hyperfine shifts, temperature-dependent heme methyl resonance line broadening, low rhombic magnetic anisotropy, and a magnetic axes orientation consistent with Met orientational averaging. Analysis of NMR properties of PA-N64Q demonstrates that the heme pocket of the mutant resembles that of HT. This result confirms the importance of peripheral interactions and, in particular, residue 64 in determining axial Met orientation and heme electronic structure in proteins in the cyt c8 family.

Crystal Structures of Cytochrome cL and Methanol Dehydrogenase from Hyphomicrobium denitrificans: Structural and Mechanistic Insights into Interactions between the Two Proteins,

Methanol dehydrogenase (Hd-MDH) and its physiological electron acceptor, cytochrome c(L) (Hd-Cyt c(L)), isolated from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans A3151, have been kinetically and structurally characterized; the X-ray structures of Hd-MDH and Hd-Cyt c(L) have been determined using molecular replacement at 2.5 and 2.0 A resolution, respectively. To explain the mechanism for electron transfer between these proteins, the dependence of MDH activity on the concentration of Hd-Cyt c(L) has been investigated at pH 4.5-7.0. The Michaelis constant for Hd-Cyt c(L) shows the smallest value (approximately 0.3 microM) at pH 5.5. The pseudo-first-order rate constant (k(obs)) of the reduction of Hd-Cyt c(L) exhibits a hyperbolic concentration dependence of Hd-MDH at pH 5.5, although k(obs) linearly increases at pH 6.5. These findings indicate formation of a transient complex between these proteins during an electron transfer event. Hd-MDH (148 kDa) is a large tetrameric protein with an alpha(2)beta(2) subunit composition, showing a high degree of structural similarity with other MDHs. Hd-Cyt c(L) (19 kDa) exhibiting the alpha-band at 550.7 nm has a unique C-terminal region involving a disulfide bond between Cys47 and Cys165. Moreover, there is a pair of Hd-Cyt c(L) monomers related with a pseudo-2-fold axis of symmetry in the asymmetric unit, and the two monomers tightly interact with each other through three hydrogen bonds. This configuration is the first example in the studies of cytochrome c as the physiological electron acceptor for MDH. The docking simulation between the coupled Hd-Cyt c(L) molecules and the heterotetrameric Hd-MDH molecule has been carried out.

Structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c″ from Methylophilus methylotrophus

The crystal structures of the oxidized and reduced forms of cytochrome c" from Methylophilus methylotrophus were solved from X-ray synchrotron data to atomic resolution. The overall fold of the molecule in the two redox states is very similar and is comparable to that of the oxygen-binding protein from the purple phototrophic bacterium Rhodobacter sphaeroides. However, significant modifications occur near the haem group, in particular the detachment from axial binding of His95 observed upon reduction as well as the adoption of different conformations of some protonatable residues that form a possible proton path from the haem pocket to the protein surface. These changes are associated with the previously well characterized redox-Bohr behaviour of this protein. Furthermore they provide a model for one of the presently proposed mechanisms of proton translocation in the much more complex protein cytochrome c oxidase.

Bis-methionine ligation to heme iron in mutants of cytochrome b562. 2. Characterization by NMR of heme-ligand interactions

Previous work has shown that, in variants of cytochrome b562 containing the H102M mutation, methionine residues provide both axial ligands to the heme iron. NMR spectroscopic studies of such bis-methionine-coordinated cytochrome have not previously been feasible, since the only other cytochrome with such a ligand arrangement, bacterioferritin, is too large to be studied by current NMR methods. The present work provides the first NMR characterization of 6-coordinate, bis-methionine-ligated heme centers in both ferrous and ferric oxidation states. We have used one and two dimensional, homonuclear NMR spectroscopy to assign the proton resonances of the heme group and ligand side chains in the reduced, cytochrome b562 variants, H102M and covR98C/H102M. The latter protein has heme covalently attached to the protein, and our results prove that the covalent linkage is a c-type thioether bond formed between the cysteine at residue 98 and the heme 2-vinyl group. Spectra of the ferrous H102M variant are consistent with the presence of two species differing in the orientation of the heme in the protein. We have interpreted results from NOESY experiments on the ferrous covR98C/H102M protein in terms of the conformation of the two methionine side chains, and we present a model for the structure of the heme ligand arrangement. The Met7 side chain adopts an extended conformation almost identical to that observed in the wild type protein with R stereochemistry at the chiral sulfur ligand. The Met102 side chain has a different, buckled side chain conformation and has S stereochemistry at the chiral center. Our NMR derived model is consistent with the spectroscopic data presented in the previous paper. Studies on the ferric forms of these proteins confirm that the double variant at low pH has a "stable" bis-methionine ligation arrangement, but that it is a thermal mixture of species with differing spin states. No hyperfine coupled proton resonances can be identified in spectra of the high-spin forms of either of these proteins.

Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy

The solution of a primary 16S rRNA-binding ribosomal protein, S17, was investigated by two- and three-dimensional homonuclear and heteronuclear magnetic resonance spectroscopy. Almost complete chemical shift assignments for the 1H, 15N, and 13C resonances have been obtained. The NMR data have been rigorously analyzed using a combination of distance geometry, back-calculation, and simulated annealing refinement techniques, and a high-resolution three-dimensional structure has been deduced. The protein consists of a single twisted antiparallel beta-pleated sheet with Greek-key topology. The five beta-strands are connected by extended loops that are flexible compared to the beta-sheet core structure and appear not to adopt one definite conformation in solution. Two of these loops contain many of the residues that have been implicated in binding ribosomal RNA. The location and distribution of these residues and other positively charged side chains on the protein surface suggest an interaction with two distinct regions of ribosomal RNA.