3dhi Citations

Structural consequences of effector protein complex formation in a diiron hydroxylase.

Proc Natl Acad Sci U S A 105 19194-8 (2008)
Related entries: 3dhg, 3dhh

Cited: 61 times
EuropePMC logo PMID: 19033467

Abstract

Carboxylate-bridged diiron hydroxylases are multicomponent enzyme complexes responsible for the catabolism of a wide range of hydrocarbons and as such have drawn attention for their mechanism of action and potential uses in bioremediation and enzymatic synthesis. These enzyme complexes use a small molecular weight effector protein to modulate the function of the hydroxylase. However, the origin of these functional changes is poorly understood. Here, we report the structures of the biologically relevant effector protein-hydroxylase complex of toluene 4-monooxygenase in 2 redox states. The structures reveal a number of coordinated changes that occur up to 25 A from the active site and poise the diiron center for catalysis. The results provide a structural basis for the changes observed in a number of the measurable properties associated with effector protein binding. This description provides insight into the functional role of effector protein binding in all carboxylate-bridged diiron hydroxylases.

Reviews - 3dhi mentioned but not cited (1)

Articles - 3dhi mentioned but not cited (6)

  1. Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. Cooley RB, Arp DJ, Karplus PA. J. Mol. Biol. 404 232-246 (2010)
  2. Structural consequences of effector protein complex formation in a diiron hydroxylase. Bailey LJ, McCoy JG, Phillips GN, Fox BG. Proc. Natl. Acad. Sci. U.S.A. 105 19194-19198 (2008)
  3. Coupling Oxygen Consumption with Hydrocarbon Oxidation in Bacterial Multicomponent Monooxygenases. Wang W, Liang AD, Lippard SJ. Acc. Chem. Res. 48 2632-2639 (2015)
  4. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. J. Am. Chem. Soc. 133 7384-7397 (2011)
  5. Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system. Acheson JF, Bailey LJ, Elsen NL, Fox BG. Nat Commun 5 5009 (2014)
  6. Aberrant coordination geometries discovered in the most abundant metalloproteins. Yao S, Flight RM, Rouchka EC, Moseley HN. Proteins 85 885-907 (2017)


Reviews citing this publication (6)

  1. Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis. Blank LM, Ebert BE, Buehler K, Bühler B. Antioxid. Redox Signal. 13 349-394 (2010)
  2. Substrate tunnels in enzymes: structure-function relationships and computational methodology. Kingsley LJ, Lill MA. Proteins 83 599-611 (2015)
  3. Structural and biophysical insight into cholesteryl ester-transfer protein. Hall J, Qiu X. Biochem. Soc. Trans. 39 1000-1005 (2011)
  4. Assembly of nonheme Mn/Fe active sites in heterodinuclear metalloproteins. Griese JJ, Srinivas V, Högbom M. J. Biol. Inorg. Chem. 19 759-774 (2014)
  5. Soluble Methane Monooxygenase. Banerjee R, Jones JC, Lipscomb JD. Annu Rev Biochem 88 409-431 (2019)
  6. Engineering non-heme mono- and dioxygenases for biocatalysis. Dror A, Fishman A. Comput Struct Biotechnol J 2 e201209011 (2012)

Articles citing this publication (48)

