Resonance Raman spectroscopic evidence for heme iron-hydroxide ligation in peroxidase alkaline forms.

Sitter, Andrew J.; Shifflett, John R.; Terner, James

doi:10.1016/s0021-9258(18)37667-1

Cited by 74 publications

(53 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, no hydroxo ligation is displayed in the variants of Kp DyP where Arg-232 is replaced by an alanine. This agrees with the general observation that binding of OH − in heme peroxidases is accommodated by a distal arginine forming a hydrogen bond [ 52 , 53 , 54 ]. The presence of hydrogen bonding can be deduced from the g z component that reflects the strength of the stabilization [ 33 ].…”

Section: Discussionsupporting

confidence: 91%

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Nys

Pfanzagl

Roefs

et al. 2021

IJMS

View full text Add to dashboard Cite

Dye-decolorizing peroxidases (DyPs) have gained interest for their ability to oxidize anthraquinone-derived dyes and lignin model compounds. Spectroscopic techniques, such as electron paramagnetic resonance and optical absorption spectroscopy, provide main tools to study how the enzymatic function is linked to the heme-pocket architecture, provided the experimental conditions are carefully chosen. Here, these techniques are used to investigate the effect of active site perturbations on the structure of ferric P-class DyP from Klebsiella pneumoniae (KpDyP) and three variants of the main distal residues (D143A, R232A and D143A/R232A). Arg-232 is found to be important for maintaining the heme distal architecture and essential to facilitate an alkaline transition. The latter is promoted in absence of Asp-143. Furthermore, the non-innocent effect of the buffer choice and addition of the cryoprotectant glycerol is shown. However, while unavoidable or indiscriminate experimental conditions are pitfalls, careful comparison of the effects of different exogenous molecules on the electronic structure and spin state of the heme iron contains information about the inherent flexibility of the heme pocket. The interplay between structural flexibility, key amino acids, pH, temperature, buffer and glycerol during in vitro spectroscopic studies is discussed with respect to the poor peroxidase activity of bacterial P-class DyPs.

show abstract

Section: Discussionsupporting

confidence: 91%

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Nys

Pfanzagl

Roefs

et al. 2021

IJMS

View full text Add to dashboard Cite

show abstract

“…(A) X = F – : (red circles) heme proteins with Arg in their distal pocket, (black squares) other heme proteins with no H-bonding to bound F – , (blue triangles) other heme proteins with H-bonding to bound F – . ,,− (B) X = OH – . Low-spin heme hydroxide complexes: (red circles) heme proteins with Arg in their distal pocket, ,, (black squares) heme proteins with distal His, ,− and (gray triangles) HRP proteins with His and/or Arg available as the H-bond donator in the pocket. The HRP-C(H42L) variant contains only a distal Arg.…”

Section: Resultsmentioning

confidence: 99%

“…This approach has the potential to clarify assignments that may be ambiguous on the basis of ν(Fe III –OH) frequency alone. For example, for HRP enzymes whose distal pockets comprise both Arg and His, the positions of HRP-A1 and HRP-C on the (Fe III –OH)/ν(Fe II –His) plot suggest that these two amino acids contribute differently to distal H-bonding in these isozymes. The HRP-C variant HRP-C(H42L), which has no distal His, leaves only the distal Arg to stabilize anion coordination by H-bond donation.…”

Section: Discussionmentioning

confidence: 99%

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

et al. 2017

View full text Add to dashboard Cite

O2-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO2− to O2 and Cl−. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate and chlorate respiring bacteria. The Cld from the Gram-negative, human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic and spectroscopic behaviors of their fluorides, chlorides and hydroxides. Cooperative Cl− binding to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(FeIII−F) bands at 385 and 390 cm−1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond-donation to the F− ligand, indicating that atoms directly coordinated to heme iron are accessible by distal H-bond donation. New vibrational frequency correlations between either ν(FeIII−F) or ν(FeIII−OH) and ν(FeII−His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe−X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.

show abstract

“…39 The 776-cm -1 band has been assigned to a H-bonded Fe IV dO moiety and the 788-cm -1 band, being insensitive to deuterium exchange, to a non-H-bonded Fe IV dO group. 39 HRP-II is a kinetically competent one-electron oxidant (eq 1c) at low pH but not at high pH, with a transition midpoint at pH 8.6. 40 Since ν(Fe-O) of MbFe IV dO is high (797 cm -1 ) compared to that of the peroxidases (745-779 cm -1 ), 41 and the 797-cm -1 band is both insensitive to pH in the range 6-12 and to substitution of D 2 O for H 2 O, 42 H-bonding to the oxene ligand in MbFe IV dO is highly unlikely.…”

mentioning

confidence: 99%

pH and Driving Force Dependence of Intramolecular Oxyferryl Heme Reduction in Myoglobin

1997

View full text Add to dashboard Cite

The kinetics of oxyferryl (Fe IV dO) heme reduction in horse heart myoglobin (Mb) by a 4 LRu II (a ) NH 3 ; L ) NH 3 , pyridine, isonicotinamide) bound at the surface His48 were investigated with pulse radiolysis. The observed first-order rate constants (k obs1 ) decreased with increasing pH and reduction potential for the a 4 LRu centers (E°/ Ru III/II) 77, 330, and 400 mV for L ) NH 3 , Pyr, and Isn). Rate-pD data obtained in D 2 O for the a 5 Ru derivative revealed the presence of an equilibrium isotope effect, and a pK a of 5.7 (6.2 in D 2 O) was obtained for the acid-base group, which is assigned to the distal His64. A mechanism where protonation precedes ET provides a good fit of the kinetic data for the three a 4 LRu derivatives. Marcus theory analysis of the k ET (0.74, 1.8, and 3.6 s -1 for L ) Isn, Pyr, and NH 3 ) extracted from the k obs1 values yielded a reorganization energy (λ) of 1.8 for Ru II f Fe IV dO ET in the a 4 LRu derivatives but a λ of 2.1 eV for the a 5 Ru derivative. From the latter, it is concluded that ET is strongly gated in the a 5 Ru derivative, and this is assumed to be the major reason for the low reactivity of Fe IV dO in Mb at high -∆G°.

show abstract

Resonance Raman spectroscopic evidence for heme iron-hydroxide ligation in peroxidase alkaline forms.

Cited by 74 publications

References 62 publications

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

pH and Driving Force Dependence of Intramolecular Oxyferryl Heme Reduction in Myoglobin

Contact Info

Product

Resources

About

Resonance Raman spectroscopic evidence for heme iron-hydroxide ligation in peroxidase alkaline forms.

Cited by 74 publications

References 62 publications

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase—The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

pH and Driving Force Dependence of Intramolecular Oxyferryl Heme Reduction in Myoglobin

Contact Info

Product

Resources

About

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations