Calculated and experimental spin state of seleno cytochrome p450

Full text of DOI:10.1002/anie.200901485

Angewandte
Chemie
DOI: 10.1002/anie.200901485
Cytochrome P450
Calculated and Experimental Spin State of Seleno Cytochrome P450**
Yongying Jiang, Santhosh Sivaramakrishnan, Takahiro Hayashi, Shimrit Cohen, Pierre Moꢀnne-
Loccoz, Sason Shaik, and Paul R. Ortiz de Montellano*
The cysteine thiolate ligand coordinated to the heme iron
atom in cytochrome P450 is thought to be responsible for the
unique spectroscopic and catalytic properties of these
enzymes. To explore the role of the proximal ligand in these
proteins, the cysteine has been replaced by a variety of other
ligands by site-specific mutagenesis, including a histidine,[1a–c]
methionine,[1d] and serine.[1e] None of these ligand substitu-
tions resulted in a protein with the spectroscopic or catalytic
properties of a cytochrome P450 monooxygenase. However,
recent computational studies suggested that a P450-like
species might result from substitution of the thiolate ligand
by a selenolate, and furthermore, that this substitution might
accelerate the rate of formation and decelerate the rate of
decay of the catalytic ferryl species, possibly making it
observable.[2]
this substitution because the proximal ligand is the only
cysteine in its sequence. The seleno protein was expressed in a
cysteine auxotroph BL21(DE3)CysE strain of Escherichia
coli that cannot synthesize cysteine owing to a mutation in the
CysE gene.[5] A pCWori vector containing the CYP119 gene
encoding a 6-His tag at the C-terminus was transformed into
the auxotrophic BL21(DE3)Cys cells, and the seleno protein
was expressed in minimal media containing l-selenocystine
(see the Supporting Information for the detailed procedure).
The protein yield was 2.6 mgLÀ1 of culture after affinity
purification, which is approximately 8–10 times lower than
that of the normal thiolate-ligated protein. This approach
results in over 70% replacement of the cysteine by a
selenocysteine as judged by the relative peak intensities of
the Cys and SeCys proteins by LC/ESI-MS.
No selenolate-coordinated heme protein was known until
our recent demonstration that such a protein is generated by
the binding of PhSeH to a heme oxygenase cavity mutant in
which the proximal histidine ligand had been replaced by an
alanine.[3] Furthermore, binding of PhSeH to cytochrome
P450cam yielded a hyperporphyrin spectrum that is analo-
gous to that observed when a distal thiolate ligand is
coordinated to the iron along with the proximal cysteine
thiolate.[3] Nevertheless, only a brief meeting abstract exists
describing a P450 enzyme in which the proximal cysteine has
been replaced by a selenocysteine.[4]
The UV/Vis spectrum of ferric SeCYP119, the selenocys-
teine-substituted enzyme, has a Soret maximum at 417 nm,
which is very similar to the 416 nm maximum of wild-type
(WT) CYP119.[6] Furthermore, the Q bands of the SeCYP119
protein correlate well with those of WT CYP119 (Figure 1a).
Herein we report the expression and characterization of a
seleno cytochrome P450 in which the cysteine thiolate iron
ligand is replaced by a selenocysteine. CYP119 was used for
Figure 1. Comparison of the UV/Vis spectra of circa 1.5 mm
WT CYP119 (c) and SeCYP119 (g) proteins in 100 mm potas-
sium phosphate buffer, pH 7.4. a) Ferric resting state, and b) ferrous
CO complex.
[*] Dr. Y. Jiang, Dr. S. Sivaramakrishnan, Prof. P. R. Ortiz de Montellano
Department of Pharmaceutical Chemistry, University of California
600 16th street, San Francisco, CA 94158 (USA)
Fax: (+001) 415-502-4728
E-mail: ortiz@cgl.ucsf.edu
The similarities in the UV/Vis spectra of ferric SeCYP119 and
WT CYP119 are consistent with the presence in both proteins
of a six-coordinate low-spin heme iron with a distal water
ligand.
