An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective

Gumiero, A.; Murphy, Emma J.; Metcalfe, Clive; Moody, P.C.E.; Raven, Emma Lloyd

doi:10.1016/j.abb.2010.02.015

Cited by 73 publications

(83 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…19). The most similar structures to the E140G-guaiacol complex were those of HRP-ferulic acid and HRP-cyanide-ferulic acid complexes (40).…”

Section: Discussionmentioning

confidence: 99%

“…However, the two enzymes show different kinetic constants oxidizing substrates at this site, due to differences in the amino acid residues forming the catalytic tryptophan environment (18). VP, like all other heme peroxidases, presents an access channel to the distal heme pocket enabling the entrance of H 2 O 2 for activation of the cofactor (19). In several peroxidases, such as horseradish peroxidase (HRP) (EC 1.11.1.7) and Coprinopsis cinerea peroxidase (CiP) (EC 1.11.1.7), it is assumed that phenolic compounds are oxidized through this channel in direct contact with the heme (20), and the same site has been suggested for LiP oxidation of anionic dyes (21).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Two Oxidation Sites for Low Redox Potential Substrates

Morales¹,

Mate²,

Romero

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background:Versatile peroxidases oxidize different substrates, including low redox potential aromatics. Results: To investigate this activity, 13 variants were characterized, and five x-ray structures obtained. Conclusion: Phenols and dyes are oxidized in a low efficiency site in the heme channel and a high efficiency site at an exposed tryptophan. Significance: This study supplies new structural-functional information on versatile peroxidase, and provides variants with improved activity on phenols.

show abstract

“…19). The most similar structures to the E140G-guaiacol complex were those of HRP-ferulic acid and HRP-cyanide-ferulic acid complexes (40).…”

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Two Oxidation Sites for Low Redox Potential Substrates

Morales¹,

Mate²,

Romero

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…In the case of the substrate-bound enzyme, the evidence suggests that, rather than there being an interaction between NO and the water pool, BHA displaces the water from near the haem, disrupting the pool and making H-bonding interactions with the 35 NO ligand, consistent with the structures revealed in the crystalline phase. 5,16 This would explain the removal of the isotope dependence of the data. Given this scenario, it may be considered that interactions between the larger head-group of BHA and the NO ligand might be expected to yield slower spectral diffusion timescales than those found when smaller, more mobile water molecules are 40 responsible for the dynamics.…”

Section: Created Using the Rsc Report Template (Ver 31) -See Wwwrsmentioning

confidence: 99%

“…In the un-liganded form of the protein, a single water molecule is observable by crystallography located in a position 2.6 Å above the haem iron that is most consistent with a weak interaction with the Fe centre. 5,16,17 In the case of a 10 haem centre with the diatomic CN ligand bound to it, the binding of BHA has been shown to be similar but there are indications of a rotated BHA head group in order to better accommodate interactions with the haem ligand. 5 In light of this, the FTIR data are consistent with a major change in the local environment of the NO ligand occurring upon substrate coordination.…”

Section: Ftir Spectroscopymentioning

confidence: 99%

“…5,16 Under conditions where the haem is not ligated by a diatomic molecule, BHA binding promotes the formation of a 6-coordinate aqua complex of the ferric haem 17,18 but, otherwise, BHA binding seems to exclude water from the normally solvent- 15 accessible pocket. In part, this is apparently achieved through competitive replacement of hydrogen bonding links near the haem but the binding of BHA also leads to a reorientation of the F68 residue, which serves to occlude the solvent access channel to the haem pocket.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase

et al. 2015

View full text Add to dashboard Cite

This version is available at https://strathprints.strath.ac.uk/50089/ Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (https://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge.Any correspondence concerning this service should be sent to the Strathprints administrator: strathprints@strath.ac.ukThe Strathprints institutional repository (https://strathprints.strath.ac.uk) is a digital archive of University of Strathclyde research outputs. It has been developed to disseminate open access research outputs, expose data about those outputs, and enable the management and persistent access to Strathclyde's intellectual output.

show abstract

Phylogenetic analysis, molecular modeling, substrate–inhibitor specificity, and active site comparison of bacterial, fungal, and plant heme peroxidases

Singh

Pandey

Naaz

et al. 2012

Biotech and App Biochem

View full text Add to dashboard Cite

Phylogenetic analysis of 40 heme peroxidases, belonging to both prokaryotes and eukaryotes, revealed their clustering into three major classes. Class I represented sequences from plants, bacteria, fungi, and algae, whereas classes II and III exclusively represented plant and fungal peroxidases, respectively. Modeling of three representative classes of peroxidases, belonging to each of bacterial, plant, and fungal categories, revealed a similar kind of folding; however, superimposition analysis revealed relatively more closeness between plant and fungal peroxidases than that of the bacterial peroxidase. The docking analysis of three representative modeled peroxidases with three common substrates, namely, H₂O₂, guaiacol, and ascorbate, and three arginine-specific inhibitors, namely, phenylglyoxal, 1,2-cyclohexanedione, and 2,3-butanedione, revealed that all three inhibitors competed for guaiacol- and ascorbate-binding sites of peroxidases, except for phenylglyoxal binding in the case of plant peroxidase. Phenylglyoxal, 1,2-cyclohexanedione, and 2,3-butanedione were found to be most potent inhibitors of bacterial, fungal, and plant peroxidases, respectively.

show abstract

An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective

Cited by 73 publications

References 76 publications

Two Oxidation Sites for Low Redox Potential Substrates

Two Oxidation Sites for Low Redox Potential Substrates

The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase

Phylogenetic analysis, molecular modeling, substrate–inhibitor specificity, and active site comparison of bacterial, fungal, and plant heme peroxidases

Contact Info

Product

Resources

About