Dynamic states of the DNA repair enzyme AlkB regulate product release

EMBO Reports

Volumn 9, Issue 9, 2008, Pages 872-877

  Bleijlevens, Boris ^a   Shivarattan, Tara ^a   Flashman, Emily ^b   Yang, Yi ^a   Simpson, Pete J ^a   Koivisto, Pertti ^c   Sedgwick, Barbara ^c   Schofield, Christopher J ^b   Matthews, Steve J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PROTEIN ALKB; SUCCINIC ACID;

ARTICLE; BETA SHEET; BINDING AFFINITY; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DECARBOXYLATION; DNA DAMAGE; DNA METHYLATION; ENZYME SUBSTRATE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; STRUCTURE ACTIVITY RELATION;

CALORIMETRY; CIRCULAR DICHROISM; ESCHERICHIA COLI PROTEINS; KETOGLUTARIC ACIDS; MAGNETIC RESONANCE SPECTROSCOPY; MIXED FUNCTION OXYGENASES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SUCCINIC ACID;

EID: 51049115752     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/embor.2008.120     Document Type: Article

References (17)

1. Aas PA et al (2003) Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421: 859-863
2. Bertini I, Fragai M, Lee YM, Luchinat C, Terni B (2004) Paramagnetic metal ions in ligand screening: The Co-II matrix metalloproteinase 12. Angew Chem Int Ed 43: 2254-2256
3. Clifton IJ, McDonough MA, Ehrismann D, Kershaw NJ, Granatino N, Schofield CJ (2006) Structural studies on 2-oxoglutarate oxygenases and related double-stranded β-helix fold proteins. J Inorg Biochem 100: 644-669
4. Duncan T, Trewick SC, Koivisto P, Bates PA, Lindahl T, Sedgwick B (2002) Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci USA 99: 16660-16665
5. Falnes PO, Johansen RF, Seeberg E (2002) AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419: 178-182
6. Henshaw TF, Feig M, Hausinger RP (2004) Aberrant activity of the DNA repair enzyme AlkB. J Inorg Biochem 98: 856-861
7. Hewitson KS, Lienard BM, McDonough MA, Clifton IJ, Butler D, Soares AS, Oldham NJ, McNeill LA, Schofield CJ (2007) Structural and mechanistic studies on the inhibition of the hypoxia-inducible transcription factor hydroxylases by tricarboxylic acid cycle intermediates. J Biol Chem 282: 3293-3301
8. McDonough MA et al (2006) Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2). Proc Natl Acad Sci USA 103: 9814-9819
9. McNeill LA, Flashman E, Buck MR, Hewitson KS, Clifton IJ, Jeschke G, Claridge TD, Ehrismann D, Oldham NJ, Schofield CJ (2005) Hypoxia-inducible factor prolyl hydroxylase 2 has a high affinity for ferrous iron and 2-oxoglutarate. Mol Biosyst 1: 321-324
10. Mishina Y, Chen LX, He C (2004) Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli. J Am Chem Soc 126: 16930-16936
11. Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T (2007) Repair of alkylated DNA: Recent advances. DNA Repair 6: 429-442
12. Selak MA, Armour SM, MacKenzie ED, Boulahbel H, Watson DG, Mansfield KD, Pan Y, Simon MC, Thompson CB, Gottlieb E (2005) Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-α prolyl hydroxylase. Cancer Cell 7: 77-85
13. Shivarattan T, Chen HA, Simpson P, Sedgwick B, Matthews S (2005) Resonance assignments of Escherichia coli AlkB: A key 2-oxoglutarate and Fe(II) dependent dioxygenase of the adaptive DNA-repair response. J Biomol NMR 33: 138
14. Solomon EI, Decker A, Lehnert N (2003) Non-heme iron enzymes: Contrasts to heme catalysis. Proc Natl Acad Sci USA 100: 3589-3594
15. Sundheim O, Vagbo CB, Bjoras M, Sousa MML, Talstad V, Aas PA, Drablos F, Krokan HE, Tainer JA, Slupphaug G (2006) Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J 25: 3389-3397
16. Trewick SC, Henshaw TF, Hausinger RP, Lindahl T, Sedgwick B (2002) oxidative demethylation by Escherichia coli AlkB-directly reverts DNA base damage. Nature 419: 174-178
17. Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) Crystal structures of catalytic complexes of the oxidative DNA/ RNA repair enzyme AlkB. Nature 439: 879-884