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Crystal structure of substrate-free Pseudomonas putida cytochrome P-450.

Poulos TL, Finzel BC, Howard AJ
Biochemistry 25 5314-22 (1986)
Cited: 219 times
EuropePMC logo PMID: 3768350

Abstract

The crystal structure of Pseudomonas putida cytochrome P-450cam in the substrate-free form has been refined at 2.20-A resolution and compared to the substrate-bound form of the enzyme. In the absence of the substrate camphor, the P-450cam heme iron atom is hexacoordinate with the sulfur atom of Cys-357 providing one axial heme ligand and a water molecule or hydroxide ion providing the other axial ligand. A network of hydrogen-bonded solvent molecules occupies the substrate pocket in addition to the iron-linked aqua ligand. When a camphor molecule binds, the active site waters including the aqua ligand are displaced, resulting in a pentacoordinate high-spin heme iron atom. Analysis of the Fno camphor - F camphor difference Fourier and a quantitative comparison of the two refined structures reveal that no detectable conformational change results from camphor binding other than a small repositioning of a phenylalanine side chain that contacts the camphor molecule. However, large decreases in the mean temperature factors of three separate segments of the protein centered on Tyr-96, Thr-185, and Asp-251 result from camphor binding. This indicates that camphor binding decreases the flexibility in these three regions of the P-450cam molecule without altering the mean position of the atoms involved.

Reviews - 1phc mentioned but not cited (3)

  1. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. Lawton TJ, Rosenzweig AC. J Am Chem Soc 138 9327-9340 (2016)
  2. Functional and protective hole hopping in metalloenzymes. Gray HB, Winkler JR. Chem Sci 12 13988-14003 (2021)
  3. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)

Articles - 1phc mentioned but not cited (16)

  1. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. Huang B, Schroeder M. BMC Struct Biol 6 19 (2006)
  2. PocketPicker: analysis of ligand binding-sites with shape descriptors. Weisel M, Proschak E, Schneider G. Chem Cent J 1 7 (2007)
  3. Mechanisms of Cytochrome P450-Catalyzed Oxidations. Guengerich FP. ACS Catal 8 10964-10976 (2018)
  4. Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments. Shimizu S. Proc Natl Acad Sci U S A 101 1195-1199 (2004)
  5. Identification of a functional water channel in cytochrome P450 enzymes. Oprea TI, Hummer G, Garcia AE. Proc Natl Acad Sci U S A 94 2133-2138 (1997)
  6. Real-time ligand binding pocket database search using local surface descriptors. Chikhi R, Sael L, Kihara D. Proteins 78 2007-2028 (2010)
  7. Solution structural ensembles of substrate-free cytochrome P450(cam). Asciutto EK, Young MJ, Madura J, Pochapsky SS, Pochapsky TC. Biochemistry 51 3383-3393 (2012)
  8. Binding cavities and druggability of intrinsically disordered proteins. Zhang Y, Cao H, Liu Z. Protein Sci 24 688-705 (2015)
  9. Predicting protein function from structure: unique structural features of proteases. Stawiski EW, Baucom AE, Lohr SC, Gregoret LM. Proc Natl Acad Sci U S A 97 3954-3958 (2000)
  10. Hydrophobic moments of protein structures: spatially profiling the distribution. Silverman BD. Proc Natl Acad Sci U S A 98 4996-5001 (2001)
  11. Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. Miao Y, Baudry J. Biophys J 101 1493-1503 (2011)
  12. Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes. Karunakaran V, Denisov I, Sligar SG, Champion PM. J Phys Chem B 115 5665-5677 (2011)
  13. Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4. Gorokhov A, Negishi M, Johnson EF, Pedersen LC, Perera L, Darden TA, Pedersen LG. Biophys J 84 57-68 (2003)
  14. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area. Cao C, Xu S. Sci Rep 6 33232 (2016)
  15. A new definition and properties of the similarity value between two protein structures. Saberi Fathi SM. J Biol Phys 42 621-636 (2016)
  16. Reconciling conformational heterogeneity and substrate recognition in cytochrome P450. Dandekar BR, Ahalawat N, Mondal J. Biophys J 120 1732-1745 (2021)


Reviews citing this publication (41)

  1. Purification and characterization of hepatic microsomal cytochrome P-450. Ryan DE, Levin W. Pharmacol Ther 45 153-239 (1990)
  2. Diversity of P450 enzymes in the biosynthesis of natural products. Podust LM, Sherman DH. Nat Prod Rep 29 1251-1266 (2012)
  3. Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. Munro AW, Girvan HM, McLean KJ. Nat Prod Rep 24 585-609 (2007)
  4. Oxygen and xenobiotic reductase activities of cytochrome P450. Goeptar AR, Scheerens H, Vermeulen NP. Crit Rev Toxicol 25 25-65 (1995)
  5. Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology. Reece SY, Hodgkiss JM, Stubbe J, Nocera DG. Philos Trans R Soc Lond B Biol Sci 361 1351-1364 (2006)
  6. Recent Structural Insights into Cytochrome P450 Function. Guengerich FP, Waterman MR, Egli M. Trends Pharmacol Sci 37 625-640 (2016)
  7. How similar are P450s and what can their differences teach us? Graham SE, Peterson JA. Arch Biochem Biophys 369 24-29 (1999)
  8. What makes a P450 tick? Munro AW, Girvan HM, Mason AE, Dunford AJ, McLean KJ. Trends Biochem Sci 38 140-150 (2013)
  9. Fatty acid hydroperoxide lyase: a plant cytochrome p450 enzyme involved in wound healing and pest resistance. Noordermeer MA, Veldink GA, Vliegenthart JF. Chembiochem 2 494-504 (2001)
  10. Comparative aspects of the mammalian cytochrome P450 IV gene family. Gibson GG. Xenobiotica 19 1123-1148 (1989)
  11. Substrate binding to cytochromes P450. Isin EM, Guengerich FP. Anal Bioanal Chem 392 1019-1030 (2008)
  12. Conformational plasticity and structure/function relationships in cytochromes P450. Pochapsky TC, Kazanis S, Dang M. Antioxid Redox Signal 13 1273-1296 (2010)
  13. Cytochrome P450 biosensors-a review. Bistolas N, Wollenberger U, Jung C, Scheller FW. Biosens Bioelectron 20 2408-2423 (2005)
  14. The status of high-valent metal oxo complexes in the P450 cytochromes. Makris TM, von Koenig K, Schlichting I, Sligar SG. J Inorg Biochem 100 507-518 (2006)
  15. Transient complexes of redox proteins: structural and dynamic details from NMR studies. Prudêncio M, Ubbink M. J Mol Recognit 17 524-539 (2004)
  16. Structural determinants of cytochrome P450 substrate specificity, binding affinity and catalytic rate. Lewis DF, Eddershaw PJ, Dickins M, Tarbit MH, Goldfarb PS. Chem Biol Interact 115 175-199 (1998)
  17. Biotransformations using prokaryotic P450 monooxygenases. Urlacher V, Schmid RD. Curr Opin Biotechnol 13 557-564 (2002)
  18. Modeling kinetics of subcellular disposition of chemicals. Balaz S. Chem Rev 109 1793-1899 (2009)
  19. Interactions between cytochrome P450 and cytochrome b5. Schenkman JB, Jansson I. Drug Metab Rev 31 351-364 (1999)
  20. Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s. Pylypenko O, Schlichting I. Annu Rev Biochem 73 991-1018 (2004)
  21. Pharmacophore modeling of cytochromes P450. de Groot MJ, Ekins S. Adv Drug Deliv Rev 54 367-383 (2002)
  22. The P450 catalytic cycle and oxygenation mechanism. Lewis DF, Pratt JM. Drug Metab Rev 30 739-786 (1998)
  23. The involvement of free radicals in the mechanisms of monooxygenases. White RE. Pharmacol Ther 49 21-42 (1991)
  24. Cytochrome P450: molecular architecture, mechanism, and prospects for rational inhibitor design. Poulos TL. Pharm Res 5 67-75 (1988)
  25. Ligand Access Channels in Cytochrome P450 Enzymes: A Review. Urban P, Lautier T, Pompon D, Truan G. Int J Mol Sci 19 E1617 (2018)
  26. P450 structures and oxidative metabolism of xenobiotics. Lewis DF. Pharmacogenomics 4 387-395 (2003)
  27. New cytochrome P450 mechanisms: implications for understanding molecular basis for drug toxicity at the level of the cytochrome. Shakunthala N. Expert Opin Drug Metab Toxicol 6 1-15 (2010)
  28. Protein engineering of cytochromes P-450. Miles CS, Ost TW, Noble MA, Munro AW, Chapman SK. Biochim Biophys Acta 1543 383-407 (2000)
  29. Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures. Li H, Poulos TL. Structure 2 461-464 (1994)
  30. Cytochromes P450: their active-site structure and mechanism of oxidation. Koymans L, Donné-op den Kelder GM, Koppele Te JM, Vermeulen NP. Drug Metab Rev 25 325-387 (1993)
  31. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. J Biomol Struct Dyn 31 630-648 (2013)
  32. Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions. Maréchal JD, Kemp CA, Roberts GC, Paine MJ, Wolf CR, Sutcliffe MJ. Br J Pharmacol 153 Suppl 1 S82-9 (2008)
  33. Progress in cytochrome P450 active site modeling. Kemp CA, Maréchal JD, Sutcliffe MJ. Arch Biochem Biophys 433 361-368 (2005)
  34. New findings in studies of cytochromes P450. Myasoedova KN. Biochemistry (Mosc) 73 965-969 (2008)
  35. Miniaturized hemoproteins. Nastri F, Lombardi A, D'Andrea LD, Sanseverino M, Maglio O, Pavone V. Biopolymers 47 5-22 (1998)
  36. Autoxidation of oxymyoglobin: a meeting point of the stabilization and the activation of molecular oxygen. Shikama K. Biol Rev Camb Philos Soc 65 517-527 (1990)
  37. Modeling the active sites of cytochrome P450s and glutathione S-transferases, two of the most important biotransformation enzymes. De Groot MJ, Vermeulen NP. Drug Metab Rev 29 747-799 (1997)
  38. H93G myoglobin cavity mutant as versatile template for modeling heme proteins: magnetic circular dichroism studies of thiolate- and imidazole-ligated complexes. Dawson JH, Pond AE, Roach MP. Biopolymers 67 200-206 (2002)
  39. Recombinant Technologies Facilitate Drug Metabolism, Pharmacokinetics, and General Biomedical Research. Cronin JM, Yu AM. Drug Metab Dispos 51 685-699 (2023)
