The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Crystal structures of dye‐decolorizing peroxidase with ascorbic acid and 2,6‐dimethoxyphenol
Abstract
The structure of dye‐decolorizing peroxidase (DyP)‐type peroxidase differs from that of other peroxidase families, indicating that DyP‐type peroxidases have a different reaction mechanism. We have determined the crystal structures of DyP with ascorbic acid and 2,6‐dimethoxyphenol at 1.5 and 1.4 Å, respectively. The common binding site for both substrates was located at the entrance of the second cavity leading from the DyP molecular surface to heme. This resulted in a hydrogen bond network connection between each substrate and the heme distal side. This network consisted of water molecules occupying the second cavity, heme 6‐propionate, Arg329, and Asn313. This network is consistent with the proton transfer pathway from substrate to DyP.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Although their action mechanism resembles that of other peroxidases, anthraquinone dye degradation is not yet fully mapped 129-134 .”
From Degradation of anthraquinone dyes from effluents: A review focusing on enzymatic dye degradation with industrial potential (2020) · cites this paper as [134]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Porphyrins and Metalloporphyrins
(1978) · Coordination Chemistry Reviews · doi:10.1016/s0010-8545(00)80351-3 · Cited by 1,716
Wariishi, H., Valli, K., & Gold, M. H. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)35893-9 · Cited by 1,006
Nelson, D. P., & Kiesow, L. A. (1972) · Analytical Biochemistry · doi:10.1016/0003-2697(72)90451-4 · Cited by 925
Identification by ENDOR of Trp 191 as the Free-Radical Site in Cytochrome c Peroxidase Compound ES
Sivaraja, M., Goodin, D. B., Smith, M., & Hoffman, B. M. (1989) · Science · doi:10.1126/science.2549632 · Cited by 479
Structural basis of enzyme encapsulation into a bacterial nanocompartment
Sutter, M., Boehringer, D., Gutmann, S., Günther, S., Prangishvili, D., Loessner, M. J., Stetter, K. O., Weber-Ban, E., & Ban, N. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1473 · Cited by 411
Kim, S. J., & Shoda, M. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.3.1029-1035.1999 · Cited by 274
DyP-type peroxidases comprise a novel heme peroxidase family
Sugano, Y. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-8651-8 · Cited by 254
Self-citationTwo Substrate Interaction Sites in Lignin Peroxidase Revealed by Site-Directed Mutagenesis
Doyle, W. A., Blodig, W., Veitch, N. C., Piontek, K., & SMITH, A. T. (1998) · Biochemistry · doi:10.1021/bi981633h · Cited by 247
DyP, a Unique Dye-decolorizing Peroxidase, Represents a Novel Heme Peroxidase Family
Sugano, Y., Muramatsu, R., Ichiyanagi, A., Sato, T., & Shoda, M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m706996200 · Cited by 222
Self-citationLiers, C., Bobeth, C., Pecyna, M. J., Ullrich, R., & Hofrichter, M. (2009) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2173-7 · Cited by 210
Ruiz-Dueñas, F. J., Martı́nez, M. J., & Martı́nez, Á. T. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01164.x · Cited by 203
van Bloois, E., Torres Pazmiño, D. E., Winter, R. T., & Fraaije, M. W. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2369-x · Cited by 180
PeroxiBase: a database with new tools for peroxidase family classification
Koua, D., Cerutti, L., Falquet, L., Sigrist, C. J. A., Theiler, G., Hulo, N., & Dunand, C. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn680 · Cited by 173
Characterization of Dye-Decolorizing Peroxidases from Rhodococcus jostii RHA1
