Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution.

Cytochrome P450terp is a class I (mitochondrial/bacterial) P450 that catalyzes the hydroxylation of alpha-terpineol as part of the catabolic assimilation of this compound by a pseudomonad species. Crystals grown from the purified protein have the symmetry of space group P6(1)22, and cell dimensions a = b = 69.4 A, c = 456.6 A, alpha = beta = 90 degrees, gamma = 120 degrees. Diffraction data were collected at the Cornell High Energy Synchrotron Source, and the structure of P450terp was solved by a combination of molecular replacement and multiple isomorphous replacement techniques. A model of P450terp was built and refined against native data, to an R-factor of 18.9% for data with I > or = sigma(I) between 6.0 A and 2.3 A resolution. This model contains 412 of the 428 P450terp amino acid residues; the loop between helices F and G is disordered in the crystal. While the overall fold of P450terp is very similar to that of P450cam, only three-quarters of the C alpha positions can be superimposed, to a root-mean-square deviation of only 1.87 A. The mode of substrate binding by P450terp can be predicted, and probable substrate contact residues identified. The heme environment and side-chain positions in the adjacent I-helix suggest possible modes of proton delivery in the catalytic cycle of the enzyme.

[1]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[2]  Ortiz de Montellano,et al.  Cytochrome P-450: Structure, Mechanism, and Biochemistry , 1986 .

[3]  Eaton E. Lattman,et al.  Optimal sampling of the rotation function , 1972 .

[4]  E. Baker,et al.  Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.

[5]  U. R. Evans,et al.  Distribution of Attack on Iron or Zinc Partly Immersed in Chloride Solutions , 1942, Nature.

[6]  S. Sligar,et al.  Catalytic mechanism of cytochrome P-450: evidence for a distal charge relay , 1992 .

[7]  Andrew Howard,et al.  Crystal structures of metyrapone- and phenylimidazole-inhibited complexes of cytochrome P-450cam , 1993 .

[8]  B. Matthews Solvent content of protein crystals. , 1968, Journal of molecular biology.

[9]  A T Brünger,et al.  Slow-cooling protocols for crystallographic refinement by simulated annealing. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[10]  M. Gelb,et al.  Stereochemistry and deuterium isotope effects in camphor hydroxylation by the cytochrome P450cam monoxygenase system. , 1982, Biochemistry.

[11]  D. Nelson,et al.  Secondary structure prediction of 52 membrane-bound cytochromes P450 shows a strong structural similarity to P450cam. , 1989, Biochemistry.

[12]  B. Griffin,et al.  Pseudomonas putida cytochrome P-450. The effect of complexes of the ferric hemeprotein on the relaxation of solvent water protons. , 1975, The Journal of biological chemistry.

[13]  M. Kjeldgaard,et al.  O: A Macromolecule Modeling Environment , 1990 .

[14]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[15]  R. Raag,et al.  Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex. , 1989, Biochemistry.

[16]  P. Ortiz de Montellano,et al.  Formation, crystal structure, and rearrangement of a cytochrome P-450cam iron-phenyl complex. , 1990, Biochemistry.

[17]  Scott R. Presnell,et al.  Topological distribution of four-alpha-helix bundles. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Y. Fujii‐Kuriyama,et al.  P450 and Human Cancer , 1991, Japanese journal of cancer research : Gann.

[19]  J. Dawson,et al.  Spectroscopic investigations of ferric cytochrome P-450-CAM ligand complexes. Identification of the ligand trans to cysteinate in the native enzyme. , 1982, The Journal of biological chemistry.

[20]  J. Deisenhofer,et al.  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. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Kassner,et al.  A theoretical model for the effects of local nonpolar heme environments on the redox potentials in cytochromes. , 1973, Journal of the American Chemical Society.

[22]  R. Raag,et al.  Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation. , 1991, Biochemistry.

[23]  B C Finzel,et al.  The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450. , 1985, The Journal of biological chemistry.

[24]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[25]  A. Wilson,et al.  Determination of Absolute from Relative X-Ray Intensity Data , 1942, Nature.

[26]  T. Poulos,et al.  High-resolution crystal structure of cytochrome P450cam. , 1987, Journal of molecular biology.

[27]  S. Philson,et al.  The effect of cytochrome P-450cam on the NMR relaxation rate of water protons. , 1979, The Journal of biological chemistry.

[28]  A. Brunger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[29]  S. Sligar,et al.  The roles of active site hydrogen bonding in cytochrome P-450cam as revealed by site-directed mutagenesis. , 1988, The Journal of biological chemistry.

[30]  M. J. Coon,et al.  Cytochrome P-450 : multiplicity of isoforms, substrates, and catalytic and regulatory mechanisms , 1991 .

[31]  J. S. Miles,et al.  Developments and perspectives on the role of cytochrome P450s in chemical carcinogenesis. , 1991, Carcinogenesis.

[32]  Julian,et al.  Cytochrome P-450terp. Isolation and purification of the protein and cloning and sequencing of its operon. , 1992, The Journal of biological chemistry.

[33]  G. A. Sim,et al.  The distribution of phase angles for structures containing heavy atoms. II. A modification of the normal heavy‐atom method for non‐centrosymmetrical structures , 1959 .

[34]  F. Guengerich Reactions and significance of cytochrome P-450 enzymes. , 1991, The Journal of biological chemistry.

[35]  H. Beinert,et al.  Spin-state changes in cytochrome P-450cam on binding of specific substrates. , 1970, Proceedings of the National Academy of Sciences of the United States of America.

[36]  B C Finzel,et al.  Crystal structure of substrate-free Pseudomonas putida cytochrome P-450. , 1986, Biochemistry.

[37]  A. Fulco P450BM-3 and other inducible bacterial P450 cytochromes: biochemistry and regulation. , 1991, Annual review of pharmacology and toxicology.

[38]  R. Raag,et al.  The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P-450CAM. , 1991, Biochemistry.

[39]  S. Martinis,et al.  Crystal structure of the cytochrome P-450CAM active site mutant Thr252Ala. , 1991, Biochemistry.

[40]  R. Raag,et al.  Inhibitor-induced conformational change in cytochrome P-450CAM. , 1993, Biochemistry.

[41]  K. Hodgson,et al.  Endogenous cysteine ligation in ferric and ferrous cytochrome P-450. Direct evidence from x-ray absorption spectroscopy. , 1982, The Journal of biological chemistry.

[42]  M. J. Coon,et al.  Aliphatic hydroxylation by highly purified liver microsomal cytochrome P-450. Evidence for a carbon radical intermediate. , 1978, Biochemical and biophysical research communications.

[43]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[44]  Axel T. Brunger,et al.  Extension of molecular replacement: a new search strategy based on Patterson correlation refinement , 1990 .

[45]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[46]  B. Matthews,et al.  Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins. , 1984, Journal of molecular biology.

[47]  O. Hayaishi Molecular mechanisms of oxygen activation , 1974 .

[48]  T. Poulos Modeling of mammalian P450s on basis of P450cam X-ray structure. , 1991, Methods in enzymology.

[49]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[50]  R. Read Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[51]  R. Raag,et al.  Cytochrome P450cam: crystallography, oxygen activation, and electron transfer1 , 1992, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.