  40. Conformational analysis and computer graphics in drug research. Tollenaere JP, Janssen PA. Med Res Rev 8 1-25 (1988)
  41. Machine Learning and Computational Chemistry for the Endocannabinoid System. Atz K, Guba W, Grether U, Schneider G. Methods Mol Biol 2576 477-493 (2023)

Articles citing this publication (159)

  1. High-resolution crystal structure of cytochrome P450cam. Poulos TL, Finzel BC, Howard AJ. J Mol Biol 195 687-700 (1987)
  2. Structure and function of cytochromes P450: a comparative analysis of three crystal structures. Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J. Structure 3 41-62 (1995)
  3. Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Cupp-Vickery JR, Poulos TL. Nat Struct Biol 2 144-153 (1995)
  4. Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution. Hasemann CA, Ravichandran KG, Peterson JA, Deisenhofer J. J Mol Biol 236 1169-1185 (1994)
  5. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. Lüdemann SK, Lounnas V, Wade RC. J Mol Biol 303 797-811 (2000)
  6. Uncoupling of the cytochrome P-450cam monooxygenase reaction by a single mutation, threonine-252 to alanine or valine: possible role of the hydroxy amino acid in oxygen activation. Imai M, Shimada H, Watanabe Y, Matsushima-Hibiya Y, Makino R, Koga H, Horiuchi T, Ishimura Y. Proc Natl Acad Sci U S A 86 7823-7827 (1989)
  7. Conservation of the conformation of the porphyrin macrocycle in hemoproteins. Jentzen W, Ma JG, Shelnutt JA. Biophys J 74 753-763 (1998)
  8. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine. Winn PJ, Lüdemann SK, Gauges R, Lounnas V, Wade RC. Proc Natl Acad Sci U S A 99 5361-5366 (2002)
  9. P450cam visits an open conformation in the absence of substrate. Lee YT, Wilson RF, Rupniewski I, Goodin DB. Biochemistry 49 3412-3419 (2010)
  10. Heme proteins--diversity in structural characteristics, function, and folding. Smith LJ, Kahraman A, Thornton JM. Proteins 78 2349-2368 (2010)
  11. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. Lüdemann SK, Lounnas V, Wade RC. J Mol Biol 303 813-830 (2000)
  12. Letter The catalytic mechanism of cytochrome P450 BM3 involves a 6 A movement of the bound substrate on reduction. Modi S, Sutcliffe MJ, Primrose WU, Lian LY, Roberts GC. Nat Struct Biol 3 414-417 (1996)
  13. Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity. Cupp-Vickery J, Anderson R, Hatziris Z. Proc Natl Acad Sci U S A 97 3050-3055 (2000)
  14. Identification of a new class of cytochrome P450 from a Rhodococcus sp. Roberts GA, Grogan G, Greter A, Flitsch SL, Turner NJ. J Bacteriol 184 3898-3908 (2002)
  15. Designing better drugs: predicting cytochrome P450 metabolism. de Groot MJ. Drug Discov Today 11 601-606 (2006)
  16. Characterization of a cytochrome P450 from the acidothermophilic archaea Sulfolobus solfataricus. McLean MA, Maves SA, Weiss KE, Krepich S, Sligar SG. Biochem Biophys Res Commun 252 166-172 (1998)
  17. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Helms V, Wade RC. Biophys J 69 810-824 (1995)
  18. Activation of cytochrome P450 2C9-mediated metabolism: mechanistic evidence in support of kinetic observations. Hutzler JM, Wienkers LC, Wahlstrom JL, Carlson TJ, Tracy TS. Arch Biochem Biophys 410 16-24 (2003)
  19. Three-dimensional models of human and other mammalian microsomal P450s constructed from an alignment with P450102 (P450bm3). Lewis DF. Xenobiotica 25 333-366 (1995)
  20. The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. Podust LM, Kim Y, Arase M, Neely BA, Beck BJ, Bach H, Sherman DH, Lamb DC, Kelly SL, Waterman MR. J Biol Chem 278 12214-12221 (2003)
  21. A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam. Paulsen MD, Ornstein RL. Proteins 11 184-204 (1991)
  22. Structure conservation in cytochromes P450. Mestres J. Proteins 58 596-609 (2005)
  23. A molecular model for the enzyme cytochrome P450(17 alpha), a major target for the chemotherapy of prostatic cancer. Laughton CA, Neidle S, Zvelebil MJ, Sternberg MJ. Biochem Biophys Res Commun 171 1160-1167 (1990)
  24. Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK. Nagano S, Li H, Shimizu H, Nishida C, Ogura H, Ortiz de Montellano PR, Poulos TL. J Biol Chem 278 44886-44893 (2003)
  25. The heme monooxygenase cytochrome P450cam can be engineered to oxidize ethane to ethanol. Xu F, Bell SG, Lednik J, Insley A, Rao Z, Wong LL. Angew Chem Int Ed Engl 44 4029-4032 (2005)
  26. Interaction of Ferredoxin-NADP(+) Reductase with its Substrates: Optimal Interaction for Efficient Electron Transfer. Medina M, Gómez-Moreno C. Photosynth Res 79 113-131 (2004)
  27. A single amino acid substitution converts cytochrome P450(14DM) to an inactive form, cytochrome P450SG1: complete primary structures deduced from cloned DNAS. Ishida N, Aoyama Y, Hatanaka R, Oyama Y, Imajo S, Ishiguro M, Oshima T, Nakazato H, Noguchi T, Maitra US. Biochem Biophys Res Commun 155 317-323 (1988)
