The amino acid sequence of Nitrosomonas europaea cytochrome c-552

The complete amino acid sequence of cytochrome c-552 derived from the chemoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea was determined. The cytochrome consisted of 81 amino acid residues, and its molecular weight was calculated to be 9098 including heme c. Although the sequence of cytochrome c-552 was highly homologous to those of cytochromes c-551, which were known as the electron-donating components to dissimilatory nitrite reductase in pseudomonads, cytochrome c-552 differed from cytochrome c-551 in two points: (1) the sequence of cytochrome c-552 was shorter by two amino acid residues than that of cytochrome c-551 at the N-terminus and (2) one amino acid insertion was present in cytochrome c-552.     

Primary sequence and solution conformation of ferrocytochrome c-552 from Nitrosomonas europaea.

Cytochrome c-552 from Nitrosomonas europaea is a 9.1-kDa monoheme protein that is a member of the bacterial cytochrome c-551 family. The gene encoding for c-552 has been cloned and sequenced and the primary sequence of the product deduced. Proton resonance assignments were made for all main-chain and most side-chain protons in the diamagnetic, reduced form by two-dimensional NMR techniques. Distance constraints (1056) were determined from nuclear Overhauser enhancements, and torsion angle constraints (88) were determined from scalar coupling estimates. Solution conformations for the protein were computed by the hybrid distance geometry-simulated annealing approach. For 20 computed structures, the root mean squared deviation from the average position of equivalent atoms was 0.84 A (sigma = 0.12) for backbone atoms over all residues. Analysis by residue revealed there were three regions clearly less well defined than the rest of the protein: the first two residues at the N-terminus, the last two at the C-terminus, and a loop region from residues 34 to 40. Omitting these regions from the comparison, the root mean squared deviation was 0.61 A (sigma = 0.13) for backbone atoms, 0.86 A (sigma = 0.12) for all associated heavy atoms, and 0. 43 A (sigma = 0.17) for the heme group. The global folding of the protein is consistent with others in the c-551 family. A deletion at the N-terminus relative to other family members had no impact on the global folding, whereas an insertion at residue 65 did affect the way the polypeptide packs against the methionine-ligated side of the heme. The effects of specific substitutions will be discussed. The structure of c-552 serves to delineate essential features of the c-551 family.     

The purification and amino acid sequence of cytochrome c-552 from Euglena gracilis

Cytochrome c-552 from Euglena gracilis was purified and the amino acid sequence determined. The protein is a single peptide chain of 87 residues with the haem prosthetic group bound through two thioether linkages to two cysteine residues near the amino-terminal region. The amino acid sequence shows some similarities to mitochondrial cytochrome c and to two prokaryote c-type cytochromes. The sequence, taken with the known characteristics of cytochrome c-552, indicates that it is an f-type cytochrome. The possible functional and evolutionary significance of these features in common is discussed. Detailed evidence for the amino acid sequence of Euglena cytochrome f has been deposited as Supplementary Publication SUP 50027 at the British Library, Lending Division (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7QB, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973) 131, 5.     

Amino acid sequence of cytochrome c-552 from Thermus thermophilus HB8

The complete amino acid sequence of thermophilic cytochrome c-552 from Thermus thermophilus HB8 is presented. The 131-residue sequence was derived by analysis of three cyanogen bromide fragments of the S-carboxymethylated apo-protein and their subpeptides. The sequence is homologous to c-type cytochromes, especially in the heme-binding region.     

Localization and concentration of hydroxylamine oxidoreductase and cytochromes c-552, c-554, cm-553, cm-552 and a in Nitrosomonas europaea

