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PDBsum entry 3cpp
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Oxidoreductase(oxygenase)
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PDB id
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3cpp
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* Residue conservation analysis
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Enzyme class:
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E.C.1.14.15.1
- camphor 5-monooxygenase.
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Reaction:
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2 reduced [2Fe-2S]-[putidaredoxin] + (1R,4R)-camphor + O2 + 2 H+ = (1R,4R,5R)-5-hydroxycamphor + 2 oxidized [2Fe-2S]-[putidaredoxin] + H2O
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2
×
reduced [2Fe-2S]-[putidaredoxin]
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+
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(1R,4R)-camphor
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+
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O2
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+
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2
×
H(+)
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=
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(1R,4R,5R)-5-hydroxycamphor
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+
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2
×
oxidized [2Fe-2S]-[putidaredoxin]
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+
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H2O
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Cofactor:
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Heme-thiolate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Biochemistry
28:7586-7592
(1989)
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PubMed id:
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Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex.
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R.Raag,
T.L.Poulos.
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ABSTRACT
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The crystal structure of the ternary complex formed between carbon monoxide
(CO), camphor, and ferrous cytochrome P-450CAM has been refined to an R value of
17.9% at 1.9-A resolution. To accommodate the CO molecule, the substrate,
camphor, moves about 0.8 A while at the same time remaining in nonbonded contact
with CO. The average temperature factor of the camphor atoms is about 50% higher
in the CO complex, suggesting that the camphor is more loosely bound in this
ternary complex. The Fe-C-O angle is about 166 degrees, and thus, CO appears to
be bent from the heme normal, as it is in various CO-globin complexes, due to
steric interactions with active site groups. The oxygen atom of the CO molecule
is nestled into a groove formed by an unusual helical hydrogen bond in the
distal helix between the highly conserved Thr 252 and Gly 248 residues. In the
transition from the ferric camphor-bound binary complex to the ferrous
CO-camphor-bound ternary complex, the heme iron atom moves into the plane
defined by the pyrrole nitrogens by about 0.41 A. Although the axial Cys ligand
also moves toward the heme, the S-Fe bond stretches from about 2.20 A in the
absence of CO to about 2.41 A once CO has bound.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Tarcsay,
R.Kiss,
and
G.M.Keseru
(2010).
Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach.
|
| |
J Comput Aided Mol Des,
24,
399-408.
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|
|
T.C.Pochapsky,
S.Kazanis,
and
M.Dang
(2010).
Conformational plasticity and structure/function relationships in cytochromes P450.
|
| |
Antioxid Redox Signal,
13,
1273-1296.
|
|
|
|
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|
W.Yang,
S.G.Bell,
H.Wang,
W.Zhou,
M.Bartlam,
L.L.Wong,
and
Z.Rao
(2010).
The structure of CYP101D2 unveils a potential path for substrate entry into the active site.
|
| |
Biochem J,
433,
85-93.
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|
|
PDB codes:
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|
E.K.Asciutto,
J.D.Madura,
S.S.Pochapsky,
B.OuYang,
and
T.C.Pochapsky
(2009).
Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam.
|
| |
J Mol Biol,
388,
801-814.
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|
|
|
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|
|
S.S.Pochapsky,
M.Dang,
B.OuYang,
A.K.Simorellis,
and
T.C.Pochapsky
(2009).
Redox-dependent dynamics in cytochrome P450cam.
|
| |
Biochemistry,
48,
4254-4261.
|
|
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|
|
|
|
B.OuYang,
S.S.Pochapsky,
M.Dang,
and
T.C.Pochapsky
(2008).
A functional proline switch in cytochrome P450cam.
|
| |
Structure,
16,
916-923.
|
|
|
|
|
|
|
D.Kim,
Y.S.Heo,
and
P.R.Ortiz de Montellano
(2008).
Efficient catalytic turnover of cytochrome P450(cam) is supported by a T252N mutation.
|
| |
Arch Biochem Biophys,
474,
150-156.
|
|
|
|
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|
|
M.Freindorf,
Y.Shao,
J.Kong,
and
T.R.Furlani
(2008).
Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin.
|
| |
J Inorg Biochem,
102,
427-432.
|
|
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O.Kweon,
S.J.Kim,
S.Baek,
J.C.Chae,
M.D.Adjei,
D.H.Baek,
Y.C.Kim,
and
C.E.Cerniglia
(2008).
A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases.
|
| |
BMC Biochem,
9,
11.
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H.Yao,
C.R.McCullough,
A.D.Costache,
P.K.Pullela,
and
D.S.Sem
(2007).
Structural evidence for a functionally relevant second camphor binding site in P450cam: model for substrate entry into a P450 active site.
|
| |
Proteins,
69,
125-138.
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L.Mouawad,
C.Tetreau,
S.Abdel-Azeim,
D.Perahia,
and
D.Lavalette
(2007).
CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.
|
| |
Protein Sci,
16,
781-794.
|
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B.OuYang,
S.S.Pochapsky,
G.M.Pagani,
and
T.C.Pochapsky
(2006).
Specific effects of potassium ion binding on wild-type and L358P cytochrome P450cam.
|
| |
Biochemistry,
45,
14379-14388.
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L.Rui,
S.S.Pochapsky,
and
T.C.Pochapsky
(2006).
Comparison of the complexes formed by cytochrome P450cam with cytochrome b5 and putidaredoxin, two effectors of camphor hydroxylase activity.
|
| |
Biochemistry,
45,
3887-3897.
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C.Tetreau,
L.Mouawad,
S.Murail,
P.Duchambon,
Y.Blouquit,
and
D.Lavalette
(2005).
Disentangling ligand migration and heme pocket relaxation in cytochrome P450cam.
|
| |
Biophys J,
88,
1250-1263.
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J.Y.Wei,
T.C.Pochapsky,
and
S.S.Pochapsky
(2005).
Detection of a high-barrier conformational change in the active site of cytochrome P450cam upon binding of putidaredoxin.
|
| |
J Am Chem Soc,
127,
6974-6976.
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S.Nagano,
T.Tosha,
K.Ishimori,
I.Morishima,
and
T.L.Poulos
(2004).
Crystal structure of the cytochrome p450cam mutant that exhibits the same spectral perturbations induced by putidaredoxin binding.
|
| |
J Biol Chem,
279,
42844-42849.
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PDB codes:
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T.Tosha,
S.Yoshioka,
K.Ishimori,
and
I.Morishima
(2004).
L358P mutation on cytochrome P450cam simulates structural changes upon putidaredoxin binding: the structural changes trigger electron transfer to oxy-P450cam from electron donors.
|
| |
J Biol Chem,
279,
42836-42843.
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D.F.Lewis
(2003).
P450 structures and oxidative metabolism of xenobiotics.
|
| |
Pharmacogenomics,
4,
387-395.
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|
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J.K.Yano,
F.Blasco,
H.Li,
R.D.Schmid,
A.Henne,
and
T.L.Poulos
(2003).
Preliminary characterization and crystal structure of a thermostable cytochrome P450 from Thermus thermophilus.
|
| |
J Biol Chem,
278,
608-616.
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PDB code:
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M.Strickler,
B.M.Goldstein,
K.Maxfield,
L.Shireman,
G.Kim,
D.S.Matteson,
and
J.P.Jones
(2003).
Crystallographic studies on the complex behavior of nicotine binding to P450cam (CYP101).
|
| |
Biochemistry,
42,
11943-11950.
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PDB codes:
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T.Tosha,
S.Yoshioka,
S.Takahashi,
K.Ishimori,
H.Shimada,
and
I.Morishima
(2003).
NMR study on the structural changes of cytochrome P450cam upon the complex formation with putidaredoxin. Functional significance of the putidaredoxin-induced structural changes.
|
| |
J Biol Chem,
278,
39809-39821.
|
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|
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|
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B.Bühler,
B.Witholt,
B.Hauer,
and
A.Schmid
(2002).
Characterization and application of xylene monooxygenase for multistep biocatalysis.
|
| |
Appl Environ Microbiol,
68,
560-568.
|
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|
|
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|
|
A.V.Grinberg,
F.Hannemann,
B.Schiffler,
J.Müller,
U.Heinemann,
and
R.Bernhardt
(2000).
Adrenodoxin: structure, stability, and electron transfer properties.
|
| |
Proteins,
40,
590-612.
|
|
|
|
|
|
|
C.Jung
(2000).
Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy.
|
| |
J Mol Recognit,
13,
325-351.
|
|
|
|
|
|
|
C.Mouro,
A.Bondon,
C.Jung,
J.D.De Certaines,
and
G.Simonneaux
(2000).
Assignment of heme methyl 1H-NMR resonances of high-spin and low-spin ferric complexes of cytochrome p450cam using one-dimensional and two-dimensional paramagnetic signals enhancement (PASE) magnetization transfer experiments.
|
| |
Eur J Biochem,
267,
216-221.
|
|
|
|
|
|
|
C.Tetreau,
M.Tourbez,
and
D.Lavalette
(2000).
Conformational relaxation in hemoproteins: the cytochrome P-450cam case.
|
| |
Biochemistry,
39,
14219-14231.
|
|
|
|
|
|
|
H.Shimizu,
E.Obayashi,
Y.Gomi,
H.Arakawa,
S.Y.Park,
H.Nakamura,
S.Adachi,
H.Shoun,
and
Y.Shiro
(2000).
Proton delivery in NO reduction by fungal nitric-oxide reductase. Cryogenic crystallography, spectroscopy, and kinetics of ferric-NO complexes of wild-type and mutant enzymes.
|
| |
J Biol Chem,
275,
4816-4826.
|
|
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PDB codes:
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J.D.Pikus,
K.H.Mitchell,
J.M.Studts,
K.McClay,
R.J.Steffan,
and
B.G.Fox
(2000).
Threonine 201 in the diiron enzyme toluene 4-monooxygenase is not required for catalysis.
|
| |
Biochemistry,
39,
791-799.
|
|
|
|
|
|
|
M.Couture,
D.J.Stuehr,
and
D.L.Rousseau
(2000).
The ferrous dioxygen complex of the oxygenase domain of neuronal nitric-oxide synthase.
|
| |
J Biol Chem,
275,
3201-3205.
|
|
|
|
|
|
|
J.Contzen,
and
C.Jung
(1999).
Changes in secondary structure and salt links of cytochrome P-450cam induced by photoreduction: a Fourier transform infrared spectroscopic study.
|
| |
Biochemistry,
38,
16253-16260.
|
|
|
|
|
|
|
L.C.Bell-Parikh,
and
F.P.Guengerich
(1999).
Kinetics of cytochrome P450 2E1-catalyzed oxidation of ethanol to acetic acid via acetaldehyde.
|
| |
J Biol Chem,
274,
23833-23840.
|
|
|
|
|
|
|
M.Schalk,
S.Nedelkina,
G.Schoch,
Y.Batard,
and
D.Werck-Reichhart
(1999).
Role of unusual amino acid residues in the proximal and distal heme regions of a plant P450, CYP73A1.
|
| |
Biochemistry,
38,
6093-6103.
|
|
|
|
|
|
|
M.Sundaramoorthy,
J.Terner,
and
T.L.Poulos
(1998).
Stereochemistry of the chloroperoxidase active site: crystallographic and molecular-modeling studies.
|
| |
Chem Biol,
5,
461-473.
|
|
|
|
|
|
|
M.Vidakovic,
S.G.Sligar,
H.Li,
and
T.L.Poulos
(1998).
Understanding the role of the essential Asp251 in cytochrome p450cam using site-directed mutagenesis, crystallography, and kinetic solvent isotope effect.
|
| |
Biochemistry,
37,
9211-9219.
|
|
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PDB codes:
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C.Tétreau,
C.Di Primo,
R.Lange,
H.Tourbez,
and
D.Lavalette
(1997).
Dynamics of carbon monoxide binding with cytochromes P-450.
|
| |
Biochemistry,
36,
10262-10275.
|
|
|
|
|
|
|
H.Li,
and
T.L.Poulos
(1997).
The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid.
|
| |
Nat Struct Biol,
4,
140-146.
|
|
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PDB code:
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J.Wang,
D.J.Stuehr,
and
D.L.Rousseau
(1997).
Interactions between substrate analogues and heme ligands in nitric oxide synthase.
|
| |
Biochemistry,
36,
4595-4606.
|
|
|
|
|
|
|
S.Y.Park,
H.Shimizu,
S.Adachi,
A.Nakagawa,
I.Tanaka,
K.Nakahara,
H.Shoun,
E.Obayashi,
H.Nakamura,
T.Iizuka,
and
Y.Shiro
(1997).
Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum.
|
| |
Nat Struct Biol,
4,
827-832.
|
|
|
PDB codes:
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G.C.Roberts
(1996).
The other kind of biological NMR--studies of enzyme-substrate interactions.
|
| |
Neurochem Res,
21,
1117-1124.
|
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|
|
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|
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H.Schulze,
G.H.Hoa,
V.Helms,
R.C.Wade,
and
C.Jung
(1996).
Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor.
|
| |
Biochemistry,
35,
14127-14138.
|
|
|
|
|
|
|
K.Wakasugi,
K.Ishimori,
and
I.Morishima
(1996).
NMR studies of recombinant cytochrome P450cam mutants.
|
| |
Biochimie,
78,
763-770.
|
|
|
|
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|
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M.Unno,
H.Shimada,
Y.Toba,
R.Makino,
and
Y.Ishimura
(1996).
Role of Arg112 of cytochrome p450cam in the electron transfer from reduced putidaredoxin. Analyses with site-directed mutants.
|
| |
J Biol Chem,
271,
17869-17874.
|
|
|
|
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|
|
O.Sibbesen,
J.J.De Voss,
and
P.R.Montellano
(1996).
Putidaredoxin reductase-putidaredoxin-cytochrome p450cam triple fusion protein. Construction of a self-sufficient Escherichia coli catalytic system.
|
| |
J Biol Chem,
271,
22462-22469.
|
|
|
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|
S.Modi,
M.J.Sutcliffe,
W.U.Primrose,
L.Y.Lian,
and
G.C.Roberts
(1996).
The catalytic mechanism of cytochrome P450 BM3 involves a 6 A movement of the bound substrate on reduction.
|
| |
Nat Struct Biol,
3,
414-417.
|
|
|
|
|
|
|
T.C.Pochapsky,
T.A.Lyons,
S.Kazanis,
T.Arakaki,
and
G.Ratnaswamy
(1996).
A structure-based model for cytochrome P450cam-putidaredoxin interactions.
|
| |
Biochimie,
78,
723-733.
|
|
|
|
|
|
|
T.L.Poulos
(1996).
Ligands and electrons and haem proteins.
|
| |
Nat Struct Biol,
3,
401-403.
|
|
|
|
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|
|
Uvarov VYu,
Y.D.Ivanov,
A.N.Romanov,
M.O.Gallyamov,
O.I.Kiselyova,
and
I.V.Yaminsky
(1996).
Scanning tunneling microscopy study of cytochrome P450 2B4 incorporated in proteoliposomes.
|
| |
Biochimie,
78,
780-784.
|
|
|
|
|
|
|
C.A.Hasemann,
R.G.Kurumbail,
S.S.Boddupalli,
J.A.Peterson,
and
J.Deisenhofer
(1995).
Structure and function of cytochromes P450: a comparative analysis of three crystal structures.
|
| |
Structure,
3,
41-62.
|
|
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|
|
C.Di Primo,
E.Deprez,
G.H.Hoa,
and
P.Douzou
(1995).
Antagonistic effects of hydrostatic pressure and osmotic pressure on cytochrome P-450cam spin transition.
|
| |
Biophys J,
68,
2056-2061.
|
|
|
|
|
|
|
C.Jung,
G.Hui Bon Hoa,
D.Davydov,
E.Gill,
and
K.Heremans
(1995).
Compressibility of the heme pocket of substrate analogue complexes of cytochrome P-450cam-CO. The effect of hydrostatic pressure on the Soret band.
|
| |
Eur J Biochem,
233,
600-606.
|
|
|
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|
|
L.D.Gruenke,
K.Konopka,
M.Cadieu,
and
L.Waskell
(1995).
The stoichiometry of the cytochrome P-450-catalyzed metabolism of methoxyflurane and benzphetamine in the presence and absence of cytochrome b5.
|
| |
J Biol Chem,
270,
24707-24718.
|
|
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|
|
M.Kato,
R.Makino,
and
T.Iizuka
(1995).
Thermodynamic aspects of the CO-binding reaction to cytochrome P-450cam. Relevance with their biological significance and structure.
|
| |
Biochim Biophys Acta,
1246,
178-184.
|
|
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|
|
S.Graham-Lorence,
B.Amarneh,
R.E.White,
J.A.Peterson,
and
E.R.Simpson
(1995).
A three-dimensional model of aromatase cytochrome P450.
|
| |
Protein Sci,
4,
1065-1080.
|
|
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|
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H.Schulze,
O.Ristau,
and
C.Jung
(1994).
The carbon monoxide stretching modes in camphor-bound cytochrome P-450cam. The effect of solvent conditions, temperature, and pressure.
|
| |
Eur J Biochem,
224,
1047-1055.
|
|
|
|
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|
|
C.Di Primo,
G.Hui Bon Hoa,
P.Douzou,
and
S.G.Sligar
(1992).
Heme-pocket-hydration change during the inactivation of cytochrome P-450camphor by hydrostatic pressure.
|
| |
Eur J Biochem,
209,
583-588.
|
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|
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M.B.Bass,
M.D.Paulsen,
and
R.L.Ornstein
(1992).
Substrate mobility in a deeply buried active site: analysis of norcamphor bound to cytochrome P-450cam as determined by a 201-psec molecular dynamics simulation.
|
| |
Proteins,
13,
26-37.
|
|
|
|
|
|
|
S.S.Boddupalli,
C.A.Hasemann,
K.G.Ravichandran,
J.Y.Lu,
E.J.Goldsmith,
J.Deisenhofer,
and
J.A.Peterson
(1992).
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.
|
| |
Proc Natl Acad Sci U S A,
89,
5567-5571.
|
|
|
|
|
|
|
M.D.Paulsen,
and
R.L.Ornstein
(1991).
A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam.
|
| |
Proteins,
11,
184-204.
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C.Di Primo,
G.Hui Bon Hoa,
P.Douzou,
and
S.Sligar
(1990).
Effect of the tyrosine 96 hydrogen bond on the inactivation of cytochrome P-450cam induced by hydrostatic pressure.
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Eur J Biochem,
193,
383-386.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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