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PMID: 17003127 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 103 ·No. 40 ·2006-10-03 ·Pages 14738-43

Hoffart LM, Barr EW, Guyer RB, Bollinger JM, Krebs C

Abstract

The Fe(II)- and alpha-ketoglutarate (alphaKG)-dependent dioxygenases use mononuclear nonheme iron centers to effect hydroxylation of their substrates and decarboxylation of their cosubstrate, alphaKG, to CO(2) and succinate. Our recent dissection of the mechanism of taurine:alphaKG dioxygenase (TauD), a member of this enzyme family, revealed that two transient complexes accumulate during catalysis in the presence of saturating substrates. The first complex contains the long-postulated C-H-cleaving Fe(IV)-oxo intermediate, J, and the second is an enzyme.product(s) complex. Here, we demonstrate the accumulation of two transient complexes in the reaction of a prolyl-4-hydroxylase (P4H), a functional homologue of human alphaKG-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing. The kinetic and spectroscopic properties of these two P4H complexes suggest that they are homologues of the TauD intermediates. Most notably, the first exhibits optical absorption and Mössbauer spectra similar to those of J and, like J, a large substrate deuterium kinetic isotope on its decay. The close correspondence of the accumulating states in the P4H and TauD reactions supports the hypothesis of a conserved mechanism for substrate hydroxylation by enzymes in this family.