Two membrane-associated cytochromes, cytochrome c_m-553 and cytochrome c_m-552, were derived from Nitrosomonas europaea. The major c-type cytochrome, cytochrome c_m-553, accounted for 92% of the c heme found in the membrane. It had absorption maxima at 410 nm in the oxidized form and at 417, 523 and 553 nm in the dithionite reduced form. Cytochrome c_m-552 possessed absorption maxima at 409 nm in the oxidized form, at 421, 522 and 552 in the dithionite reduced form, and at 418 in the dithionite reduced plus CO form. The concentration and cellular distribution of the two c-type membrane cytochromes, hydroxylamine oxidoreductase and cytochromes c-552, c-554, and a were determined. Over 95% of the soluble cytochromes (hydroxylamine oxidoreductase cytochromes and c-552 and c-554) were periplasmic, whereas cytochrome c_m-553, cytochrome c_m-552 and cytochrome a were associated with the cell membrane. The outer membrane and cytoplasm were devoid of cytochromes. The extracytoplasmic location of the proton-yielding hydroxylamine oxidizing system (NH₂OH ™ HNO + 2H⁺ + 2e⁻) may contribute to an energy-linked proton gradient. The heme concentrations of hydroxylamine oxidoreductase and cytochromes c-552, c-554, c_m-553, c_m-552 and a were approx. 2.4, 1.2, 0.3, 1.3, 0.1 and 1.1 nmol/mg cell protein, respectively. The corresponding molar ratios of heme were 22:11:2.9:12:1.0:10. The enzyme or cytochrome concentrations for hydroxylamine oxidoreductase and cytochromes c-552, c-554, c_m-553, c_m-552 and a were approx. 0.13, 1.05, 0.09, 0.63, 0.055 and 0.56 nmol/mg cell protein, respectively. The corresponding molar ratios were 0.24:2.2:0.16:1.2:0.1:1.0.     

Amino acid sequence of cytochrome c-552 from a thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus.

The complete amino acid sequence of cytochrome c-552 from an extremely thermophilic hydrogen bacterium, Hydrogenobacter thermophilus TK-6 (IAM 12695), was determined. It is a single polypeptide chain of 80 residues, and its molecular weight, including heme, was calculated to be 7,599. The sequence of cytochrome c-552 from H. thermophilus TK-6 closely resembles that of cytochromes c-551 from Pseudomonas species. Moreover, the tertiary structure of Hydrogenobacter cytochrome c-552 is suggested to be similar to that of cytochrome c-551 from Pseudomonas aeruginosa. The sequence similarity between Hydrogenobacter cytochrome c-552 and that of other bacteria physiologically related to H. thermophilus is not high.     

Conformational change accompanies redox reactions of the tetraheme cytochrome c-554 of Nitrosomonas europaea

Cytochrome c-554 of the ammonia-oxidizing chemolithoautotropic bacteria is thought to mediate electron transfer from hydroxylamine oxidoreductase to a terminal oxidase and/or to ammonia monooxygenase. The cytochrome has four c hemes which interact magnetically and have the same redox potential. We report that the kinetics of reduction of ferric cytochrome c-554 by dithionite or the oxidation of ferrous cytochrome c-554 by O2 or H2O2 are complex and multiphasic. Transient rapid-scan difference spectra indicate discrete maxima at approximately 418 nm, 425 nm and 432 nm. Absorbance changes at all three difference maxima appear to occur in all kinetic phases, although not in equal amounts for each wavelength. Reduction by 20 mM dithionite was biphasic. At pH 7.5 the first phase, which involved approximately 50% of the total absorbance change, had a rate constant (20 degrees C) of 140 s-1 and energy of activation of 20 kJ X mol-1. The slow phase had a rate constant 0.43 s-1 and a relatively high energy of activation, 87 kJ X mol-1, suggesting that a change in protein configuration accompanied the reaction. As the pH of the solution increased, the rate constant for both phases decreased and the fraction of absorbance change in the rapid phase increased. Oxidation of ferrous cytochrome c-554 by O2 involved a discrete rapid phase with a rate constant of 14 s-1, accounting for 6% of the absorbance. The remainder of the reaction was multiphasic with rate constants in the range 0.1-0.01 s-1. With H2O2 as the oxidant, the rapid phase involved 39% of the change in absorbance with a rate constant of 19 s-1. The remainder of the reoxidation was multiphasic with rate constants ranging over 0.4-0.01 s-1.     