  28. Crystal structure of the human prostacyclin synthase. Chiang CW, Yeh HC, Wang LH, Chan NL. J Mol Biol 364 266-274 (2006)
  29. Flavocytochrome P450 BM3 mutant A264E undergoes substrate-dependent formation of a novel heme iron ligand set. Girvan HM, Marshall KR, Lawson RJ, Leys D, Joyce MG, Clarkson J, Smith WE, Cheesman MR, Munro AW. J Biol Chem 279 23274-23286 (2004)
  30. The iron environment in heme and heme-antimalarial complexes of pharmacological interest. Adams PA, Berman PA, Egan TJ, Marsh PJ, Silver J. J Inorg Biochem 63 69-77 (1996)
  31. Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel. Lee YT, Glazer EC, Wilson RF, Stout CD, Goodin DB. Biochemistry 50 693-703 (2011)
  32. Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. Markwick PR, Pierce LC, Goodin DB, McCammon JA. J Phys Chem Lett 2 158-164 (2011)
  33. The pea gene LH encodes ent-kaurene oxidase. Davidson SE, Smith JJ, Helliwell CA, Poole AT, Reid JB. Plant Physiol 134 1123-1134 (2004)
  34. Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4. De Rienzo F, Fanelli F, Menziani MC, De Benedetti PG. J Comput Aided Mol Des 14 93-116 (2000)
  35. Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state. Harris DL, Park JY, Gruenke L, Waskell L. Proteins 55 895-914 (2004)
  36. Determinants of the substrate specificity of human cytochrome P-450 CYP2D6: design and construction of a mutant with testosterone hydroxylase activity. Smith G, Modi S, Pillai I, Lian LY, Sutcliffe MJ, Pritchard MP, Friedberg T, Roberts GC, Wolf CR. Biochem J 331 ( Pt 3) 783-792 (1998)
  37. Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity. Knudsen GM, Nishida CR, Mooney SD, Ortiz de Montellano PR. J Biol Chem 278 31814-31824 (2003)
  38. 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands. Lozano JJ, Pastor M, Cruciani G, Gaedt K, Centeno NB, Gago F, Sanz F. J Comput Aided Mol Des 14 341-353 (2000)
  39. A functional proline switch in cytochrome P450cam. OuYang B, Pochapsky SS, Dang M, Pochapsky TC. Structure 16 916-923 (2008)
  40. Identification of intermediates in the catalytic cycle of chloroperoxidase. Wagenknecht HA, Woggon WD. Chem Biol 4 367-372 (1997)
  41. Marketed Drugs Can Inhibit Cytochrome P450 27A1, a Potential New Target for Breast Cancer Adjuvant Therapy. Mast N, Lin JB, Pikuleva IA. Mol Pharmacol 88 428-436 (2015)
  42. Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy. Thielges MC, Chung JK, Fayer MD. J Am Chem Soc 133 3995-4004 (2011)
  43. Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods. Liu LV, Bell CB, Wong SD, Wilson SA, Kwak Y, Chow MS, Zhao J, Hodgson KO, Hedman B, Solomon EI. Proc Natl Acad Sci U S A 107 22419-22424 (2010)
  44. Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance. Colthart AM, Tietz DR, Ni Y, Friedman JL, Dang M, Pochapsky TC. Sci Rep 6 22035 (2016)
  45. Purification and characterization of benzoate-para-hydroxylase, a cytochrome P450 (CYP53A1), from Aspergillus niger. Faber BW, van Gorcom RF, Duine JA. Arch Biochem Biophys 394 245-254 (2001)
  46. Antagonistic effects of hydrostatic pressure and osmotic pressure on cytochrome P-450cam spin transition. Di Primo C, Deprez E, Hoa GH, Douzou P. Biophys J 68 2056-2061 (1995)
  47. Clay-bridged electron transfer between cytochrome p450(cam) and electrode. Lei C, Wollenberger U, Jung C, Scheller FW. Biochem Biophys Res Commun 268 740-744 (2000)
  48. Substrate-assisted catalysis in cytochrome P450eryF. Cupp-Vickery JR, Han O, Hutchinson CR, Poulos TL. Nat Struct Biol 3 632-637 (1996)
  49. Conformational states of cytochrome P450cam revealed by trapping of synthetic molecular wires. Hays AM, Dunn AR, Chiu R, Gray HB, Stout CD, Goodin DB. J Mol Biol 344 455-469 (2004)
  50. Spectroscopic studies of peroxyacetic acid reaction intermediates of cytochrome P450cam and chloroperoxidase. Schünemann V, Jung C, Terner J, Trautwein AX, Weiss R. J Inorg Biochem 91 586-596 (2002)
  51. A comprehensive test set of epoxidation rate constants for iron(iv)-oxo porphyrin cation radical complexes. Sainna MA, Kumar S, Kumar D, Fornarini S, Crestoni ME, de Visser SP. Chem Sci 6 1516-1529 (2015)
  52. Cytochrome P450 conformation and substrate interactions as probed by CO binding kinetics. Koley AP, Robinson RC, Friedman FK. Biochimie 78 706-713 (1996)
  53. NMR study on the structural changes of cytochrome P450cam upon the complex formation with putidaredoxin. Functional significance of the putidaredoxin-induced structural changes. Tosha T, Yoshioka S, Takahashi S, Ishimori K, Shimada H, Morishima I. J Biol Chem 278 39809-39821 (2003)
  54. Structural motif-based homology modeling of CYP27A1 and site-directed mutational analyses affecting vitamin D hydroxylation. Prosser DE, Guo Y, Jia Z, Jones G. Biophys J 90 3389-3409 (2006)
  55. Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6. Kirton SB, Kemp CA, Tomkinson NP, St-Gallay S, Sutcliffe MJ. Proteins 49 216-231 (2002)
