Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP.

The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C-C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in the predominantly hydrophobic active-site pocket where it undergoes peroxide radical-mediated heterolysis.

Flavoenzyme catalysed oxidation of amines: roles for flavin and protein-based radicals.

Amines are a carbon source for the growth of a number of bacterial species and they also play key roles in neurotransmission, cell growth and differentiation, and neoplastic cell proliferation. Enzymes have evolved to catalyse these reactions and these oxidoreductases can be grouped into the flavoprotein and quinoprotein families. The mechanism of amine oxidation catalysed by the quinoprotein amine oxidases is understood reasonably well and occurs through the formation of enzyme-substrate covalent adducts with TPQ (topaquinone), TTQ (tryptophan tryptophylquinone), CTQ (cysteine tryptophylquinone) and LTQ (lysine tyrosyl quinone) redox centres. Oxidation of amines by flavoenzymes is less well understood. The role of protein-based radicals and flavin semiquinone radicals in the oxidation of amines is discussed.

Aerobic synthesis of vitamin B12: ring contraction and cobalt chelation.

The aerobic biosynthetic pathway for vitamin B12 (cobalamin) biosynthesis is reviewed. Particular attention is focused on the ring contraction process, whereby an integral carbon atom of the tetrapyrrole-derived macrocycle is removed. Previous work had established that this chemically demanding step is facilitated by the action of a mono-oxygenase called CobG, which generates a hydroxy lactone intermediate. This mono-oxygenase contains both a non-haem iron and an Fe-S centre, but little information is known about its mechanism. Recent work has established that in bacteria such as Rhodobacter capsulatus, CobG is substituted by an isofunctional protein called CobZ. This protein has been shown to contain flavin, haem and Fe-S centres. A mechanism is proposed to explain the function of CobZ. Another interesting aspect of the aerobic cobalamin biosynthetic pathway is cobalt insertion, which displays some similarity to the process of magnesium chelation in chlorophyll synthesis. The genetic requirements of cobalt chelation and the subsequent reduction of the metal ion are discussed.

Evidence from time resolved studies of the P700(.+)/A1(.-) radical pair for photosynthetic electron transfer on both the PsaA and PsaB branches of the photosystem I reaction centre.

Kinetic analysis using pulsed electron paramagnetic resonance (EPR) of photosynthetic electron transfer in the photosystem I reaction centres of Synechocystis 6803, in wild-type Chlamydomonas reinhardtii, and in site directed mutants of the phylloquinone binding sites in C. reinhardtii, indicates that electron transfer from the reaction centre primary electron donor, P700, to the iron-sulphur centres, Fe-S(X/A/B), can occur through either the PsaA or PsaB side phylloquinone. At low temperature reaction centres are frozen in states which allow electron transfer on one side of the reaction centre only. A fraction always donates electrons to the PsaA side quinone, the remainder to the PsaB side.

Site-directed mutagenesis of PsaA residue W693 affects phylloquinone binding and function in the photosystem I reaction center of Chlamydomonas reinhardtii.

To investigate the environment of the phylloquinone secondary electron acceptor A(1) within the photosystem I reaction center, we have carried out site-directed mutagenesis of two tryptophan residues (W693 and W702) in the PsaA subunit of Chlamydomonas reinhardtii. One of these conserved tryptophans (W693) is predicted to be close to the phylloquinone and has been implicated in the interaction of A(1) with an aromatic residue through pi--pi stacking. We find that replacement of W702 with either histidine or leucine has no effect on the electronic structure of A(1)(*-) or on forward electron transfer from A(1)(*-) to the iron--sulfur center F(x). In contrast, the same mutations of W693 alter the electronic structure of the photoaccumulated A(1)(*-) and slow forward electron transfer as measured by the decay of the electron spin-polarized signal arising from the P700(*+)/A(1)(*-) radical pair. These results provide support for the hypothesis that W693 has a role in poising the redox potential of A(1)/A(1)(*-) so it can reduce F(x), and they indirectly provide evidence for electron transfer along the PsaA-side branch of cofactors in PSI.

ENDOR spectroscopic studies of stable semiquinone radicals bound to the Escherichia coli cytochrome bo3 quinol oxidase.