The complete amino acid sequence of Nitrobacter agilis cytochrome c-550

The amino acid sequence of cytochrome c-550 from the chemoautotroph, Nitrobacter agilis, was completed by using solid-phase sequencing and conventional procedures. The cytochrome was composed of 109 amino acid residues and its molecular weight was calculated to be 12375 including haem c. The cytochrome was homologous to eukaryotic cytochromes c and some photosynthetic bacterial cytochromes c2. In particular, its primary structure was very similar to that of Rhodopseudomonas viridis cytochrome c2. Some of its properties were compared with those of other cytochromes c on the basis of the primary structure.     

The amino acid sequence of cytochrome c-556 from Agrobacterium tumefaciens strain Apple 185

The evidence for the amino acid sequence of cytochrome c-556 from Agrobacterium tumefaciens strain Apple 185 is reported. The sequence was determined by manual Edman degradation of tryptic and chymotryptic peptides using the DABITC/PITC double-coupling method; some peptides were further cleaved by partial acid hydrolysis and with Staphylococcus aureus protease. The sequence overlaps 13-15, 83-85 and 106-108 as well as the region 113-118 involving the haem-binding sequence Cys-Xaa-Xaa-Cys-His were deduced by homology with cytochrome c-556 from Agrobacterium tumefaciens strain B2a. The identity of histidine at position 6 has been inferred from fast-atom bombardment experiments on the N-terminal tryptic peptide, and Asp-63 was deduced from the electrophoretic mobility of the peptides in which it occurs. The cytochrome from A. tumefaciens Apple 185 contains 125 amino acids of which 71 are identical in the protein from strain B2a. Together with cytochrome c-556 from the photosynthetic prokaryote Rhodopseudomonas palustris strain 2.1.37, the presently studied protein is the third known example of a monohaem class II cytochrome of the low-spin type having the single haem group covalently linked near the C terminus of the polypeptide chain. The only methionine residue in the Apple protein, methionine-13, is the most likely candidate to be the sixth haem ligand and therefore to be responsible for the low-spin character of the haem iron.     

The amino acid sequence of cytochrome c-555 from the methane-oxidizing bacterium Methylococcus capsulatus.

The amino acid sequence of the cytochrome c-555 from the obligate methanotroph Methylococcus capsulatus strain Bath (N.C.I.B. 11132) was determined. It is a single polypeptide chain of 96 residues, binding a haem group through the cysteine residues at positions 19 and 22, and the only methionine residue is a position 59. The sequence does not closely resemble that of any other cytochrome c that has yet been characterized. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50131 (12 pages) at the British Library Lending Division, Boston Spa, West Yorkshire LS23 7BQ, U.K., from whom copies are available on prepayment.     

Catalytic properties of cytochrome c oxidase purified from Nitrosomonas europaea

Cytochrome c oxidase of Nitrosomonas europaea reacts with not only the native cytochrome c (N. europaea cytochrome c-552) but also horse and yeast cytochromes c. The effects on its reactivity of various reagents were very different between the reactions with the native and eukaryotic cytochromes c as the electron donors. The oxidation of eukaryotic ferrocytochrome c by the oxidase was activated by addition of anionic detergents such as sodium dodecyl sulfate and sodium cholate, and anionic phospholipids such as cardiolipin, phosphatidylserine, phosphatidylinositol, and phosphatidylethanolamine, while the reaction was not activated by Triton X-100, Tween 20, or phosphatidylcholine. However, the reaction with the native cytochrome c of the enzyme was hardly affected by any of the detergents and phospholipids mentioned above, while it was activated by the presence of poly-L-lysine.     

Secondary transport of amino acids in Nitrosomonas europaea

Nitrosomonas europaea is capable of incorporating exogenously supplied amino acids. Studies in whole cells revealed that at least eight amino acids are actively accumulated, probably by the action of three different transport systems, each with high affinity ( molar range) for several amino acids. Evidence for the action of secondary mechanisms of transport was obtained from efflux, counterflow and exchange experiments. More detailed information was obtained from studies in liposomes in which solubilized integral membrane proteins of N. europaea were incorporated. Uptake of l-alanine in these liposomes could be driven by artificially imposed pH gradients and electrical potentials, but not by chemical sodium-ion gradients. These observations indicate that l-alanine is transported by a H⁺/alanine symport system. The ecological significance of secondary amino acid transport systems in autotrophic ammonium-oxidizing bacteria is discussed.