Skip to main content
Article thumbnail
Location of Repository

Geometric and Electronic Structures of the NiI and Methyl−NiIII Intermediates of Methyl-Coenzyme M Reductase†

By Ritimukta Sarangi, Mishtu Dey and Stephen W. Ragsdale
Topics:
Publisher: American Chemical Society
OAI identifier: oai:pubmedcentral.nih.gov:2667316
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Citations

    1. (2004)ORCA: An ab initio, DFT and semiempirical Electronic Structure Package.
    2. (2004). 03, revision C.02.
    3. (1998). 6-31G* basis set for atoms K through Zn.
    4. (2002). A mechanism from quantum chemical studies for methane formation in methanogenesis.
    5. (1997). A multiplet analysis of Fe K-edge 1s f 3d pre-edge features of iron complexes.
    6. (2008). A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations.
    7. (2006). A nickel-alkyl bond in an inactivated state of the enzyme catalyzing methane formation.
    8. A polarization type basis set for 2nd-row elements.
    9. (1991). Ab initio curved wave X-ray absoprtion fine structure.
    10. (1980). Ab initio studies of the X-ray absorption edge in copper complexes.
    11. (2004). Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin.
    12. (2001). Adenosylcobalamindependent isomerases: New insights into structure and mechanism.
    13. Although the resolution of k ) 2-17 Å EXAFS data is ∼0.1 Å, the standard deviation of the first shell obtained from the EXAFS data presented here is
    14. (2007). Biochemical and spectroscopic studies of the electronic structure and reactivity of a methyl-Ni species formed on methyl-coenzyme M reductase.
    15. (1998). Biochemistry of methanogenesis: A tribute to Marjory Stephenson.
    16. (2003). Catalysis by methylcoenzyme M reductase: A theoretical study for heterodisulfide product formation.
    17. (2007). Characterization of alkyl-nickel adducts generated by reaction of methyl-coenzyme M reductase with brominated acids.
    18. (2008). Characterization of the thioether product formed from the thiolytic cleavage of the 3154
    19. (1991). Coenzyme F430 from methanogenic bacteria: Complete assignment of configuration based on X-ray analysis of 12,13-Diepi-F430 pentamethyl ester and on NMR spectroscopy.
    20. (2000). Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: Unusual amino acid modification, conservation and adaptation.
    21. (2003). Coordination and geometry of the nickel atom in active methyl-coenzyme M reductase from Methanothermobacter marburgensis as detected by X-ray absorption spectroscopy.
    22. (1989). Coordination chemistry of F430: Axial ligation equilibrium between squareplanar and bis-aquo species in aqueous solution.
    23. (2001). Cryoreduction of methyl-coenzyme M reductase: EPR characterization of forms, MCRox1 and MCRred1.
    24. (1997). Crystal structure of methyl-coenzyme M reductase: The key enzyme of biological methane formation.
    25. (1993). Density functional theromochemistry: 3. The role of exact exchange.
    26. (2003). Description of the ground state wave functions of Ni dithiolenes using sulfur K-edge X-ray absorption spectroscopy.
    27. (1988). Development of the ColleSalvetti correlation-energy formula into a functional of the electron density.
    28. (2002). Efficient use of the resolution of the identity approximation in time-dependent density functional calculations with hybrid density functionals.
    29. (1990). EXAFS studies of nickel(II) and nickel(I) factor 430M. Conformational flexibility of the F430 skeleton.
    30. (1986). EXAFS: Basic Principles and Data Analysis,
    31. EXAFSPAK and EDG-FIT.
    32. (1991). Extension of Gaussian-1 (G1) theory to bromine-containing molecules.
    33. (1995). Extension of Gaussian-2 theory to molecules containing 3rd row atoms Ga-Kr.
    34. (2007). Formation of a nickel-methyl species in methyl-coenzyme M reductase, an enzyme catalyzing methane formation.
    35. (1992). Fully optimized contracted Gaussian basis sets for atoms Li to Kr.
    36. (1994). Fully optimized contracted Gaussian basis sets of triple- valence quality for atoms Li to Kr.
    37. (1994). How a protein binds B12: A 3.0 Å X-ray structure of B12-binding domains of methionine synthase.
    38. (1999). Identification of a rearranged-substrate, product radical intermediate and the contribution of a product radical trap in vitamin B-12 coenzymedependent ethanolamine deaminase catalysis.
    39. (2008). Methane as fuel for anaerobic microorganisms.
    40. (2000). Methane formation by reaction of a methyl thioether with a photo-excited nickel thiolate: A process mimicking methanogenesis in archaea.