  1. Docking, scoring, and affinity prediction in CAPRI. Lensink MF, Wodak SJ. Proteins 81 2082-2095 (2013)
  2. Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O2 with a nonheme diiron center. Vu VV, Emerson JP, Martinho M, Kim YS, Münck E, Park MH, Que L. Proc. Natl. Acad. Sci. U.S.A. 106 14814-14819 (2009)
  3. Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway. Tinberg CE, Lippard SJ. Biochemistry 48 12145-12158 (2009)
  4. Control of substrate access to the active site in methane monooxygenase. Lee SJ, McCormick MS, Lippard SJ, Cho US. Nature 494 380-384 (2013)
  5. A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold. Andersson CS, Högbom M. Proc. Natl. Acad. Sci. U.S.A. 106 5633-5638 (2009)
  6. Determination of tyrosinase substrate-binding modes reveals mechanistic differences between type-3 copper proteins. Goldfeder M, Kanteev M, Isaschar-Ovdat S, Adir N, Fishman A. Nat Commun 5 4505 (2014)
  7. Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate. Pandelia ME, Li N, Nørgaard H, Warui DM, Rajakovich LJ, Chang WC, Booker SJ, Krebs C, Bollinger JM. J. Am. Chem. Soc. 135 15801-15812 (2013)
  8. Characterization of a peroxodiiron(III) intermediate in the T201S variant of toluene/o-xylene monooxygenase hydroxylase from Pseudomonas sp. OX1. Song WJ, Behan RK, Naik SG, Huynh BH, Lippard SJ. J. Am. Chem. Soc. 131 6074-6075 (2009)
  9. Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex. Grishin AM, Ajamian E, Tao L, Zhang L, Menard R, Cygler M. J. Biol. Chem. 286 10735-10743 (2011)
  10. Active site threonine facilitates proton transfer during dioxygen activation at the diiron center of toluene/o-xylene monooxygenase hydroxylase. Song WJ, McCormick MS, Behan RK, Sazinsky MH, Jiang W, Lin J, Krebs C, Lippard SJ. J. Am. Chem. Soc. 132 13582-13585 (2010)
  11. Structure of a dinuclear iron cluster-containing β-hydroxylase active in antibiotic biosynthesis. Makris TM, Knoot CJ, Wilmot CM, Lipscomb JD. Biochemistry 52 6662-6671 (2013)
  12. Tracking a defined route for O₂ migration in a dioxygen-activating diiron enzyme. Song WJ, Gucinski G, Sazinsky MH, Lippard SJ. Proc. Natl. Acad. Sci. U.S.A. 108 14795-14800 (2011)
  13. Analysis of substrate access to active sites in bacterial multicomponent monooxygenase hydroxylases: X-ray crystal structure of xenon-pressurized phenol hydroxylase from Pseudomonas sp. OX1. McCormick MS, Lippard SJ. Biochemistry 50 11058-11069 (2011)
  14. Multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas sp. OX1. Tinberg CE, Song WJ, Izzo V, Lippard SJ. Biochemistry 50 1788-1798 (2011)
  15. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Proteins 81 2192-2200 (2013)
  16. Performance of ZDOCK in CAPRI rounds 20-26. Vreven T, Pierce BG, Hwang H, Weng Z. Proteins 81 2175-2182 (2013)
  17. Improving biocatalyst performance by integrating statistical methods into protein engineering. Brouk M, Nov Y, Fishman A. Appl. Environ. Microbiol. 76 6397-6403 (2010)
  18. Electron transfer control in soluble methane monooxygenase. Wang W, Iacob RE, Luoh RP, Engen JR, Lippard SJ. J. Am. Chem. Soc. 136 9754-9762 (2014)
  19. Comment Frontiers in enzymatic C-H-bond activation. Bollinger JM, Broderick JB. Curr Opin Chem Biol 13 51-57 (2009)
  20. In-crystal reaction cycle of a toluene-bound diiron hydroxylase. Acheson JF, Bailey LJ, Brunold TC, Fox BG. Nature 544 191-195 (2017)
  21. Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. Griese JJ, Kositzki R, Schrapers P, Branca RM, Nordström A, Lehtiö J, Haumann M, Högbom M. J. Biol. Chem. 290 25254-25272 (2015)
  22. Structural Studies of the Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel. Jones JC, Banerjee R, Shi K, Aihara H, Lipscomb JD. Biochemistry 59 2946-2961 (2020)
  23. Study of the TmoS/TmoT two-component system: towards the functional characterization of the family of TodS/TodT like systems. Silva-Jiménez H, García-Fontana C, Cadirci BH, Ramos-González MI, Ramos JL, Krell T. Microb Biotechnol 5 489-500 (2012)
  24. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou X. Proteins 81 2183-2191 (2013)
  25. The targets of CAPRI rounds 20-27. Janin J. Proteins 81 2075-2081 (2013)
