Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms

Nagashima, So; Nakasako, Masayoshi; Dohmae, Naoshi; Tsujimura, Maki; Takio, Koji; Odaka, Masafumi; Yohda, Masafumi; Kamiya, Nobuo; Endo, Itaru

doi:10.1038/nsb0598-347

Cited by 348 publications

(376 citation statements)

References 34 publications

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“…Addition of 1.07 equiv of HBF 4 to 5b at −40°C in MeCN (reaction 3) causes the color to change from grape-purple to cobalt-blue, and the πS→Fe d xy CT band red- (3) shifts by 47 nm (3.76 kcal/mol; Table 5) with very little loss of intensity ( Figure 11). This spectral change is reversed upon the addition of 1.02 equiv of Et 3 N ( Figure S-3, Supporting Information).…”

Section: Proton Additionmentioning

confidence: 99%

How Does Single Oxygen Atom Addition Affect the Properties of an Fe−Nitrile Hydratase Analogue? The Compensatory Role of the Unmodified Thiolate

et al. 2006

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Nitrile hydratase (NHase) is one of a growing number of enzymes shown to contain posttranslationally modified cysteine sulfenic acids (Cys-SOH). Cysteine sulfenic acids have been shown to play diverse roles in cellular processes, including transcriptional regulation, signal transduction, and the regulation of oxygen metabolism and oxidative stress responses. The function of the cysteine sulfenic acid coordinated to the iron active site of NHase is unknown. Herein we report the first example of a sulfenate-ligated iron complex, [Fe III (ADIT)(ADIT-O)] + (5), and compare its electronic and magnetic properties with those of structurally related complexes in which the sulfur oxidation state and protonation state have been systematically altered. Oxygen atom addition was found to decrease the unmodified thiolate Fe-S bond length and blue-shift the ligand-to-metal charge-transfer band (without loss of intensity). S K-edge X-ray absorption spectroscopy and density functional theory calculations show that, although the modified RS-O − fragment is incapable of forming a π bond with the Fe III center, the unmodified thiolate compensates for this loss of π bonding by increasing its covalent bond strength. The redox potential shifts only slightly (75 mV), and the magnetic properties are not affected (the S = ½ spin state is maintained). The coordinated sulfenate S-O bond is activated and fairly polarized (S + -O − ). Addition of strong acids at low temperatures results in the reversible protonation of sulfenateligated 5. An X-ray structure demonstrates that Zn 2+ binds to the sulfenate oxygen to afford [Fe III HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript unmodified NHase thiolate, involving its ability to "tune" the electronics in response to protonation of the sulfenate (RS-O − ) oxygen and/or substrate binding, is discussed.Nitrile hydratases (NHases) are non-heme iron enzymes that convert nitriles to less toxic amides cleanly, and rapidly, under mild conditions. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] It is unusual for a hydrolytic metalloenzyme to incorporate iron, as opposed to zinc, 17,18 presumably because, unlike other metal ions, Zn 2+ is not complicated by redox chemistry. Iron, on the other hand, can promote unwanted side reactions with dioxygen (i.e., Fenton chemistry involving OH · radicals) upon reduction to the Fe 2+ oxidation state. 19,20 The NHase iron site is, however, redox inactive and stabilized in the 3+ oxidation state. The stabilization of Fe 3+ is accomplished by placing the iron in an electron-rich environment consisting of five anionic ligands-two deprotonated peptide amides and three cysteinates (Figure 1). Two of the three coordinated cysteinate sulfurs are oxidized (post-translationally modified) in NHase -one to a sulfenic acid ( 114 Cys-S-(OH)) and the other to a sulfinate 112 CysSO 2 −.3,21 The third cysteinate sulfur, which is trans to the inhibitor/substrate binding site and less accessible to solvent, remains unmodifie...

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Section: Proton Additionmentioning

confidence: 99%

How Does Single Oxygen Atom Addition Affect the Properties of an Fe−Nitrile Hydratase Analogue? The Compensatory Role of the Unmodified Thiolate

et al. 2006

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“…One trypsin molecule is shown by stick models. (b) F 0 Ϫ F c omit-difference Fourier maps of water molecules around nitrile hydratase (Nagashima et al 1998). One ␣ 2 ␤ 2 hetero-tetrameric enzyme (blue and green, ␣-subunits; yellow and pink, ␤-subunits) schematically is shown as cylinder-ribbon models.…”

Section: Introductionmentioning

confidence: 99%

Water–protein interactions from high–resolution protein crystallography

Nakasako

2004

Phil. Trans. R. Soc. Lond. B

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165

119

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To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

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“…The nitrile hydratase enzymes, which catalyze the hydrolysis of nitriles to amides, have an active site consisting of either Co(III) or Fe(III) in an N 2 S 3 X coordination sphere comprised of two deprotonated amide N donors from the protein backbone, three cysteine thiolates, two of which have been post-translationally modified to sulfenic and sulfinic acid groups, and an exogenous hydroxide ligand [10,[27][28]. This unusual active site geometry is likely to be relevant in terms of tuning the electronics of the active-site metal.…”

Section: Introductionmentioning

confidence: 99%

Incorporation of thiolate donation using 2,2′-dithiodibenzaldehyde: Complexes of a pentadentate N2S3 ligand with relevance to the active site of Co nitrile hydratase

Smucker

VanStipdonk

Eichhorn

2007

Journal of Inorganic Biochemistry

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The use of 2,2′-dithiodibenzaldehyde (DTDB) as a reactant for incorporating thiolate donors into the coordination sphere of a transition metal complex without the need for protecting groups is expanded to include the synthesis of complexes with pentadentate ligands. The ligand N,N′-bis (thiosalicylideneimine)-2,2′-thiobis(ethylamine) (tsaltp) is synthesized at a cobalt center by the reaction of DTDB with a Co complex of thiobis(ethylamine). The resulting Co complexes are thus coordinated by the N 2 S 3 pentadentate ligand through two imine N atoms, two thiolate S atoms, and one thioether S atom. A dimeric, bis-thiolate-bridged complex (1) is isolated and converted to a monomeric CN adduct (2) by treatment with KCN. The N 2 S 3 coordination environment provided by the tsaltp ligand is similar to that provided by the protein donors at the active site of the nitrile hydratase enzymes, with 2 being the first octahedral Co complex reported with such a coordination sphere.

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Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms

Cited by 348 publications

References 34 publications

How Does Single Oxygen Atom Addition Affect the Properties of an Fe−Nitrile Hydratase Analogue? The Compensatory Role of the Unmodified Thiolate

How Does Single Oxygen Atom Addition Affect the Properties of an Fe−Nitrile Hydratase Analogue? The Compensatory Role of the Unmodified Thiolate

Water–protein interactions from high–resolution protein crystallography

Incorporation of thiolate donation using 2,2′-dithiodibenzaldehyde: Complexes of a pentadentate N2S3 ligand with relevance to the active site of Co nitrile hydratase

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