T. Hayashi, Prof. P. Moꢀnne-Loccoz
Department of Science and Engineering
Oregon Health & Science University, Beaverton, OR 97006 (USA)
S. Cohen, Prof. S. Shaik
The catalytic activity of the enzymes was examined using a
hydrogen peroxide mediated shunt pathway in the presence
of the substrate dodecanoic (lauric) acid. The specific activity
of SeCYP119 was estimated to be 90 Æ 20 pmolminÀ1 per
nmol of enzyme, which is approximately half that for the
WT CYP119 (170 Æ 18 pmolminÀ1 per nmol of enzyme).[7]
Oxidation of lauric acid resulted in hydroxylation at the w,
w-1 and w-2 positions, as determined by GC-MS. Interest-
ingly, the regiospecificity of hydroxylation showed the same
trend for both the WTand SeCYP119 proteins, with w-1 being
the predominant product, followed by w-2 and w (see the
Institute of Chemistry and the Lise Meitner-Minerva Center for
Computational Quantum Chemistry
The Hebrew University, Jerusalem, 91904 (Israel)
[**] This work is supported by NIH grants GM25515 (to P.R.O.M.) and
GM74785 (to P.M.-L.) and by an ISF grant (to S.S.). Mass
spectrometry was provided by the UCSF Mass Spectrometry Facility
(A. L. Burlingame, Director) supported by the Biomedical Research
Technology Program of the National Center for Research Resources,
NIH NCRR BRTP 01614. We thank Dr. Hugues Ouellet for helpful
discussions and suggestions.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200901485.
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Communications
Supporting Information). Overall, our results suggest that the
novel seleno mutant is indeed catalytically active.
and n(C-O) frequencies (Supporting Information, Figure S6).
Therefore, in the ferrous carbon monoxide complexes, and in
contrast with the ferric-NO complexes, the trans effect of the
selenolate and thiolate ligands on the Fe-C-O unit are
equivalent.
To model the three-dimensional structure of the selenium
resting state in SeCYP119, we used theoretical DFT(B3LYP)/
MM calculations to probe an analogous SeCYP101 mu-
tant.[2,12a] Three snapshots (60 ps, 120 ps, and 200 ps) from the
equilibrium trajectory of the WT enzyme were mutated by
replacing cysteine by selenocysteine and fully optimized by
DFT(B3LYP)/MM geometry optimization for the spin states
S = 1/2, 3/2, and 5/2.[12b] (For further details, see the Support-
ing Information). All three snapshots display similar proper-
ties, and Figure 3 depicts representative geometric data,
The EPR spectrum of ferric SeCYP119 is characteristic of
a rhombic S = 1/2 low-spin heme iron(III) with g values that
are distinct from those of the WT protein (Supporting
Information, Figure S4). Interpreting the changes in g values
in electronic or structural terms is not straightforward,
because the selenium substitution may affect tetragonal and
rhombic splittings of the low-spin iron(III) d orbitals and also
the spin-orbit coupling constant.[8] The EPR spectra also
support the presence of a WT CYP119 contaminant that
varies from preparation to preparation but remains below
30%. The resonance Raman spectrum of ferric SeCYP119
also supports a six-coordinate low-spin configuration[9] with
porphyrin skeletal modes n3, n2, and n10 at 1502, 1583, and
1636 cmÀ1, respectively (Figure 2). These frequencies are
within 1 cmÀ1 of those observed in WT CYP119. The n4
mode shows a 1 cmÀ1 downshift upon substitution of sulfur
by selenium, which reflects an increased electron density on
the antibonding porphyrin p* orbitals.[10]
Figure 3. B3LYP/MM calculated geometric features and spin-state
energies of the SeCys mutant of CYP101: a) Detailed structure of a
representative snapshot (60 ps) in the doublet 2A state. b) Relative
QM/MM energies (kcalmolÀ1) and key geometric parameters for
different snapshots calculated with the largest basis set (BL//B1 in the
Supporting Information). The geometric parameters correspond to
snapshots at 60, 120, and 200 ps (arranged vertically) in the A(4A)[6A]
spin states.
2
Figure 2. Resonance Raman spectra of ferric wild-type (WT) CYP119
(black) and SeCYP119 (red) at room temperature. Excitation wave-
length=413 nm.