  26. Tuning the specificity of the recombinant multicomponent toluene o-xylene monooxygenase from Pseudomonas sp. strain OX1 for the biosynthesis of tyrosol from 2-phenylethanol. Notomista E, Scognamiglio R, Troncone L, Donadio G, Pezzella A, Di Donato A, Izzo V. Appl. Environ. Microbiol. 77 5428-5437 (2011)
  27. Mechanistic studies of reactions of peroxodiiron(III) intermediates in T201 variants of toluene/o-xylene monooxygenase hydroxylase. Song WJ, Lippard SJ. Biochemistry 50 5391-5399 (2011)
  28. A flexible glutamine regulates the catalytic activity of toluene o-xylene monooxygenase. Liang AD, Wrobel AT, Lippard SJ. Biochemistry 53 3585-3592 (2014)
  29. Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond. Qin S, Zhou HX. Proteins 81 2229-2236 (2013)
  30. Component interactions and electron transfer in toluene/o-xylene monooxygenase. Liang AD, Lippard SJ. Biochemistry 53 7368-7375 (2014)
  31. Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB. Liao RZ, Siegbahn PEM. Chem Sci 6 2754-2764 (2015)
  32. Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complex. Grishin AM, Ajamian E, Zhang L, Cygler M. Acta Crystallogr Sect F Struct Biol Cryst Commun 66 1045-1049 (2010)
  33. Recombinant expression, purification, and characterization of ThmD, the oxidoreductase component of tetrahydrofuran monooxygenase. Oppenheimer M, Pierce BS, Crawford JA, Ray K, Helm RF, Sobrado P. Arch. Biochem. Biophys. 496 123-131 (2010)
  34. Family of phenylacetyl-CoA monooxygenases differs in subunit organization from other monooxygenases. Grishin AM, Ajamian E, Tao L, Bostina M, Zhang L, Trempe JF, Menard R, Rouiller I, Cygler M. J. Struct. Biol. 184 147-154 (2013)
  35. Ligand-Constraint-Induced Peroxide Activation for Electrophilic Reactivity. Chandra A, Ansari M, Monte-Pérez I, Kundu S, Rajaraman G, Ray K. Angew Chem Int Ed Engl 60 14954-14959 (2021)
  36. Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase. Bím D, Chalupský J, Culka M, Solomon EI, Rulíšek L, Srnec M. J Am Chem Soc 142 10412-10423 (2020)
  37. Cavity residue leucine 95 and channel residues glutamine 204, aspartic acid 211, and phenylalanine 269 of toluene o-xylene monooxygenase influence catalysis. Kurt C, Sönmez B, Vardar N, Yanık-Yıldırım KC, Vardar-Schara G. Appl. Microbiol. Biotechnol. 100 7599-7609 (2016)
  38. Deoxycholate-Enhanced Shigella Virulence Is Regulated by a Rare π-Helix in the Type Three Secretion System Tip Protein IpaD. Bernard AR, Jessop TC, Kumar P, Dickenson NE. Biochemistry 56 6503-6514 (2017)
  39. Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy. Wang Z, Wang M, Zhao Z, Zheng P. Protein Sci 32 e4583 (2023)
  40. Saturation mutagenesis of Bradyrhizobium sp. BTAi1 toluene 4-monooxygenase at alpha-subunit residues proline 101, proline 103, and histidine 214 for regiospecific oxidation of aromatics. Yanık-Yıldırım KC, Vardar-Schara G. Appl. Microbiol. Biotechnol. 98 8975-8986 (2014)
  41. Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR. Jones JC, Banerjee R, Shi K, Semonis MM, Aihara H, Pomerantz WCK, Lipscomb JD. Biochemistry 60 1995-2010 (2021)
  42. The YHS-Domain of an Adenylyl Cyclase from Mycobacterium phlei Is a Probable Copper-Sensor Module. Linder JU. PLoS ONE 10 e0141843 (2015)
  43. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Banerjee R, Srinivas V, Lebrette H. Subcell Biochem 99 109-153 (2022)
  44. research-article Metalloenzymes: Put a ring on it. Rosenzweig AC. Nat. Chem. Biol. 9 220-221 (2013)
  45. On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all-Atom Molecular Dynamics Investigation in Water Solution. Pietra F. Chem. Biodivers. 14 (2017)
  46. Purification and Characterization of the Isoprene Monooxygenase from Rhodococcus sp. Strain AD45. Sims LP, Lockwood CWJ, Crombie AT, Bradley JM, Le Brun NE, Murrell JC. Appl Environ Microbiol 88 e0002922 (2022)
  47. Substrate-Triggered μ-Peroxodiiron(III) Intermediate in the 4-Chloro-l-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate. McBride MJ, Nair MA, Sil D, Slater JW, Neugebauer ME, Chang MCY, Boal AK, Krebs C, Bollinger JM. Biochemistry 61 689-702 (2022)
  48. π-Helix controls activity of oxygen-sensing diguanylate cyclases. Walker JA, Wu Y, Potter JR, Weinert EE. Biosci Rep 40 (2020)