The putative oxidation of ubiquinol by the cytochrome bo3 terminal oxidase of Escherichia coli in sequential one-electron steps requires stabilization of the semiquinone. ENDOR spectroscopy has recently been used to study the native ubisemiquinone radical formed in the cytochrome bo3 quinone-binding site [Veselov, A.V., Osborne, J.P., Gennis, R.B. & Scholes, C.P. (2000) Biochemistry 39, 3169-3175]. Comparison of these spectra with those from the decyl-ubisemiquinone radical in vitro indicated that the protein induced large changes in the electronic structure of the ubisemiquinone radical. We have used quinone-substitution experiments to obtain ENDOR spectra of ubisemiquinone, phyllosemiquinone and plastosemiquinone anion radicals bound at the cytochrome bo3 quinone-binding site. Large changes in the electronic structures of these semiquinone anion radicals are induced on binding to the cytochrome bo3 oxidase. The changes in electronic structure are, however, independent of the electronic structures of these semiquinones in vitro. Thus it is shown to be the structure of this binding site in the protein, not the covalent structure of the bound quinone, that determines the electronic structure of the protein-bound semiquinone.

Reaction of bovine cytochrome c oxidase with hydrogen peroxide produces a tryptophan cation radical and a porphyrin cation radical.

Oxidized bovine cytochrome c oxidase reacts with hydrogen peroxide to generate two electron paramagnetic resonance (EPR) free radical signals (Fabian, M., and Palmer, G. (1995) Biochemistry 34, 13802-13810). These radicals are associated with the binuclear center and give rise to two overlapped EPR signals, one signal being narrower in line width (DeltaHptp = 12 G) than the other (DeltaHptp = 45 G). We have used electron nuclear double resonance (ENDOR) spectrometry to identify the two different chemical species giving rise to these two EPR signals. Comparison of the ENDOR spectrum associated with the narrow signal with that of compound I of horseradish peroxidase (formed by reaction of that enzyme with hydrogen peroxide) demonstrates that the two species are virtually identical. The chemical species giving rise to the narrow signal is therefore identified as an exchange-coupled porphyrin cation radical similar to that formed in horseradish peroxidase compound I. Comparison of the ENDOR spectrum of compound ES (formed by the reaction of hydrogen peroxide with cytochrome c peroxidase) with that of the broad signal indicates that the chemical species giving rise to the broad EPR signal in cytochrome c oxidase is probably an exchange coupled tryptophan cation radical. This is substantiated using H(2)O/D(2)O solvent exchange experiments where the ENDOR difference spectrum of the broad EPR signal of cytochrome c oxidase shows a feature consistent with hyperfine coupling to the exchangeable N(1) proton of a tryptophan cation radical.

ENDOR and special TRIPLE resonance spectroscopy of photoaccumulated semiquinone electron acceptors in the reaction centers of green sulfur bacteria and heliobacteria.

Photoaccumulation at 205 K in the presence of dithionite produces EPR signals in anaerobically prepared membranes from Chlorobium limicola and Heliobacterium chlorum that resemble the EPR spectrum of phyllosemiquinone (A1*-) photoaccumulated in photosystem I. We have used ENDOR and special TRIPLE resonance spectroscopy to demonstrate conclusively that these signals arise from menasemiquinone electron acceptors reduced by photoaccumulation. Hyperfine couplings to two protons H-bonded to the semiquinone oxygens have been identified by exchange of H. chlorum into D2O, and hyperfine couplings to the methyl group, and the methylene group of the phytyl side chain, of the semiquinone have also been assigned. The electronic structure of these menasemiquinones in these reaction centers is very similar to that of phyllosemiquinone in PSI, and shows a distorted electron spin density distribution relative to that of phyllosemiquinone in vitro. Special TRIPLE resonance spectrometry has been used to investigate the effect of detergents and oxygen on membranes of C. limicola. Triton X-100 and oxygen affect the menaquinone binding site, but n-dodecyl beta-D-maltoside preparations exhibit a relatively unaltered special TRIPLE spectrum for the photoaccumulated menasemiquinone.

Photoaccumulation in photosystem I does produce a phylloquinone (A1.-) radical.

Previous work has challenged the assignment of a photoaccumulated EPR signal to the phylloquinone electron acceptor in photosystem I, A1.-. Biosynthetic deuteration of the phylloquinone in the cyanobacterium Anabaena variabilis has been shown to narrow this photoaccumulated signal, demonstrating that the signal arises from A1.-. The ESP signal attributed to P700.+A1.- is also narrowed by this deuteration, showing that the photoaccumulated EPR signal and the ESP signal are monitoring the same redox component. Confirmation that the photoaccumulated EPR signal comes from deuterated phylloquinone was obtained by exchanging the deuterated for protonated phylloquinone, which broadened the photoaccumulated EPR signal.

ENDOR and special triple resonance spectroscopy of A1.- of photosystem 1.

