Structural and mechanistic studies on the inhibition of the hypoxia-inducible transcription factor hydroxylases by tricarboxylic acid cycle intermediates
Open accessAbstract
In humans both the levels and activity of the alpha-subunit of the hypoxia-inducible transcription factor (HIF-alpha) are regulated by its post-translation hydroxylation as catalyzed by iron- and 2-oxoglutarate (2OG)-dependent prolyl and asparaginyl hydroxylases (PHD1-3 and factor-inhibiting HIF (FIH), respectively). One consequence of hypoxia is the accumulation of tricarboxylic acid cycle intermediates (TCAIs). In vitro assays were used to assess non-2OG TCAIs as inhibitors of purified PHD2 and FIH. Under the assay conditions, no significant FIH inhibition was observed by the TCAIs or pyruvate, but fumarate, succinate, and isocitrate inhibited PHD2. Mass spectrometric analyses under nondenaturing conditions were used to investigate the binding of TCAIs to PHD2 and supported the solution studies. X-ray crystal structures of FIH in complex with Fe(II) and fumarate or succinate revealed similar binding modes for each in the 2OG co-substrate binding site. The in vitro results suggest that the cellular inhibition of PHD2, but probably not FIH, by fumarate and succinate may play a role in the Warburg effect providing that appropriate relative concentrations of the components are achieved under physiological conditions.
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
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 HIF hydroxylases have been reported to be inhibited by citrate, isocitrate, succinate, fumarate, malate, oxaloacetate, and pyruvate.
“In addition to requiring 2-oxoglutarate as a cosubstrate, the HIF hydroxylases have been reported to be inhibited by citrate, isocitrate, succinate, fumarate, malate, oxaloacetate, and pyruvate (Dalgard et al., 2004; Hewitson et al., 2007; Isaacs et al., 2005; Koivunen et al., 2007a; Selak et al., 2005).”
From Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. (2008) · cites this paper as Hewitson et al., 2007
The paper reports that fumarate, succinate, and isocitrate inhibited PHD2 under its assay conditions (opening summary; results on TCAI inhibition). It does not establish inhibition by every compound listed: the “TCAIs as Inhibitors of HIF Hydroxylases” section says its purified-enzyme assays found neither pyruvate nor oxaloacetate inhibited PHD2, and the opening summary reports no significant FIH inhibition by the tested compounds. Citrate and malate are not reported as PHD2 inhibitors in the cited results. (LLM, conf=0.91)
Experimental — accuracy not yet measuredFumarate and succinate are less-effective inhibitors of FIH1, which appears more sensitive to citrate and oxaloacetate.
“These two molecules are less-effective inhibitors of FIH1, which appears more sensitive to citrate and oxaloacetate (Hewitson et al., 2007; Koivunen et al., 2007a).”
From Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. (2008) · cites this paper as Hewitson et al., 2007
The crystal-structure results describe fumarate and succinate as weak inhibitors of FIH, supporting the first part of the claim. The inhibition results report that none of the selected TCA intermediates substantially inhibited FIH under the assay conditions; they do not establish that FIH is more sensitive to citrate or oxaloacetate. (LLM, conf=0.88)
Experimental — accuracy not yet measuredSuccinate and fumarate inhibit prolyl hydroxylase domain-containing enzymes that regulate hypoxia-inducible factor stability, so FH- and SDH-deficient cancers activate the hypoxic gene expression program even under normoxic conditions.
“Additionally, succinate and fumarate inhibit the prolyl hydroxylase domain-containing (PHD) enzymes that regulate stability of hypoxia-inducible factors (HIFs), such that FH and SDH deficient cancers activate the hypoxic gene expression program even under normoxic conditions (Hewitson et al., 2007; Pollard et al., 2005; Selak et al., 2005).”
From Targeting Metabolism for Cancer Therapy (2017) · cites this paper as Hewitson et al., 2007
The crystallographic analyses indicate that both R-2HG and S-2HG have the potential to bind active-site Fe(II) and compete with 2OG for binding.
“Overall, the crystallographic analyses indicte that, similarly to succinate and fumarate (Fig 2C,F; Hewitson et al, 2007), both R-and S-2HG have the potential to bind to the active site Fe(II) and compete with 2OG for binding.”
From The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases (2011) · cites this paper as Hewitson et al, 2007
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 65 · Cited by 235
Research works printed but not linked: 6
- Semenza, G. L., Nejfelt, M. K., Chi, S. M., and Antonarakis, S. E. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 5680 -5684
- Ivan, M., Haberberger, T., Gervasi, D. C., Michelson, K. S., Gunzler, V., Kondo, K., Yang, H. F., Sorokina, I., Conaway, R. C., Conaway, J. W., and Kaelin, W. G. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 13459 -13464
- Chandel, N. S., Maltepe, E., Goldwasser, E., Mathieu, C. E., Simon, M. C., and Schumacker, P. T. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 11715-11720
- McDonough, M. A., Li, V., Flashman, E., Chowdhury, R., Mohr, C., Lien- ard, B. M. R., Zondlo, J., Oldham, N. J., Clifton, I. J., Lewis, J., McNeill, L. A., Kurzeja, R. J. M., Hewitson, K. S., Yang, E., Jordan, S., Syed, R. S., and Schofield, C. J. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 9814 -9819
- Launonen, V., Vierimaa, O., Kiuru, M., Isola, J., Roth, S., Pukkala, E., Sistonen, P., Herva, R., and Aaltonen, L. A. (2001) Proc. Natl. Acad. Sci.
- Percy, M. J., Zhao, Q., Flores, A., Harrison, C., Lappin, T. R., Maxwell, P. H., McMullin, M. F., and Lee, F. S. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 654 -659
- Authors
- Hewitson, K. S., Liénard, B. M. R., McDonough, M. A., Clifton, I. J., Butler, D., Soares, A. S., Oldham, N. J., McNeill, L. A., & Schofield, C. J.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Hewitson, Kirsty S.
- Schofield, Christopher J.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2007-02
- Volume
- 282
- Issue
- 5
- Pages
- 3293-3301
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2005917601
- Cited by
- 235
- References
- 65
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 13 · 2023: 9 · 2022: 10 · 2021: 14 · 2020: 9 · 2019: 16 · 2018: 9 · 2017: 12 · 2016: 10 · 2015: 11 · 2014: 20 · 2013: 19 · 2012: 13
- FWCI
- 4.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BBS/B/07683)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
- Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- hypoxia-inducible factor alpha, prolyl hydroxylase 2, factor inhibiting HIF, tricarboxylic acid cycle intermediates, fumarate, succinic acid, isocitrate, pyruvate, Warburg effect, hypoxia, crystal structure, ligand binding
- MeSH terms
- Breast, Breast Neoplasms, Citric Acid Cycle, Female, Humans, Mixed Function Oxygenases, Protein-Lysine 6-Oxidase, Placental Lactogen, Cell Line, Tumor, Basic Helix-Loop-Helix Transcription Factors, Basic Helix-Loop-Helix Proteins, Hypoxia-Inducible Factor 1, alpha Subunit
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
