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PDBsum entry 2cpp
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Oxidoreductase(oxygenase)
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PDB id
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2cpp
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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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J Mol Biol
195:687-700
(1987)
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PubMed id:
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High-resolution crystal structure of cytochrome P450cam.
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T.L.Poulos,
B.C.Finzel,
A.J.Howard.
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ABSTRACT
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The crystal structure of Pseudomonas putida cytochrome P450cam with its
substrate, camphor, bound has been refined to R = 0.19 at a normal resolution of
1.63 A. While the 1.63 A model confirms our initial analysis based on the 2.6 A
model, the higher resolution structure has revealed important new details. These
include a more precise assignment of sequence to secondary structure, the
identification of three cis-proline residues, and a more detailed picture of
substrate-protein interactions. In addition, 204 ordered solvent molecules have
been found, one of which appears to be a cation. The cation stabilizes an
unfavorable polypeptide conformation involved in forming part of the active site
pocket, suggesting that the cation may be the metal ion binding site associated
with the well-known ability of metal ions to enhance formation of the
enzyme-substrate complex. Another unusual polypeptide conformation forms the
proposed oxygen-binding pocket. A localized distortion and widening of the
distal helix provides a pocket for molecular oxygen. An intricate system of
side-chain to backbone hydrogen bonds aids in stabilizing the required local
disruption in helical geometry. Sequence homologies strongly suggest a common
oxygen-binding pocket in all P450 species. Further sequence comparisons between
P450 species indicate common three-dimensional structures with changes focused
in a region of the molecule postulated to be associated with the control of
substrate specificity.
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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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Changing the substrate specificity of P450cam towards diphenylmethane by semi-rational enzyme engineering.
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| |
Protein Eng Des Sel,
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M.Dang,
S.S.Pochapsky,
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Spring-loading the active site of cytochrome P450cam.
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| |
Metallomics,
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L.L.Wong,
and
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(2011).
Structural Analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444.
|
| |
Chembiochem,
12,
88-99.
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PDB codes:
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|
N.Kirischian,
A.G.McArthur,
C.Jesuthasan,
B.Krattenmacher,
and
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(2011).
Phylogenetic and functional analysis of the vertebrate cytochrome p450 2 family.
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and
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(2011).
Three clusters of conformational States in p450cam reveal a multistep pathway for closing of the substrate access channel .
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| |
Biochemistry,
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Molecular characterization and isolation of cytochrome P450 genes from the filamentous fungus Aspergillus oryzae.
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Arabidopsis CYP72C1 is an atypical cytochrome P450 that inactivates brassinosteroids.
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and
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(2010).
The structure of CYP101D2 unveils a potential path for substrate entry into the active site.
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| |
Biochem J,
433,
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PDB codes:
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Y.T.Lee,
R.F.Wilson,
I.Rupniewski,
and
D.B.Goodin
(2010).
P450cam visits an open conformation in the absence of substrate.
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| |
Biochemistry,
49,
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PDB codes:
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A.Dey,
Y.Jiang,
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J Am Chem Soc,
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Investigating the structural plasticity of a cytochrome P450: three-dimensional structures of P450 EryK and binding to its physiological substrate.
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J Biol Chem,
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PDB codes:
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C.Sheng,
Z.Miao,
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Three-dimensional model of lanosterol 14 alpha-demethylase from Cryptococcus neoformans: active-site characterization and insights into azole binding.
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and
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Substrate binding induces structural changes in cytochrome P450cam.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
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PDB codes:
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L.Tian,
and
R.A.Friesner
(2009).
QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism.
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| |
J Chem Theory Comput,
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S.Balaz
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Modeling kinetics of subcellular disposition of chemicals.
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| |
Chem Rev,
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S.P.de Visser,
L.Tahsini,
and
W.Nam
(2009).
How does the axial ligand of cytochrome P450 biomimetics influence the regioselectivity of aliphatic versus aromatic hydroxylation?
|
| |
Chemistry,
15,
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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,
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|
Z.R.Yang
(2009).
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy.
