CoChat
Sign Up
Cited by 286Metalloenzymes and iron-sulfur proteinsMetal-Catalyzed Oxygenation MechanismsEnzyme Structure and Function

The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition

Open access
Okamoto, Ken, Matsumoto, Koji, Hille, Russ, Eger, Bryan T., Pai, Emil F., Nishino, Takeshi·2004·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0400973101PMC PMC419534
Open this paper in CoChat — free account

Abstract

Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon–oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge–transfer band at ≈640 nm. The crystal structure of the complex indicates that the catalytically labile Mo—OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the Mo⋕S group of the oxidized enzyme has become protonated to afford Mo—SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide.

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.0400973101

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

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.

A few free checks a day · papers already verified open instantly · results are public

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?

  • Febuxostat is a XO inhibitor developed by Teijin, with higher selectivity and potency than allopurinol and oxypurinol.

    “Febuxostat (2-(3-cyano-4-isobutoxyphenyl)-4-methyl-5-thiazole carboxylic acid) (TEI-6720, TMX-67) (FIGURE 16) is a XO inhibitor developed by Teijin, with higher selectivity and potency than allopurinol and oxypurinol (702).”

    From Sources of Vascular Nitric Oxide and Reactive Oxygen Species and Their Regulation (2019) · cites this paper as [702]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 30

  1. [1]Hille, R. & Nishino, T. (1995) FASEB J. 9, 995–1003. [PubMed] [Google Scholar]
  2. [2]Hille, R. (1996) Chem. Rev. 96, 2757–2816. [DOI] [PubMed] [Google Scholar]
  3. [3]Elion, G. B. (1989) Science 244, 41–47. [DOI] [PubMed] [Google Scholar]
  4. [4]Massey, V. & Harris, C. M. (1997) Biochem. Soc. Trans. 25, 750–755. [DOI] [PubMed] [Google Scholar]
  5. [5]Enroth, C., Eger, B. T., Okamoto, K., Nishino, T., Nishino, T. & Pai, E. F. (2000) Proc. Natl. Acad. Sci. USA 97, 10723–10738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. [6]Kuwabara, Y., Nishino, T., Okamoto, K., Matsumura, T., Eger, B. T., Pai, E. F. & Nishino, T. (2003) Proc. Natl. Acad. Sci. USA 100, 8170–8175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. [7]Romao, M. J., Archer, M., Moura, I., Moura, J. J., LeGall, J., Engh, R., Schneider, M., Hof, P. & Huber, R. (1995) Science 270, 1170–1176. [DOI] [PubMed] [Google Scholar]
  8. [8]Huber, R., Hof, P., Duarte, R. O., Moura, J. J., Moura, I., Liu, M. Y., LeGall, J., Hille, R., Archer, M. & Romao, M. J. (1996) Proc. Natl. Acad. Sci. USA 93, 8846–8851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. [9]Hille, R. & Sprecher, H. (1987) J. Biol. Chem. 262, 10914–10917. [PubMed] [Google Scholar]
  10. [10]Howes, B. D., Bray, R. C., Richards, R. L., Turner, N. A., Bennet, B. & Lowe, D. J. (1996) Biochemistry 35, 1432–1443. [DOI] [PubMed] [Google Scholar]
  11. [11]Xia, M., Dempski, R. & Hille, R. (1999) J. Biol. Chem. 274, 3323–3330. [DOI] [PubMed] [Google Scholar]
  12. [12]Eger, B. T., Okamoto, K., Enroth, C., Sato, M., Nishino, T., Pai, E. F. & Nishino, T. (2000) Acta Crystallogr. D 56, 1656–1658. [DOI] [PubMed] [Google Scholar]
  13. [13]Nishino, T., Nishino, T. & Tsushima, K. (1981) FEBS Lett. 131, 369–372. [DOI] [PubMed] [Google Scholar]
  14. [14]Massey, V., Brumby, P. E. & Komai, H. (1969) J. Biol. Chem. 244, 1682–1691. [PubMed] [Google Scholar]
  15. [15]Seefeldt, L. C. & Ensign, S. A. (1994) Anal. Biochem. 221, 379–386. [DOI] [PubMed] [Google Scholar]
  16. [16]Codd, R., Astashkin, A. V., Pacheco, A., Raitsimring, A. M. & Enemark, J. H. (2002) J. Biol. Inorg. Chem. 7, 338–350. [DOI] [PubMed] [Google Scholar]
  17. [17]Kissinger, C. R., Gehlhaar, D. K. & Fogel, D. B. (1999) Acta Crystallogr. D 55, 484–491. [DOI] [PubMed] [Google Scholar]
  18. [18]Kleywegt, G. J. & Jones, T. A. (1996) Acta Crystallogr. D 52, 829–832. [DOI] [PubMed] [Google Scholar]
  19. [19]Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) Acta Crystallogr. D 54, 905–921. [DOI] [PubMed] [Google Scholar]
  20. [20]Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946–950. [Google Scholar]
  21. [21]Merritt, E. A. & Bacon, D. J. (1997) Methods Enzymol. 277, 505–524. [DOI] [PubMed] [Google Scholar]
  22. [22]Esnouf, R. M. (1997) J. Mol. Graphics Model. 15, 132–134. [DOI] [PubMed] [Google Scholar]
  23. [23]Ryan, M. G., Ratnam, K. & Hille, R. (1995) J. Biol. Chem. 270, 19209–19212. [DOI] [PubMed] [Google Scholar]
  24. [24]Oertling, W. A. & Hille, R. (1990) J. Biol. Chem. 265, 17446–17450. [PubMed] [Google Scholar]
  25. [25]Okamoto, K., Eger, B. T., Nishino, T., Kondo, S., Pai, E. F. & Nishino, T. (2003) J. Biol. Chem. 278, 1848–1855. [DOI] [PubMed] [Google Scholar]
  26. [26]Jones, R. M., Inscore, F. E., Hille, R. & Kirk, M. L. (1999) Inorg. Chem. 38, 4963–4970. [DOI] [PubMed] [Google Scholar]
  27. [27]Holm, R. H. (1990) Coord. Chem. Rev. 100, 183–221. [Google Scholar]
  28. [28]Dobbek, H., Gremer, L., Kiefersauer, R., Huber, R. & Meyer, O. (2002) Proc. Natl. Acad. Sci. USA 99, 15971–15976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. [29]Lorigan, G. A., Britt, R. D., Kim, J. H. & Hille, R. (1994) Biochim. Biophys. Acta 1185, 284–294. [DOI] [PubMed] [Google Scholar]
  30. [30]Manikandan, P., Choi, E.-Y., Hille, R. & Hoffman, B. M. (2001) J. Am. Chem. Soc. 123, 2658–2663. [DOI] [PubMed] [Google Scholar]

