How a protein generates a catalytic radical from coenzyme B12: X-ray structure of a diol-dehydratase–adeninylpentylcobalamin complex

Masuda, Jun; Shibata, Naoki; Morimoto, Yukio; Toraya, Tetsuo; Yasuoka, Noritake

doi:10.1016/s0969-2126(00)00164-7

Cited by 139 publications

(268 citation statements)

References 53 publications

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“…Such a rotation mechanism for propagation of the radical was proposed earlier by Toraya and co-workers based on the crystal structure of the enzyme from K. oxytoca (44). The two positions of the anhydroadenosyl radical observed in the presence and absence of substrate in the current study provides direct evidence in support of this rotation mechanism.…”

Section: Discussionsupporting

confidence: 86%

“…A) The distance between C5′ and Co 2+ is 3.5 Å. The position of the adenine ring is very similar to that observed in the crystal structure of the DDH-adeninylpentylcobalamin complex (RMSD, 0.67 Å) (44). B) The distance between C5′ and Co 2+ is 4.1 Å.…”

Section: Discussionsupporting

confidence: 75%

“…The starting coordinates for the analysis were obtained by placing the geometry optimized cob (II)alamin fragment and the adenine ring of the anhydroadenosyl radical in the positions observed in the crystal structure of DDH complexed with adeninylpentylcobalamin (44). The position of the anhydroribosyl moiety was varied by rotation about the glycosidic bond and small overall rotations and translations of the anhydroadenosyl radical were performed to find the best match of the experimentally observed and calculated ZFS tensors in the global minimization.…”

Section: Analysis and Decomposition Of The Zfs Tensormentioning

confidence: 99%

“…The structure corresponding to the minimum in the analysis is not necessarily unique in its ability to reproduce the ZFS tensor. However, it represents the structure that best reproduces the ZFS tensor and while minimizing changes in the geometry from that expected from the crystallographic data (44).…”

Section: Analysis and Decomposition Of The Zfs Tensormentioning

confidence: 99%

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Analysis of the Cob(II)alamin−5‘-Deoxy-3‘,4‘-anhydroadenosyl Radical Triplet Spin System in the Active Site of Diol Dehydrase

et al. 2006

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A triplet spin system (S = 1) is detected by low-temperature electron paramagnetic resonance (EPR) spectroscopy in samples of diol dehydrase and the functional adenosylcobalamin (AdoCbl) analog 5′-deoxy-3′,4′-anhydroadenosylcobalamin (anAdoCbl). Different spectra are observed in the presence and absence of the substrate (R,S)-1,2-propanediol. In both cases, the spectra include a prominent half-field transition (ΔM S = 2) that is a hallmark of strongly-coupled triplet spin systems. The appearance of 59 Co-hyperfine splitting in the EPR signals as well as the positions (g-values) of the signals in the spectra show that half of the triplet spin is contributed by the low spin Co 2+ of cob (II)alamin. Linewidth effects from isotopic labeling ( 13 C and 2 H) in the 5′-deoxy-3′,4′-anhydroribosyl ring demonstrate that the other half of the spin triplet is from an allylic 5′-deoxy-3′, 4′-anhydroadenosyl (anhydroadenosyl) radical. The zero-field splitting (ZFS) tensors describing the magnetic dipole-dipole interactions of the component spins of the triplets have rhombic symmetry because of electron spin delocalization within the organic radical component and nearness of the radical to the low spin Co 2+ . The dipole-dipole interaction was modeled as a summation of pointdipole interactions involving the spin-bearing orbitals of the anhydroadenosyl radical and cob(II) alamin. Geometries which are consistent with the ZFS tensors in the presence and absence of substrate position the 5′-carbon of the anhydroadenosyl radical 3.5 Å and 4.1 Å and from Co 2+ , respectively. Homolytic cleavage of the cobalt-carbon bond of the analog in the absence of substrate indicates that, in diol dehydrase, binding of the coenzyme to the protein weakens the bond prior to binding of substrate.A common characteristic of AdoCbl 1 -dependent enzymes is the generation and utilization of enzyme-bound organic radicals (1-3). The Co-C5′ bond of AdoCbl is relatively weak having a bond dissociation energy of ~ 30 kcal mol −1 (4). A prevalent mechanism for AdoCbldependent enzymes begins with the homolytic cleavage of the Co-C5′ bond to give cob(II) alamin and the 5′-deoxyadenosyl radical (1). The 5′-deoxyadenosyl radical being an unstabilized, primary alkyl radical is expected to have a short lifetime, low concentration, and a high reactivity towards H atom abstraction. Thus far, these properties of the 5′-deoxyadenosyl radical have precluded direct observation of the radical by EPR spectroscopy.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionsupporting

confidence: 75%

Section: Analysis and Decomposition Of The Zfs Tensormentioning

confidence: 99%

Section: Analysis and Decomposition Of The Zfs Tensormentioning

confidence: 99%

See 2 more Smart Citations

Analysis of the Cob(II)alamin−5‘-Deoxy-3‘,4‘-anhydroadenosyl Radical Triplet Spin System in the Active Site of Diol Dehydrase

et al. 2006

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“…This is in contrast to ‘organometallic’ sites, which contain bonds between metals and C atoms. Organometallic bonds are rarely observed in biological macromolecules in nature, although there are a few important examples such as cyanocobalamin (Masuda et al , 2000) and enzymes catalyzing reactions with carbon monoxide (Carlsson et al , 2005). The atomic ligands analyzed in our work are strongly electronegative (N, O, F, S, Cl and Br) and were chosen partly owing to their biological relevance.…”

Section: Introductionmentioning

confidence: 99%

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Zheng

Langner

Shields

et al. 2017

Acta Crystallogr D Struct Biol

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The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal–organic bond-valence parameters. R0 bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R0 bond-valence parameters were reproduced, except for iron–nitrogen bonds, for which distinct R0 parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.

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Cation‐Activated Enzymes

Glusker

2005

Encyclopedia of Inorganic Chemistry

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Cation‐activated enzymes are those that require a cation for maximal activity but which still have some activity in the absence of the cation, that is, the activating cation is not an essential part of the enzyme mechanism. The cations involved are generally metal or ammonium ions. The metal ions used are generally Na + , K + , Mg 2+ , or Ca 2+ , those that are abundant in nature. In the last 10 years, many crystal structures of cation‐activated enzymes have been determined and, in these studies, potassium is the most common activating cation. The geometry of binding and possible conclusions about this activity are the subject of this review. Chosen for description are thrombin (a sodium‐activated enzyme), pyruvate kinase, dialkylglycine decarboxylase, diol dehydrase, inosine monophosphate dehydrogenase, and tryptophanase (all potassium‐activated enzymes), and alkaline phosphatase (a magnesium‐activated enzyme). In some enzymes, the activating cation is near the active site, but in others it is distant. This implies that its function in these two possibilities involves the modification of the charge distribution in the reaction center or else stabilization of the enzyme conformation most suited to the reaction to be catalyzed. These studies provide information on one way in which nature controls enzyme activity, and hopefully further studies will help us learn more possibilities for utilizing these enzyme‐control strategies in medicine.

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How a protein generates a catalytic radical from coenzyme B12: X-ray structure of a diol-dehydratase–adeninylpentylcobalamin complex

Cited by 139 publications

References 53 publications

Analysis of the Cob(II)alamin−5‘-Deoxy-3‘,4‘-anhydroadenosyl Radical Triplet Spin System in the Active Site of Diol Dehydrase

Analysis of the Cob(II)alamin−5‘-Deoxy-3‘,4‘-anhydroadenosyl Radical Triplet Spin System in the Active Site of Diol Dehydrase

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Cation‐Activated Enzymes

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