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| |
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|
B.OuYang,
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M.Dang,
and
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A functional proline switch in cytochrome P450cam.
|
| |
Structure,
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C.Jung
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Fourier transform infrared spectroscopy as a tool to study structural properties of cytochromes P450 (CYPs).
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| |
Anal Bioanal Chem,
392,
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|
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|
|
D.K.Ro,
M.Ouellet,
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D.Eng,
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J.D.Newman,
and
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(2008).
Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic acid.
|
| |
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E.M.Isin,
and
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Substrate binding to cytochromes P450.
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| |
Anal Bioanal Chem,
392,
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|
|
J.F.Martín,
E.Gudiña,
and
J.L.Barredo
(2008).
Conversion of beta-carotene into astaxanthin: Two separate enzymes or a bifunctional hydroxylase-ketolase protein?
|
| |
Microb Cell Fact,
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|
|
|
|
|
|
|
L.Li,
Z.Chang,
Z.Pan,
Z.Q.Fu,
and
X.Wang
(2008).
Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase.
|
| |
Proc Natl Acad Sci U S A,
105,
13883-13888.
|
|
|
PDB codes:
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P.J.Mak,
D.Kaluka,
M.E.Manyumwa,
H.Zhang,
T.Deng,
and
J.R.Kincaid
(2008).
Defining resonance Raman spectral responses to substrate binding by cytochrome P450 from Pseudomonas putida.
|
| |
Biopolymers,
89,
1045-1053.
|
|
|
|
|
|
|
S.Huang,
D.Sun,
and
L.B.Brattsten
(2008).
Novel cytochrome P450s, CYP6BB1 and CYP6P10, from the salt marsh mosquito Aedes sollicitans (Walker) (Diptera: Culicidae).
|
| |
Arch Insect Biochem Physiol,
67,
139-154.
|
|
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|
|
T.A.Pechurskaya,
O.P.Lukashevich,
A.A.Gilep,
and
S.A.Usanov
(2008).
Engineering, expression, and purification of "soluble" human cytochrome P45017alpha and its functional characterization.
|
| |
Biochemistry (Mosc),
73,
806-811.
|
|
|
|
|
|
|
W.Li,
Y.Tang,
H.Liu,
J.Cheng,
W.Zhu,
and
H.Jiang
(2008).
Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking.
|
| |
Proteins,
71,
938-949.
|
|
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|
|
|
|
Y.Hamuro,
K.S.Molnar,
S.J.Coales,
B.OuYang,
A.K.Simorellis,
and
T.C.Pochapsky
(2008).
Hydrogen-deuterium exchange mass spectrometry for investigation of backbone dynamics of oxidized and reduced cytochrome P450cam.
|
| |
J Inorg Biochem,
102,
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|
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|
|
|
|
A.Dey,
F.E.Jenney,
M.W.Adams,
M.K.Johnson,
K.O.Hodgson,
B.Hedman,
and
E.I.Solomon
(2007).
Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity.
|
| |
J Am Chem Soc,
129,
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|
|
A.W.Munro,
H.M.Girvan,
and
K.J.McLean
(2007).
Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily.
|
| |
Nat Prod Rep,
24,
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|
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|
|
|
|
|
C.Berne,
D.Pignol,
J.Lavergne,
and
D.Garcia
(2007).
CYP201A2, a cytochrome P450 from Rhodopseudomonas palustris, plays a key role in the biodegradation of tributyl phosphate.
|
| |
Appl Microbiol Biotechnol,
77,
135-144.
|
|
|
|
|
|
|
D.A.Landfried,
D.A.Vuletich,
M.P.Pond,
and
J.T.Lecomte
(2007).
Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins.
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| |
Gene,
398,
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|
|
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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,
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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.
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| |
Protein Sci,
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A.Cavalli,
M.Masetti,
A.Carotti,
and
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Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes.
|
| |
Proteins,
62,
1074-1087.
|
|
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PDB code:
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B.K.Muralidhara,
S.Negi,
C.C.Chin,
W.Braun,
and
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Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling.