  56. In vitro cytochrome P450 46A1 (CYP46A1) activation by neuroactive compounds. Mast N, Anderson KW, Johnson KM, Phan TTN, Guengerich FP, Pikuleva IA. J Biol Chem 292 12934-12946 (2017)
  57. Binding of a cyano- and fluoro-containing drug bicalutamide to cytochrome P450 46A1: unusual features and spectral response. Mast N, Zheng W, Stout CD, Pikuleva IA. J Biol Chem 288 4613-4624 (2013)
  58. Calculation of the electronic structure and spectra of model cytochrome P450 compound I. Harris D, Loew G, Waskell L. J Inorg Biochem 83 309-318 (2001)
  59. Hydration energy landscape of the active site cavity in cytochrome P450cam. Helms V, Wade RC. Proteins 32 381-396 (1998)
  60. Intermediates in the reaction of substrate-free cytochrome P450cam with peroxy acetic acid. Schünemann V, Jung C, Trautwein AX, Mandon D, Weiss R. FEBS Lett 479 149-154 (2000)
  61. Optical detection of cytochrome P450 by sensitizer-linked substrates. Dmochowski IJ, Crane BR, Wilker JJ, Winkler JR, Gray HB. Proc Natl Acad Sci U S A 96 12987-12990 (1999)
  62. Conformational transitions and redox potential shifts of cytochrome P450 induced by immobilization. Todorovic S, Jung C, Hildebrandt P, Murgida DH. J Biol Inorg Chem 11 119-127 (2006)
  63. Crystallization and preliminary x-ray diffraction analysis of P450terp and the hemoprotein domain of P450BM-3, enzymes belonging to two distinct classes of the cytochrome P450 superfamily. Boddupalli SS, Hasemann CA, Ravichandran KG, Lu JY, Goldsmith EJ, Deisenhofer J, Peterson JA. Proc Natl Acad Sci U S A 89 5567-5571 (1992)
  64. Double electron-electron resonance shows cytochrome P450cam undergoes a conformational change in solution upon binding substrate. Stoll S, Lee YT, Zhang M, Wilson RF, Britt RD, Goodin DB. Proc Natl Acad Sci U S A 109 12888-12893 (2012)
  65. Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes. Guengerich FP, Wilkey CJ, Phan TTN. J Biol Chem 294 10928-10941 (2019)
  66. The extreme dwarf phenotype of the GA-sensitive mutant of sunflower, dwarf2, is generated by a deletion in the ent-kaurenoic acid oxidase1 (HaKAO1) gene sequence. Fambrini M, Mariotti L, Parlanti S, Picciarelli P, Salvini M, Ceccarelli N, Pugliesi C. Plant Mol Biol 75 431-450 (2011)
  67. Compressibility of the heme pocket of substrate analogue complexes of cytochrome P-450cam-CO. The effect of hydrostatic pressure on the Soret band. Jung C, Hui Bon Hoa G, Davydov D, Gill E, Heremans K. Eur J Biochem 233 600-606 (1995)
  68. Homology modeling and substrate binding study of human CYP2C9 enzyme. Payne VA, Chang YT, Loew GH. Proteins 37 176-190 (1999)
  69. Homology modeling and substrate binding study of human CYP4A11 enzyme. Chang YT, Loew GH. Proteins 34 403-415 (1999)
  70. CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase. Ly TT, Khatri Y, Zapp J, Hutter MC, Bernhardt R. Appl Microbiol Biotechnol 95 123-133 (2012)
  71. Characterization of the oxygenated intermediate of the thermophilic cytochrome P450 CYP119. Denisov IG, Hung SC, Weiss KE, McLean MA, Shiro Y, Park SY, Champion PM, Sligar SG. J Inorg Biochem 87 215-226 (2001)
  72. DNA haplotype-dependent differences in the amino acid sequence of debrisoquine 4-hydroxylase (CYP2D6): evidence for two major allozymes in extensive metabolisers. Panserat S, Mura C, Gérard N, Vincent-Viry M, Galteau MM, Jacqz-Aigrain E, Krishnamoorthy R. Hum Genet 94 401-406 (1994)
  73. Mutations at the distal and proximal sites of cytochrome P-450d changed regio-specificity of acetanilide hydroxylations. Furuya H, Shimizu T, Hatano M, Fujii-Kuriyama Y. Biochem Biophys Res Commun 160 669-676 (1989)
  74. The sequence homologies of cytochromes P-450 and active-site geometries. Lewis DF, Moereels H. J Comput Aided Mol Des 6 235-252 (1992)
  75. Species differences in coumarin metabolism: a molecular modelling evaluation of CYP2A interactions. Lewis DF, Lake BG. Xenobiotica 32 547-561 (2002)
  76. Stability of the heme environment of the nitric oxide synthase from Staphylococcus aureus in the absence of pterin cofactor. Chartier FJ, Couture M. Biophys J 87 1939-1950 (2004)
  77. The role of tryptophan 97 of cytochrome P450 BM3 from Bacillus megaterium in catalytic function. Evidence against the 'covalent switching' hypothesis of P-450 electron transfer. Munro AW, Malarkey K, McKnight J, Thomson AJ, Kelly SM, Price NC, Lindsay JG, Coggins JR, Miles JS. Biochem J 303 ( Pt 2) 423-428 (1994)
  78. Cloning and expression of a member of a new cytochrome P-450 family: cytochrome P-450lin (CYP111) from Pseudomonas incognita. Ropp JD, Gunsalus IC, Sligar SG. J Bacteriol 175 6028-6037 (1993)
  79. Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, Jain N, Smith JC. Biophys J 103 2167-2176 (2012)
  80. N-(2-ferrocene-ethyl)maleimide: a new electroactive sulphydryl-specific reagent for cysteine-containing peptides and proteins. Di Gleria K, Hill HA, Wong LL. FEBS Lett 390 142-144 (1996)
  81. S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity. Dey A, Jiang Y, Ortiz de Montellano P, Hodgson KO, Hedman B, Solomon EI. J Am Chem Soc 131 7869-7878 (2009)
  82. Binding of camphor to Pseudomonas putida cytochrome p450(cam): steady-state and picosecond time-resolved fluorescence studies. Prasad S, Mazumdar S, Mitra S. FEBS Lett 477 157-160 (2000)
  83. Effect of the tyrosine 96 hydrogen bond on the inactivation of cytochrome P-450cam induced by hydrostatic pressure. Di Primo C, Hui Bon Hoa G, Douzou P, Sligar S. Eur J Biochem 193 383-386 (1990)
  84. Novel family members of CYP109 from Sorangium cellulosum So ce56 exhibit characteristic biochemical and biophysical properties. Khatri Y, Hannemann F, Girhard M, Kappl R, Même A, Ringle M, Janocha S, Leize-Wagner E, Urlacher VB, Bernhardt R. Biotechnol Appl Biochem 60 18-29 (2013)
  85. Spectroscopic studies on the active site of hydroperoxide lyase; the influence of detergents on its conformation. Noordermeer MA, Veldink GA, Vliegenthart JF. FEBS Lett 489 229-232 (2001)
  86. Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site. Yao H, McCullough CR, Costache AD, Pullela PK, Sem DS. Proteins 69 125-138 (2007)
  87. Analysis of active site motions from a 175 picosecond molecular dynamics simulation of camphor-bound cytochrome P450cam. Paulsen MD, Bass MB, Ornstein RL. J Biomol Struct Dyn 9 187-203 (1991)
  88. Conformational dynamics in cytochrome P450-substrate interactions. Li H, Poulos TL. Biochimie 78 695-699 (1996)
  89. Crystal structures of cytochrome P450nor and its mutants (Ser286-->Val, Thr) in the ferric resting state at cryogenic temperature: a comparative analysis with monooxygenase cytochrome P450s. Shimizu H, Park S, Lee D, Shoun H, Shiro Y. J Inorg Biochem 81 191-205 (2000)
  90. Drugs and Scaffold That Inhibit Cytochrome P450 27A1 In Vitro and In Vivo. Lam M, Mast N, Pikuleva IA. Mol Pharmacol 93 101-108 (2018)
  91. Heme-pocket-hydration change during the inactivation of cytochrome P-450camphor by hydrostatic pressure. Di Primo C, Hui Bon Hoa G, Douzou P, Sligar SG. Eur J Biochem 209 583-588 (1992)
  92. Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: cytochrome P450eryF. Cupp-Vickery JR, Li H, Poulos TL. Proteins 20 197-201 (1994)
  93. The influence of substrate on the spectral properties of oxyferrous wild-type and T252A cytochrome P450-CAM. Sono M, Perera R, Jin S, Makris TM, Sligar SG, Bryson TA, Dawson JH. Arch Biochem Biophys 436 40-49 (2005)
  94. Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. Tarcsay A, Kiss R, Keseru GM. J Comput Aided Mol Des 24 399-408 (2010)
  95. Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin. Deprez E, Gill E, Helms V, Wade RC, Hui Bon Hoa G. J Inorg Biochem 91 597-606 (2002)
  96. Structural Analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444. Ma M, Bell SG, Yang W, Hao Y, Rees NH, Bartlam M, Zhou W, Wong LL, Rao Z. Chembiochem 12 88-99 (2011)
  97. The critical role of substrate-protein hydrogen bonding in the control of regioselective hydroxylation in p450cin. Meharenna YT, Slessor KE, Cavaignac SM, Poulos TL, De Voss JJ. J Biol Chem 283 10804-10812 (2008)
  98. Enantiomeric discrimination of Ru-substrates by cytochrome P450cam. Dmochowski IJ, Winkler JR, Gray HB. J Inorg Biochem 81 221-228 (2000)
  99. Haem insertion, dimerization and reactivation of haem-free rat neuronal nitric oxide synthase. Hemmens B, Gorren AC, Schmidt K, Werner ER, Mayer B. Biochem J 332 ( Pt 2) 337-342 (1998)
  100. Solvation of the active site of cytochrome P450-cam. Wade RC. J Comput Aided Mol Des 4 199-204 (1990)
  101. Structure of cytochrome P450eryF: substrate, inhibitors, and model compounds bound in the active site. Cupp-Vickery JR, Poulos TL. Steroids 62 112-116 (1997)
  102. Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ. Lozano JJ, López-de-Briñas E, Centeno NB, Guigó R, Sanz F. J Comput Aided Mol Des 11 395-408 (1997)
  103. Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis. Shoji O, Fujishiro T, Nagano S, Tanaka S, Hirose T, Shiro Y, Watanabe Y. J Biol Inorg Chem 15 1331-1339 (2010)
  104. Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography. Basudhar D, Madrona Y, Kandel S, Lampe JN, Nishida CR, de Montellano PR. J Biol Chem 290 10000-10017 (2015)
  105. Common system setup for the entire catalytic cycle of cytochrome P450(cam) in quantum mechanical/molecular mechanical studies. Zheng J, Altun A, Thiel W. J Comput Chem 28 2147-2158 (2007)
  106. Hydrogen-deuterium exchange mass spectrometry for investigation of backbone dynamics of oxidized and reduced cytochrome P450cam. Hamuro Y, Molnar KS, Coales SJ, OuYang B, Simorellis AK, Pochapsky TC. J Inorg Biochem 102 364-370 (2008)
  107. 4-cyanopyridine, a versatile spectroscopic probe for cytochrome P450 BM3. Ost TW, Clark JP, Anderson JL, Yellowlees LJ, Daff S, Chapman SK. J Biol Chem 279 48876-48882 (2004)
  108. A critical role of protein-bound water in the catalytic cycle of cytochrome P-450 camphor. Di Primo C, Sligar SG, Hoa GH, Douzou P. FEBS Lett 312 252-254 (1992)
  109. Construction of a model of the Candida albicans lanosterol 14-alpha-demethylase active site using the homology modelling technique. Höltje HD, Fattorusso C. Pharm Acta Helv 72 271-277 (1998)
  110. Measurements of CO geminate recombination in cytochromes P450 and P420. Tian WD, Wells AV, Champion PM, Di Primo C, Gerber N, Sligar SG. J Biol Chem 270 8673-8679 (1995)
  111. Effects of monovalent cations on cytochrome P-450 camphor. Evidence for preferential binding of potassium. Deprez E, Di Primo C, Hoa GH, Douzou P. FEBS Lett 347 207-210 (1994)
  112. The CO stretching mode infrared spectrum of substrate-free cytochrome P-450cam-CO: the effect of solvent conditions, temperature, and pressure. Jung C, Ristau O, Schulze H, Sligar SG. Eur J Biochem 235 660-669 (1996)
  113. The electronic and vibrational structures of iron-oxo porphyrin with a methoxide or cysteinate axial ligand. Ohta T, Matsuura K, Yoshizawa K, Morishima I. J Inorg Biochem 82 141-152 (2000)
  114. Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes. Payne VA, Chang YT, Loew GH. Proteins 37 204-217 (1999)
  115. Memetic algorithms for ligand expulsion from protein cavities. Rydzewski J, Nowak W. J Chem Phys 143 124101 (2015)
  116. Resonance Raman study on the structure of the active sites of microsomal cytochrome P-450 isozymes LM2 and LM4. Hildebrandt P, Greinert R, Stier A, Taniguchi H. Eur J Biochem 186 291-302 (1989)
  117. The role of water near cytochrome a in cytochrome c oxidase. Rousseau DL, Sassaroli M, Ching YC, Dasgupta S. Ann N Y Acad Sci 550 223-237 (1988)
  118. Control of electrochemical and ferryloxy formation kinetics of cyt P450s in polyion films by heme iron spin state and secondary structure. Krishnan S, Abeykoon A, Schenkman JB, Rusling JF. J Am Chem Soc 131 16215-16224 (2009)
  119. Experimental resolution of the free energies of aqueous solvation contributions to ligand-protein binding: quinone-QA site interactions in the photosynthetic reaction center protein. Warncke K, Dutton PL. Proc Natl Acad Sci U S A 90 2920-2924 (1993)
  120. In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria. Msomi NN, Padayachee T, Nzuza N, Syed PR, Kryś JD, Chen W, Gront D, Nelson DR, Syed K. Molecules 26 1538 (2021)
  121. Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam. Das B, Helms V, Lounnas V, Wade RC. J Inorg Biochem 81 121-131 (2000)
  122. Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme. Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL. Acta Crystallogr D Biol Crystallogr 68 277-291 (2012)
  123. Using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes P450. Meharenna YT, Poulos TL. Biochemistry 49 6680-6686 (2010)
  124. Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s. de Groot MJ, Havenith RW, Vinkers HM, Zwaans R, Vermeulen NP, van Lenthe JH. J Comput Aided Mol Des 12 183-193 (1998)
  125. Characterization of the CYP3A4 active site by homology modeling. Tanaka T, Okuda T, Yamamoto Y. Chem Pharm Bull (Tokyo) 52 830-835 (2004)
  126. Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor. Park SY, Shimizu H, Adachi S, Shiro Y, Iizuka T, Nakagawa A, Tanaka I, Shoun H, Hori H. FEBS Lett 412 346-350 (1997)
  127. Low- and ultralow-temperature magnetic circular dichroism studies of reduced cytochromes P-450-LM2 and P-420-LM2 and of photo-products of their co-complexes. The spin-state and axial ligation of heme iron. Sharonov YuA, Pismensky VF, Greschner S, Ruckpaul K. Biochem Biophys Res Commun 146 165-172 (1987)
  128. Roles of two surface residues near the access channel in the substrate recognition by cytochrome P450cam. Behera RK, Mazumdar S. Biophys Chem 135 1-6 (2008)
  129. Spectroelectrochemistry of cytochrome P450cam. Bistolas N, Christenson A, Ruzgas T, Jung C, Scheller FW, Wollenberger U. Biochem Biophys Res Commun 314 810-816 (2004)
  130. Spectroscopic characterization of a newly isolated cytochrome P450 from Rhodococcus rhodochrous. Banci L, Bertini I, Eltis LD, Pierattelli R. Biophys J 65 806-813 (1993)
  131. Rapid partial degradation of DDT by a cytochrome P-450 model system. Langen H, Epprecht T, Linden M, Hehlgans T, Gutte B, Buser HR. Eur J Biochem 182 727-735 (1989)
  132. Reversible inactivation of cytochrome P450 by alkaline earth metal ions: auxiliary metal ion induced conformation change and formation of inactive P420 species in CYP101. Manna SK, Mazumdar S. J Inorg Biochem 102 1312-1321 (2008)
  133. Substrate modulates compound I formation in peroxide shunt pathway of Pseudomonas putida cytochrome P450(cam). Prasad S, Mitra S. Biochem Biophys Res Commun 314 610-614 (2004)