    41. (2005). Methyl-coenzyme M reductase and the anaerobic oxidation of methane in methanotrophic archaea.
    42. (1979). Natural widths of the atomic K-levels and L-levels, K-alpha X-ray lines and several KLL Auger lines.
    43. (2004). Nickel oxidation states of F430 cofactor in methyl-coenzyme M reductase.
    44. (1982). Nickelcontaining factor F430: Chromophore of the methyl reductase of Methanobacterium thermoautotrophicum.
    45. (1993). Number of relevant independent points in X-ray absorption fine structure spectra.
    46. (1976). Observation and interpretation of X-ray absorption edges in iron compounds and proteins.
    47. (1982). Observation of an electric quadrupole transition in the X-ray absorption spectrum of a Cu(II) complex.
    48. On the basis of ∼160 structures submitted to the Cambridge Structure Database (CSD), the average Ni-C(alkyl) bond distance in NiI- and NiII-containing complexes is ∼1.98 Å.
    49. (2001). On the mechanism of biological methane formation: Structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding.
    50. (2005). Performance of nonrelativistic and quasi-relativistic hybrid DFT for the prediction of electric and magnetic hyperfine parameters in
    51. (1984). Polarized Cu K-edge XANES of square planar
    52. (2002). Prediction and interpretation of the Fe-57 isomer shift in
    53. Pyspline and QMForge.
    54. R′ denotes the non-phase shift corrected bond distance.
    55. (2001). Radical peregrinations catalyzed by coenzyme B12-dependent enzymes.
    56. (1989). Results obtained with the correlation energy density functionals of Becke
    57. (1982). Self consistent molecular-orbital methods.
    58. (1980). Self consistent molecular-orbital methods. 20. Basis set for correlated wave functions.
    59. (2008). Solution [Cu(amm)]2 + is a strongly solvated square pyramid: A full account of the copper K-edge XAS spectrum within singleelectron theory.
    60. (2004). Spectroscopic and computational characterization of the nickel-containing F430 cofactor of methyl-coenzyme M reductase.
    61. (2006). Spectroscopic and computational studies of reduction of the metal versus the tetrapyrrole ring of coenzyme F430 from methyl-coenzyme M reductase.
    62. (2006). Spectroscopic and kinetic studies of the reaction of bromopropanesulfonate with methyl-coenzyme M reductase.
    63. (2004). Spectroscopic investigation of the nickel-containing porphinoid cofactor F430. Comparison of the free cofactor in the (+)1, (+)2 and (+)3 oxidation states with the cofactor bound to methylcoenzyme M reductase in the silent, red and ox forms.
    64. (1990). Structural consequences of nickel versus macrocycle reductions in F430 models: EXAFS studies of a Ni(I) anion and Ni(II) ·π·anion radicals.
    65. (1997). Structure-based perspectives on B12-dependent enzymes.
    66. (2007). Sulfur K-edge X-ray absorption spectroscopy as a probe of ligand-metal bond covalency: Metal vs ligand oxidation in copper and nickel dithiolene complexes.
    67. (1988). The final step in methane formation: Investigations with highly purified methyl-coenzyme M reductase (component C) from Methanobacterium thermoautotrophicum (strain Marburg).
    68. (1973). The influence of polarization functions on molecular orbital hydrogenation energies.
    69. (1989). The magnetic and electronic properties of Methanobacterium thermoautotrophicum (strain delta H) methyl coenzyme M reductase and its nickel tetrapyrrole cofactor F430. A low temperature magnetic circular dichroism study.
    70. (1989). The magnetic properties of the nickel cofactor F430 in the enzyme methyl-coenzyme M reductase of Methanobacterium thermoautotrophicum.
    71. (2000). Theoretical approaches to X-ray absorption fine structure.
    72. (1991). Theoretical X-ray absorption fine structure standards.
    73. (1990). Unusual coenzymes of methanogenesis.
    74. (2008). When identical functional groups are not identical: A DFT study of the effects of molecular environment on sulfur K-edge X-ray absorption spectra.
    75. (2002). X-ray absorption and resonance Raman studies of methyl-coenzyme M reductase indicating that ligand exchange and macrocycle reduction accompany reductive activation.
    76. (2006). X-ray absorption edge spectroscopy and computational studies on LCu O2 species: Superoxide-CuII versus peroxide-CuIII bonding.
    77. (1991). X-ray spectroscopies studies of nickel complexes, with application to the structure of nickle sites in hydrogenases.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.