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| |
J Biol Chem,
281,
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|
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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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|
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H.Morita,
H.Yoshikawa,
T.Takizawa,
M.Shirai,
F.Akahori,
and
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The formation of g=2.49-species of cytochrome P450 in the rat liver by PCB126 oral administration: identification of heme axial ligands by EPR spectroscopy.
|
| |
Biosci Biotechnol Biochem,
70,
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|
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|
|
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|
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J.Qin,
R.Perera,
L.L.Lovelace,
J.H.Dawson,
and
L.Lebioda
(2006).
Structures of thiolate- and carboxylate-ligated ferric H93G myoglobin: models for cytochrome P450 and for oxyanion-bound heme proteins.
|
| |
Biochemistry,
45,
3170-3177.
|
|
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PDB codes:
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J.Zurek,
N.Foloppe,
J.N.Harvey,
and
A.J.Mulholland
(2006).
Mechanisms of reaction in cytochrome P450: Hydroxylation of camphor in P450cam.
|
| |
Org Biomol Chem,
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|
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|
K.P.Ravindranathan,
E.Gallicchio,
R.A.Friesner,
A.E.McDermott,
and
R.M.Levy
(2006).
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study.
|
| |
J Am Chem Soc,
128,
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|
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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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|
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|
|
M.Bandell,
A.E.Dubin,
M.J.Petrus,
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and
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(2006).
High-throughput random mutagenesis screen reveals TRPM8 residues specifically required for activation by menthol.
|
| |
Nat Neurosci,
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M.Ekroos,
and
T.Sjögren
(2006).
Structural basis for ligand promiscuity in cytochrome P450 3A4.
|
| |
Proc Natl Acad Sci U S A,
103,
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|
|
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PDB codes:
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S.Y.Reece,
J.M.Hodgkiss,
J.Stubbe,
and
D.G.Nocera
(2006).
Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology.
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| |
Philos Trans R Soc Lond B Biol Sci,
361,
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T.Mouri,
J.Michizoe,
H.Ichinose,
N.Kamiya,
and
M.Goto
(2006).
A recombinant Escherichia coli whole cell biocatalyst harboring a cytochrome P450cam monooxygenase system coupled with enzymatic cofactor regeneration.
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| |
Appl Microbiol Biotechnol,
72,
514-520.
|
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T.Mouri,
N.Kamiya,
and
M.Goto
(2006).
Increasing the catalytic performance of a whole cell biocatalyst harboring a cytochrome p450cam system by stabilization of an electron transfer component.
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| |
Biotechnol Lett,
28,
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U.M.Kent,
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D.E.Mills,
K.A.Regal,
and
P.F.Hollenberg
(2006).
Identification of 17-alpha-ethynylestradiol-modified active site peptides and glutathione conjugates formed during metabolism and inactivation of P450s 2B1 and 2B6.
|
| |
Chem Res Toxicol,
19,
279-287.
|
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A.Oda,
N.Yamaotsu,
and
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(2005).
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models.
|
| |
J Comput Chem,
26,
818-826.
|
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|
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B.Zhao,
F.P.Guengerich,
A.Bellamine,
D.C.Lamb,
M.Izumikawa,
L.Lei,
L.M.Podust,
M.Sundaramoorthy,
J.A.Kalaitzis,
L.M.Reddy,
S.L.Kelly,
B.S.Moore,
D.Stec,
M.Voehler,
J.R.Falck,
T.Shimada,
and
M.R.Waterman
(2005).
Binding of two flaviolin substrate molecules, oxidative coupling, and crystal structure of Streptomyces coelicolor A3(2) cytochrome P450 158A2.
|
| |
J Biol Chem,
280,
11599-11607.
|
|
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PDB codes:
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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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|
|
F.Xu,
S.G.Bell,
J.Lednik,
A.Insley,
Z.Rao,
and
L.L.Wong
(2005).
The heme monooxygenase cytochrome P450cam can be engineered to oxidize ethane to ethanol.
|
| |
Angew Chem Int Ed Engl,
44,
4029-4032.
|
|
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H.Yasui,
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Primary and secondary structural patterns in eukaryotic cytochrome P-450 families correspond to structures of the helix-rich domain of Pseudomonas putida cytochrome P-450cam. Indications for a similar overall topology.
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Mol Microbiol,
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Where a reference describes a PDB structure, the PDB
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