Roberts, J. N., Singh, R., Grigg, J. C., Murphy, M. E. P., Bugg, T. D. H., & Eltis, L. D. (2011) · Biochemistry · doi:10.1021/bi200427h · Cited by 164
Distal Heme Pocket Residues of B-type Dye-decolorizing Peroxidase
Singh, R., Grigg, J. C., Armstrong, Z., Murphy, M. E. P., & Eltis, L. D. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.332171 · Cited by 104
YcdB from Escherichia coli Reveals a Novel Class of Tat-dependently Translocated Hemoproteins
Sturm, A., Schierhorn, A., Lindenstrauß, U., Lilie, H., & Brüser, T. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m511891200 · Cited by 103
Sugano, Y., Nakano, R., Sasaki, K., & Shoda, M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1754-1758.2000 · Cited by 99
Self-citationGumiero, A., Murphy, E. J., Metcalfe, C. L., Moody, P. C. E., & Raven, E. L. (2010) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2010.02.015 · Cited by 86
Crystal Structure and Biochemical Features of EfeB/YcdB from Escherichia coli O157
Liu, X., Du, Q., Wang, Z., Zhu, D., Huang, Y., Li, N., Wei, T., Xu, S., & Gu, L. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.197780 · Cited by 85
Zubieta, C., Krishna, S., Kapoor, M., Kozbial, P. Z., McMullan, D., Axelrod, H. L., Miller, M. D., Abdubek, P., Ambing, E., Astakhova, T., et al. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21550 · Cited by 85
Yoshida, T., Tsuge, H., Konno, H., Hisabori, T., & Sugano, Y. (2011) · FEBS Journal · doi:10.1111/j.1742-4658.2011.08161.x · Cited by 83
Self-citationZubieta, C., Joseph, R., Krishna, S., McMullan, D., Kapoor, M., Axelrod, H. L., Miller, M. D., Abdubek, P., Acosta, C., Astakhova, T., et al. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21673 · Cited by 71
Sugano, Y., Sasaki, K., & Shoda, M. (1999) · Journal of Bioscience and Bioengineering · doi:10.1016/s1389-1723(99)80087-5 · Cited by 69
Self-citationCrystal Structure of the Ascorbate Peroxidase−Salicylhydroxamic Acid Complex
Sharp, K. H., Moody, P. C. E., Brown, K. A., & Raven, E. L. (2004) · Biochemistry · doi:10.1021/bi049343q · Cited by 63
Wariishi, H., Huang, J., Dunford, H. B., & Gold, M. H. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)54764-5 · Cited by 56
Interaction of Ascorbate Peroxidase with Substrates: A Mechanistic and Structural Analysis
Macdonald, I. K., Badyal, S. K., Ghamsari, L., et al. (2006) · Biochemistry · doi:10.1021/bi0606849 · Cited by 50
Li, J., Liu, C., Li, B., Yuan, H., Yang, J., & Zheng, B. (2011) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-011-9466-x · Cited by 41
Proton Delivery to Ferryl Heme in a Heme Peroxidase: Enzymatic Use of the Grotthuss Mechanism
Efimov, I., Badyal, S. K., Metcalfe, C. L., Macdonald, I. K., Gumiero, A., Raven, E. L., & Moody, P. C. E. (2011) · Journal of the American Chemical Society · doi:10.1021/ja2007017 · Cited by 40
Crystal structure of guaiacol and phenol bound to a heme peroxidase
Murphy, E. J., Metcalfe, C. L., Nnamchi, C. I., Moody, P. C. E., & Raven, E. L. (2011) · FEBS Journal · doi:10.1111/j.1742-4658.2011.08425.x · Cited by 39
Research works printed but not linked: 1
- K.M. Smith J.H. Fuhrhop 1975 Elsevier Amsterdam
Cited by
Routoula, E., & Patwardhan, S. V. (2020) · Environmental Science & Technology · doi:10.1021/acs.est.9b03737 · Cited by 579
Metadata
- Authors
- Yoshida, T., Tsuge, H., Hisabori, T., & Sugano, Y.
- Venue
- FEBS Letters
- Publisher
- Wiley
- Published
- 2012-11-15
- Volume
- 586
- Issue
- 24
- Pages
- 4351-4356
- ISSN
- 0014-5793
- 1873-3468
- Cited by
- 46
- References
- 29
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