Cited by

Sorted by citations

Related

Authors
Okamoto, K., Matsumoto, K., Hille, R., Eger, B. T., Pai, E. F., & Nishino, T.
Affiliations
University of Toronto (CA)
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2004-05-17
Volume
101
Issue
21
Pages
7931-7936
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0400973101
PMC
PMC419534
OpenAlex
W2047276432
Cited by
286
References
31
Citations by year
2026: 6 · 2025: 9 · 2024: 12 · 2023: 17 · 2022: 15 · 2021: 20 · 2020: 11 · 2019: 10 · 2018: 13 · 2017: 10 · 2016: 12 · 2015: 9 · 2014: 17 · 2013: 10 · 2012: 15
FWCI
10.92
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Institute of General Medical Sciences (R01GM059953, GM 59953)
Topics
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
xanthine oxidoreductase, molybdenum enzymes, molybdenum hydroxylases, enzyme catalysis, reaction mechanism, enzyme inhibition, crystal structure, C–O bond formation, square pyramidal geometry, ligand displacement, oxygen atom transfer
MeSH terms
Animals, Catalysis, Enzyme Inhibitors, Hydroxides, Hydroxylation, Ligands, Milk, Models, Chemical, Models, Molecular, Molybdenum, Oxidoreductases, Oxygen, Structure-Activity Relationship, Sulfur, Xanthine Dehydrogenase, Crystallography, X-Ray, Xanthine

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