The photoaccumulated radical state of the photosystem 1 secondary electron acceptor A1, A1.-, has been studied in spinach and the cyanobacterium Anabaena variabilis strain Met27 using electron nuclear double resonance (ENDOR) and electron--nuclear--nuclear special triple (ST) resonance spectroscopies. Spectra of A1.- in both these species are very similar. ENDOR spectra of the phylloquinone anion radical in solvent glass were also obtained. Comparison of the spectra of the in vivo and in vitro radicals shows that A1.- is a phylloquinone anion radical with a distorted electron spin density distribution. Hyperfine couplings to the A1.- methyl group and to two protons hydrogen bonded to the quinone oxygens have been identified using biosynthetic deuteration in A. variabilis. Possible hyperfine coupling to a methylene proton of the phytyl side chain of the quinone has also been identified. These results are compared with those from previous studies of protein-bound semiquinones in the light of the unusual redox potential of A1.

ENDOR and special TRIPLE resonance spectroscopy of QA.- of photosystem 2.

ENDOR and special TRIPLE spectroscopies have been used to study the electron spin density distribution and hydrogen bonding of the plastosemiquinone anion radical, QA.-, of photosystem 2. The semiquinone radical was made accessible to ENDOR through the use of exogenous cyanide, which decouples the radical from the ferrous iron of the photosystem 2 ferroquinone acceptor complex [Sanakis, Y., et al. (1994) Biochemistry 33, 9922]. H2O/D2O exchange was used to assign hyperfine couplings to hydrogen-bonded protons, and orientation-selected special TRIPLE spectroscopy has revealed the orientation of hydrogen bonds relative to the quinone ring. Methyl group resonances have also been assigned. ENDOR spectra of the decylplastosemiquinone anion radical in vitro are presented for comparison. This shows that interaction with the protein leads to changes in the electron spin density distribution and the hydrogen bond orientation; both hydrogen bonds are parallel to the quinone ring plane in vitro, whereas QA.- has one parallel and one perpendicular to the plane. These results are discussed in the light of previous ENDOR studies of the ubiquinone radical QA.- of Rhodobacter sphaeroides and the predicted structure of the QA-binding region of photosystem 2.

EPR dating CO2- sites in tooth enamel apatites by ENDOR and triple resonance.

In this work we combine electron paramagnetic resonance (EPR), high-resolution electron nucleus double resonance (ENDOR) and general triple resonance (GTR) spectroscopies, to study the local environment of the CO2- groups created by ionizing radiation in fossil tooth enamel. We demonstrate that the CO2- groups occupy slightly modified phosphate sites in the hydroxyapatite lattice. In quaternary shark enamel we found these groups to be interacting with water molecules in the apatite channels. The absence of water molecules as first neighbors in mammalian samples indicate, however, that these molecules are not significantly responsible for the stabilization of CO2- dating centers in enamel.

The electronic structure of P840+. The primary donor of the Chlorobium limicola f. sp. thiosulphatophilum photosynthetic reaction centre.

The radical cation P840+. was studied in frozen suspensions of Chlorobium limicola f. sp. thiosulphatophilum membranes using ENDOR and Special TRIPLE spectroscopies. The spectra show that P840+. arises from a bacteriochlorophyll a 'special' pair with a highly symmetrical distribution of electron spin density between the constituent bacteriochlorophylls. Special TRIPLE spectroscopy has resolved the separate contributions of the two halves of the pair and revealed small deviations from a 1:1 electron spin density distribution. Nevertheless P840+. appears to come the closest yet to the symmetrical 'dimer' originally proposed for the structure of the primary donor radical cation (P870+.) in purple non-sulphur photosynthetic bacteria.

ENDOR and special triple resonance studies of chlorophyll cation radicals in photosystem 2.

Electron nuclear double resonance (ENDOR) and special triple (ST) resonance spectroscopies have been used to study the cation radicals of the primary donor, P680, and two secondary donor chlorophylls (Chl) in photosystem 2 (PS2). Two different preparations were employed, Tris-washed PS2 membranes and PS2 reaction centers (D1-D2-I-Cytb559 complex). One secondary donor Chl a cation radical, Chl1.+, was generated in the Tris-washed preparation, while the P680.+ radical cation and a further Chl a cation radical, Chl2.+, were produced in the reaction center preparation. The ENDOR spectrum of the primary donor radical cation of photosystem 1 (P700.+) is also presented for comparison. Hyperfine coupling constants for methyl groups have been measured for all three PS2 radical species and assigned by comparison with previously published spectra of Chl a radicals in vitro. Electron spin densities were calculated from these hyperfine couplings. Comparison of ENDOR spectral features with those of Chla.+ in vitro indicates similar values for Chl1.+ and Chl2.+ radicals but an apparent reduction in unpaired electron spin density for P680.+. It has been proposed from the more detailed studies of purple bacterial reaction centers that such a reduction in spin density can be interpreted as a delocalization over two Chl a molecules. Our calculations therefore suggest that P680.+ is a weakly coupled chlorophyll pair with 82% of the unpaired electron spin located on one chlorophyll of the pair at 15 K. Environmental or geometrical changes to the chlorin ring structure to give a novel monomeric primary donor are also possible.(ABSTRACT TRUNCATED AT 250 WORDS)

The dark stable tyrosine radical of photosystem 2 studied in three species using ENDOR and EPR spectroscopies.