  134. An ab initio approach to the understanding of cytochrome P450-ligand interactions. Segall MD, Payne MC, Ellis SW, Tucker GT, Boyes RN. Xenobiotica 28 15-20 (1998)
  135. Density functional studies on thromboxane biosynthesis: mechanism and role of the heme-thiolate system. Yanai TK, Mori S. Chem Asian J 3 1900-1911 (2008)
  136. NMR studies of recombinant cytochrome P450cam mutants. Wakasugi K, Ishimori K, Morishima I. Biochimie 78 763-770 (1996)
  137. Scanning tunneling microscopy study of cytochrome P450 2B4 incorporated in proteoliposomes. Uvarov VYu, Ivanov YD, Romanov AN, Gallyamov MO, Kiselyova OI, Yaminsky IV. Biochimie 78 780-784 (1996)
  138. Size-selective and reversible encapsulation of single small hydrocarbon molecules by a cavitand-porphyrin species. Nakazawa J, Hagiwara J, Mizuki M, Shimazaki Y, Tani F, Naruta Y. Angew Chem Int Ed Engl 44 3744-3746 (2005)
  139. Structure and redox properties of the haem centre in the C357M mutant of cytochrome P450cam. Murugan R, Mazumdar S. Chembiochem 6 1204-1211 (2005)
  140. Thermodynamic aspects of the CO-binding reaction to cytochrome P-450cam. Relevance with their biological significance and structure. Kato M, Makino R, Iizuka T. Biochim Biophys Acta 1246 178-184 (1995)
  141. 13C-Methyl isocyanide as an NMR probe for cytochrome P450 active sites. McCullough CR, Pullela PK, Im SC, Waskell L, Sem DS. J Biomol NMR 43 171-178 (2009)
  142. Ab initio molecular modeling in the study of drug metabolism. Segall MD, Payne MC, Ellis SW, Tucker GT, Boyes RN. Eur J Drug Metab Pharmacokinet 22 283-289 (1997)
  143. Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450. Lee JY, Kang NS, Kang YK. Biopolymers 97 219-228 (2012)
  144. First principles investigation of singly reduced cytochrome P450. Segall MD, Payne MC, Ellis SW, Tucker GT, Eddershaw PJ. Xenobiotica 29 561-571 (1999)
  145. Structural alterations of the heme environment of cytochrome P450cam and the Y96F mutant as deduced by resonance Raman spectroscopy. Niaura G, Reipa V, Mayhew MP, Holden M, Vilker VL. Arch Biochem Biophys 409 102-112 (2003)
  146. Substrate binding induces structural changes in cytochrome P450cam. Sakurai K, Shimada H, Hayashi T, Tsukihara T. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 80-83 (2009)
  147. Kinetic Evidence for an Induced Fit Mechanism in the Binding of the Substrate Camphor by Cytochrome P450cam. Guengerich FP, Child SA, Barckhausen IR, Goldfarb MH. ACS Catal 11 639-649 (2021)
  148. Molecular dynamics simulations indicate that F87W,T185F-cytochrome P450cam may reductively dehalogenate 1,1,1-trichloroethane. Manchester JI, Ornstein RL. J Biomol Struct Dyn 13 413-422 (1995)
  149. Structure-guided manipulation of the regioselectivity of the cyclosporine A hydroxylase CYP-sb21 from Sebekia benihana. Li F, Ma L, Zhang X, Chen J, Qi F, Huang Y, Qu Z, Yao L, Zhang W, Kim ES, Li S. Synth Syst Biotechnol 5 236-243 (2020)
  150. Substrate induced changes of the active site electronic states in reduced cytochrome P450cam and the photolysis product of its CO complex. Low-temperature magnetic circular dichroism data. Greschner S, Sharonov YuA, Jung C. FEBS Lett 315 153-158 (1993)
  151. The Energetics of Streptococcal Enolase Octamer Formation: The Quantitative Contributions of the Last Eight Amino Acids at the Carboxy-Terminus. Kornblatt JA, Quiros V, Kornblatt MJ. PLoS One 10 e0135754 (2015)
  152. A complete volume profile for the reversible binding of camphor to cytochrome P450(cam). Franke A, Hartmann E, Schlichting I, van Eldik R. J Biol Inorg Chem 17 447-463 (2012)
  153. Density functional studies on isomerization of prostaglandin H2 to prostacyclin catalyzed by cytochrome P450. Yanai TK, Mori S. Chemistry 15 4464-4473 (2009)
  154. General trends of dihedral conformational transitions in a globular protein. Miao Y, Baudry J, Smith JC, McCammon JA. Proteins 84 501-514 (2016)
  155. Jumpstarting the cytochrome P450 catalytic cycle with a hydrated electron. Erdogan H, Vandemeulebroucke A, Nauser T, Bounds PL, Koppenol WH. J Biol Chem 292 21481-21489 (2017)
  156. Structural and functional characterisation of the cytochrome P450 enzyme CYP268A2 from Mycobacterium marinum. Child SA, Naumann EF, Bruning JB, Bell SG. Biochem J 475 705-722 (2018)
  157. Cytochrome P450cam-monoterpene interactions. Van Roon A, Parsons JR, Govers HA. SAR QSAR Environ Res 16 369-384 (2005)
  158. Structure of cytochrome P450 2B4 with an acetate ligand and an active site hydrogen bond network similar to oxyferrous P450cam. Yang Y, Bu W, Im S, Meagher J, Stuckey J, Waskell L. J Inorg Biochem 185 17-25 (2018)
  159. The role of Ile476 in the structural stability and substrate binding of human cytochrome P450 2C8. Sun L, Wang ZH, Ni FY, Tan XS, Huang ZX. Protein J 29 32-43 (2010)


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