MeSH Terms
Absorption Amino Acid Sequence Carbon/analysis Humans Hydrogen/analysis Iron/analysis Ketoglutaric Acids/metabolism Kinetics Mixed Function Oxygenases/metabolism Molecular Sequence Data Peptides/chemistry Phycodnaviridae/enzymology Procollagen-Proline Dioxygenase/analysis,chemistry Spectroscopy, Mossbauer Substrate Specificity Titrimetry
Chemicals
Ketoglutaric Acids Peptides Carbon Hydrogen Iron Mixed Function Oxygenases Procollagen-Proline Dioxygenase
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Hoffart Lee M
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
Barr Eric W
Guyer Robert B
Bollinger J Martin
Krebs Carsten
References (48)
48 references, click to expand
  1. Theoretical spectroscopy of model-nonheme [Fe(IV)OL5]2+ complexes in their lowest triplet and quintet states using multireference ab initio and density functional theory methods.
    J Inorg Biochem. 2006 Apr;100(4):716-26 PMID: 16504299
  2. Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters.
    J Am Chem Soc. 2005 Apr 27;127(16):5840-53 PMID: 15839682
  3. Histone demethylation by hydroxylation: chemistry in action.
    ACS Chem Biol. 2006 Mar 17;1(2):75-81 PMID: 17163647
  4. FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor.
    Genes Dev. 2002 Jun 15;16(12):1466-71 PMID: 12080085
  5. A non-heme iron protein with heme tendencies: an investigation of the substrate specificity of thymine hydroxylase.
    Biochemistry. 1993 Dec 21;32(50):14023-33 PMID: 8268181
  6. Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation.
    Science. 2001 Apr 20;292(5516):468-72 PMID: 11292861
  7. Pterin-Dependent Amino Acid Hydroxylases.
    Chem Rev. 1996 Nov 7;96(7):2659-2756 PMID: 11848840
  8. Requirements for alpha-ketoglutarate, ferrous ion and ascorbate by collagen proline hydroxylase.
    Biochem Biophys Res Commun. 1966 Jul 20;24(2):179-84 PMID: 5965224
  9. Histone demethylation by a family of JmjC domain-containing proteins.
    Nature. 2006 Feb 16;439(7078):811-6 PMID: 16362057
  10. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.
    Nature. 1997 Jun 19;387(6635):827-30 PMID: 9194566
  11. Aqueous FeIV==O: spectroscopic identification and oxo-group exchange.
    Angew Chem Int Ed Engl. 2005 Oct 28;44(42):6871-4 PMID: 16206322
  12. Oxygen activation by nonheme iron(II) complexes: alpha-keto carboxylate versus carboxylate.
    J Am Chem Soc. 2003 Jul 2;125(26):7828-42 PMID: 12823001
  13. Prolyl 4-hydroxylases and their protein disulfide isomerase subunit.
    Matrix Biol. 1998 Feb;16(7):357-68 PMID: 9524356
  14. A conserved family of prolyl-4-hydroxylases that modify HIF.
    Science. 2001 Nov 9;294(5545):1337-40 PMID: 11598268
  15. HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing.
    Science. 2001 Apr 20;292(5516):464-8 PMID: 11292862
  16. Comparison of FeIV=O heme and non-heme species: electronic structures, bonding, and reactivities.
    Angew Chem Int Ed Engl. 2005 Apr 8;44(15):2252-5 PMID: 15719352
  17. The enzymology of clavam and carbapenem biosynthesis.
    Chem Commun (Camb). 2005 Sep 14;(34):4251-63 PMID: 16113715
  18. Evidence for 4-hydroxyproline in viral proteins. Characterization of a viral prolyl 4-hydroxylase and its peptide substrates.
    J Biol Chem. 1999 Aug 6;274(32):22131-4 PMID: 10428773
  19. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage.
    Nature. 2002 Sep 12;419(6903):174-8 PMID: 12226667
  20. Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates.
    Chem Rev. 2004 Feb;104(2):939-86 PMID: 14871146
  21. Geometric and electronic structure/function correlations in non-heme iron enzymes.
    Chem Rev. 2000 Jan 12;100(1):235-350 PMID: 11749238
  22. Spectroscopic studies of substrate interactions with clavaminate synthase 2, a multifunctional alpha-KG-dependent non-heme iron enzyme: correlation with mechanisms and reactivities.
    J Am Chem Soc. 2001 Aug 1;123(30):7388-98 PMID: 11472170
  23. Mechanism-based inactivation of thymine hydroxylase, an alpha-ketoglutarate-dependent dioxygenase, by 5-ethynyluracil.
    Biochemistry. 1993 Dec 21;32(50):14034-42 PMID: 8268182
  24. One motif--many different reactions.
    Nat Struct Biol. 2000 Mar;7(3):182-4 PMID: 10700270
  25. Spectroscopy and electronic structures of mono- and binuclear high-valent non-heme iron-oxo systems.
    J Inorg Biochem. 2006 Apr;100(4):697-706 PMID: 16510189
  26. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation.
    Cell. 2001 Oct 5;107(1):43-54 PMID: 11595184
  27. A stereochemical concept for the catalytic mechanism of prolylhydroxylase: applicability to classification and design of inhibitors.
    J Theor Biol. 1982 Jan 21;94(2):421-55 PMID: 6281585
  28. SyrB2 in syringomycin E biosynthesis is a nonheme FeII alpha-ketoglutarate- and O2-dependent halogenase.
    Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10111-6 PMID: 16002467
  29. EXAFS spectroscopic evidence for an Fe=O unit in the Fe(IV) intermediate observed during oxygen activation by taurine:alpha-ketoglutarate dioxygenase.
    J Am Chem Soc. 2004 Jul 7;126(26):8108-9 PMID: 15225039
  30. Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family.
    J Biol Chem. 2002 Jul 19;277(29):26351-5 PMID: 12042299
  31. Crystallographic and spectroscopic characterization of a nonheme Fe(IV)-O complex.
    Science. 2003 Feb 14;299(5609):1037-9 PMID: 12586936
  32. Targeting HIF-1 for cancer therapy.
    Nat Rev Cancer. 2003 Oct;3(10):721-32 PMID: 13130303
  33. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli.
    Nature. 2002 Sep 12;419(6903):178-82 PMID: 12226668
  34. Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis.
    Nature. 2006 Mar 16;440(7082):368-71 PMID: 16541079
  35. Rapid freeze-quench 57Fe Mössbauer spectroscopy: monitoring changes of an iron-containing active site during a biochemical reaction.
    Inorg Chem. 2005 Feb 21;44(4):742-57 PMID: 15859243
  36. Evidence for hydrogen abstraction from C1 of taurine by the high-spin Fe(IV) intermediate detected during oxygen activation by taurine:alpha-ketoglutarate dioxygenase (TauD).
    J Am Chem Soc. 2003 Oct 29;125(43):13008-9 PMID: 14570457
  37. The first direct characterization of a high-valent iron intermediate in the reaction of an alpha-ketoglutarate-dependent dioxygenase: a high-spin FeIV complex in taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli.
    Biochemistry. 2003 Jun 24;42(24):7497-508 PMID: 12809506
  38. Spectroscopic and quantum chemical characterization of the electronic structure and bonding in a non-heme FeIV[double bond]O complex.
    J Am Chem Soc. 2004 May 5;126(17):5378-9 PMID: 15113207
  39. Independent function of two destruction domains in hypoxia-inducible factor-alpha chains activated by prolyl hydroxylation.
    EMBO J. 2001 Sep 17;20(18):5197-206 PMID: 11566883
  40. Mechanism of aromatic amino acid hydroxylation.
    Biochemistry. 2003 Dec 9;42(48):14083-91 PMID: 14640675
  41. Direct detection of oxygen intermediates in the non-heme Fe enzyme taurine/alpha-ketoglutarate dioxygenase.
    J Am Chem Soc. 2004 Feb 4;126(4):1022-3 PMID: 14746461
  42. Kinetic dissection of the catalytic mechanism of taurine:alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli.
    Biochemistry. 2005 Jun 7;44(22):8138-47 PMID: 15924433
  43. Stalking intermediates in oxygen activation by iron enzymes: motivation and method.
    J Inorg Biochem. 2006 Apr;100(4):586-605 PMID: 16513177
  44. HIF-1alpha binding to VHL is regulated by stimulus-sensitive proline hydroxylation.
    Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9630-5 PMID: 11504942
  45. Oxygen sensing by HIF hydroxylases.
    Nat Rev Mol Cell Biol. 2004 May;5(5):343-54 PMID: 15122348
  46. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis.
    Nature. 2005 Aug 25;436(7054):1191-4 PMID: 16121186
  47. Giant viruses infecting algae.
    Annu Rev Microbiol. 1999;53:447-94 PMID: 10547698
  48. FeII/alpha-ketoglutarate-dependent hydroxylases and related enzymes.
    Crit Rev Biochem Mol Biol. 2004 Jan-Feb;39(1):21-68 PMID: 15121720
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0604005103
Published
2006-10-03
Epub
2006-00-26
Pages
14738-43
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1578498
Subset
IM
Grants
NIGMS NIH HHS · R01 GM069657 · United States
NIGMS NIH HHS · GM 69657 · United States
External Links
PubMed source DOI: 10.1073/pnas.0604005103 PMC Full Text View journal details
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