The dark stable neutral tyrosine radical YD. of photosystem 2 (PS2) has been studied using electron nuclear double-resonance (ENDOR) and electron paramagnetic resonance (EPR) spectroscopies. The proton hyperfine coupling constants of all four ring protons and both beta-methylene protons have been determined for YD. in three species covering the range of oxygenic organisms; a higher plant (spinach), an alga (Chlamydomonas reinhardtii), and a cyanobacterium (Phormidium laminosum). It has generally been assumed that the properties of Yd. are the same in all oxygenic organisms, while in fact there are small but significant differences. The beta-proton coupling constants are shown to be species dependent while the ring proton coupling constants are not. Estimation of the electron spin density distribution of Yd. from all three organisms has been done. This shows that changes in beta-proton coupling constants in each organism arise from the slightly different orientation of the tyrosine ring, relative to the beta-protons. The electron spin density distribution within the tyrosine ring is organism independent. The variations in the beta-proton coupling constants are reflected in the corresponding EPR spectra, where small variations in line width have been detected. These data delineate the range of natural variation in the spectroscopic properties of YD., and by assigning the features of the ENDOR spectrum, provide a basis for both the unification of studies of YD. in different organisms and the study of YZ.. The results are discussed in relation to data in the recent study (Hoganson & Babcock, 1992) using YD. in the cyanobacterium, Synechocystis PCC 6803.

Spectroscopic studies of the manganese complex of Photosystem II.

Our recent EPR and EXAFS experiments investigating the structure of the oxygen-evolving complex of PS II are discussed. PS II treatments which affect the cofactors calcium and chloride have been used to poise samples in modified forms of the S-states, S1, S2 and S3. X-ray absorption studies indicate a similar overall structure for the manganese complex between treated and native samples although the influence of the treatments and cofactors is observed. Manganese oxidation (or oxidation of a ligand to the manganese cluster) is indicated to occur on each of the transitions S1 →S2 and S2 →S3 in these modified samples. The cluster appears to contain at least two inequivalent Mn-Mn pairs. In the native samples the Mn-Mn distance is 2.7 Å, but in samples where the calcium site is affected, one of the pairs has a 3.0 Å Mn-Mn distance. The intensity of the 3.3/3.6 Å interaction is reduced on sodium chloride treatment (calcium depletion) perhaps indicating calcium binding close to the manganese cluster. From EPR data we also propose that treatments which affect calcium and chloride binding cause a modification of the native S2 state, slow the reduction of Yz (•) and allow an S3 EPR signal to be observed following illumination. The origin of the S3 EPR signal, a modified S3 or S2 X(•) where X(•) is an organic radical of unknown charge, is discussed in relation to the results from the EXAFS studies.

NMR characterization of surface interactions in the cytochrome b5-cytochrome c complex.

The complex formed in solution by native and chemically modified cytochrome c with cytochrome b5 has been studied by 1H and 13C nuclear magnetic resonance spectroscopy (NMR). Contrary to predictions of recent theoretical analysis, 1H NMR spectroscopy indicates that there is no major movement of cytochrome c residue Phe82 on binding to cytochrome b5. The greater resolution provided by 13C NMR spectroscopy permits detection of small perturbations in the environments of cytochrome c residues Ile75 and Ile85 on binding with cytochrome b5, a result that is in agreement with earlier model-building experiments. As individual cytochrome c lysyl residues are resolved in the 1H NMR spectrum of N-acetimidylated cytochrome c, the interaction of this modified protein with cytochrome b5 has been studied to evaluate the number of cytochrome c lysyl residues involved in binding to cytochrome b5. The results of this experiment indicate that at least six lysyl residues are involved, two more than predicted by static model building, which indicates that cytochrome c and cytochrome b5 form two or more structurally similar 1:1 complexes in solution.

A 1H NMR study of bovine cytochrome oxidase. Paramagnetically shifted resonances of haem a.

Dimeric and monomeric forms of mitochondrial cytochrome oxidase (EC 1.9.3.1) have been examined using 1H NMR spectroscopy. Paramagnetically shifted resonances were detected in spectra of the monomeric protein. Studies of this protein in a number of oxidation and ligation states have assigned these resonances to ferrihaem a. The temperature and pH dependence of this new probe of haem a environment is reported.