calculated at the highest basis set, of triple-zeta quality
À
The impact of the Cys317SeCys substitution in SeCYP119
was investigated further by characterizing the ferric nitrosyl
complexes using resonance Raman spectroscopy and isotopic
labeling of the nitrosyl group. In SeCYP119, the n(Fe-NO)
and n(N-O) modes are observed at 526 (D15N = 3 cmÀ1) and
1838 cmÀ1 (D15N = 37 cmÀ1), respectively (Supporting Infor-
mation, Figure S5). These frequencies are 4 and 14 cmÀ1 lower
than in the WT protein. These decreases in stretching
frequencies can be interpreted in terms of a weakening of
the Fe-NO and N-O bond strengths as the s-trans effect of the
coordinating selenolate ligand on the Fe-N-O unit increases
compared to that of the thiolate in the WT protein. Recent
DFT calculations have examined in detail the trans effect of
thiolate ligation in ferric heme nitrosyl complexes.[11]
augmented by polarization and diffuse functions. The Fe Se
distance is 2.44 ꢀ, which is within the range found in iron
seleno complexes.[13] As seen from Figure 3b, the calculations
predict small energy gaps between the three spin states, which
are packed within about 2.1 kcalmolÀ1. Given that B3LYP/
MM slightly overestimates the stability of high spin states,[12b]
along with the BLYP/MM data (Supporting Information),
which strongly prefer the doublet state, we can assign the
ground state to have a doublet spin. This feature is similar to
the computed situation for the WT and to the experimental
finding that the ground state (doublet) is in spin equilibrium
with the higher spin states.[14] Comparisons to the WT
geometries[12b] suggest that in both cases, the water ligand is
tilted by 40–608 owing to H-bond interactions within the
À
The UV/Vis spectra of the ferrous carbon monoxide
complexes show a pronounced shift in the Soret maximum
from 449 nm in WT CYP119 to 454 nm in SeCYP119
(Figure 1b), but the resonance Raman characterizations of
these carbonyl complexes show nearly identical n(Fe-CO)
protein pocket (Figure 3b). The Fe O bond length is slightly
À
À
shorter by ca 0.02 ꢀ, whilst the Fe Se bond is longer than Fe
S by circa 0.2 ꢀ, as previously reported for the seleno and
WT Cpd I species.[2] Therefore, the DFT/MM calculations
support the doublet spin-state assignment by EPR.
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[5] S. Mꢂller, H. Senn, B. Gsell, W. Vetter, C. Baron, A. Bꢃck,
In conclusion, we have expressed and characterized the
first selenium-incorporated P450 enzyme. Our preliminary
results reveal that the spectral characteristics of this novel
CYP119 are comparable to those of the corresponding WT
protein, indicating the presence of a six-coordinate low-spin
heme iron with water as a distal ligand. More importantly, the
catalytic activity of the seleno mutant is comparable to that of
the WT enzyme. Furthermore, computational calculations
clearly support the experimentally assigned spin state. Future
studies will focus on both examining how this substitution
affects the stability of the putative Cpd I species and the
development of novel catalysts.
Biochemistry 1994, 33, 3404.
[6] L. S. Koo, R. A. Tschirret-Guth, W. E. Straub, P. Moꢁnne-
Loccoz, T. M. Loehr, P. R. Ortiz de Montellano, J. Biol. Chem.
2000, 275, 14112.
[7] The catalytic activity of SeP450cam is also reported to be
twofold less than the activity of the corresponding WT control
(see Ref. [4]).
[8] G. Palmer in Iron Porphyrins, Part II (Eds.: A. B. P. Lever, H. B.
Gray), Addison-Wesley, Reading MA, 1983, pp. 43 – 88.
[9] T. G. Spiro, X. Y. Li in Biological Applications of Raman
Spectroscopy, Vol 3, Wiley, New York, 1998; T. G. Spiro in
Resonance Raman spectra of hemes and metalloproteins, Wiley,
New York, 1998, pp. 1 – 37.
[10] T. G. Spiro, J. M. Burke, J. Am. Chem. Soc. 1976, 98, 5482.
[11] F. Paulat, N. Lehnert, Inorg. Chem. 2007, 46, 1547.
[12] a) It has been shown that the spectral properties and geometric
features of CYP119 are very similar to those in CYP101 for a few
species in the catalytic cycle; see I. G. Denisov, S. C. Hung, K. E.
Weiss, M. A. McLean, Y. Shiro, S. Y. Park, P. M. Champion, S. G.
Sligar, J. Inorg. Biochem. 2001, 87, 215. In view of this similarity
of the two isozymes, we preferred to carry out the QM/MM
calculations on CYP101 for which we already have all the
necessary MM parameters, as well as QM/MM features of the
active Cpd I species: b) J. C. Schꢃneboom, W. Thiel, J. Phys.
Chem. B 2004, 108, 7468.
[13] a) R. Hauptmann, R. Kliss, G. Henkel, Angew. Chem. 1999, 111,
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Q.-M. Hu, Y. J. Liu, Organomet. Chem. 2003, 676, 80; c) L.-C.
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Gong, Chem. Eur. J. 2003, 9, 170; e) M. El-khateeb, Inorg. Chim.
Acta 2004, 357, 4341.
Received: March 18, 2009
Revised: June 22, 2009
Published online: August 28, 2009
Keywords: cytochrome P450 · proteins · Raman spectroscopy ·
.
selenium · spin states
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