spacer
spacer

PDBsum entry 7cpp
Go to PDB code: 
protein ligands links
Oxidoreductase(oxygenase) PDB id
7cpp

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
405 a.a. *
Ligands
HEM
NCM
Waters ×206
* Residue conservation analysis
PDB id:
7cpp
Name: Oxidoreductase(oxygenase)
Title: The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome p450(cam)
Structure: Cytochrome p450-cam. Chain: a. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303
Resolution:
2.00Å     R-factor:   0.180    
Authors: R.Raag,T.L.Poulos
Key ref:
R.Raag and T.L.Poulos (1989). The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P-450CAM. Biochemistry, 28, 917-922. PubMed id: 2713354 DOI: 10.1021/bi00428a077
Date:
18-May-90     Release date:   15-Jul-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00183  (CPXA_PSEPU) -  Camphor 5-monooxygenase from Pseudomonas putida
Seq:
Struc: 		415 a.a.
405 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.15.1  - camphor 5-monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 reduced [2Fe-2S]-[putidaredoxin] + (1R,4R)-camphor + O2 + 2 H+ = (1R,4R,5R)-5-hydroxycamphor + 2 oxidized [2Fe-2S]-[putidaredoxin] + H2O
2 × reduced [2Fe-2S]-[putidaredoxin]
 + (1R,4R)-camphor
 + O2
 + 2 × H(+)
 = (1R,4R,5R)-5-hydroxycamphor
 + 2 × oxidized [2Fe-2S]-[putidaredoxin]
 + H2O
      Cofactor: Heme-thiolate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1021/bi00428a077 Biochemistry 28:917-922 (1989)
PubMed id: 2713354  
 
 
The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P-450CAM.
R.Raag, T.L.Poulos.
 
  ABSTRACT  
 
The crystal structures of cytochrome P-450CAM complexed with the alternative substrates norcamphor and adamantanone have been refined at 2.0-A resolution and compared with the native, camphor-bound form of the enzyme. Norcamphor lacks the 8-, 9-, and 10-methyl groups of camphor. Thus, specific interactions between these groups and phenylalanine 87 and valines 247 and 295 are missing in the norcamphor complex. As a result, norcamphor binds about 0.9 A further from the oxygen-binding site than does camphor, which allows sufficient room for a water molecule or hydroxide ion to remain coordinated with the heme iron atom. The larger adamantanone occupies a position closer to that of camphor and, as in the camphor-bound enzyme, the heme iron remains pentacoordinate with no solvent molecule coordinated as a sixth ligand. A comparison of crystallographic temperature factors indicates that norcamphor is more "loosely" bound than are either camphor or adamantanone, as might be expected from the relative sizes of the different substrates. The looser fit of norcamphor in the active-site pocket results in a less specific pattern of hydroxylation. The presence of an aqua ligand is the likely structural basis for the norcamphor-P-450CAM complex having both a lower redox potential and higher percentage of low-spin heme than do either the camphor-P-450CAM or adamantanone-P-450CAM complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21186391 M.Dang, S.S.Pochapsky, and T.C.Pochapsky (2011).
Spring-loading the active site of cytochrome P450cam.
  Metallomics, 3, 339-343.  
20446763 T.C.Pochapsky, S.Kazanis, and M.Dang (2010).
Conformational plasticity and structure/function relationships in cytochromes P450.
  Antioxid Redox Signal, 13, 1273-1296.  
19438234 A.Dey, Y.Jiang, P.Ortiz de Montellano, K.O.Hodgson, B.Hedman, and E.I.Solomon (2009).
S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity.
  J Am Chem Soc, 131, 7869-7878.  
18619466 R.Fasan, Y.T.Meharenna, C.D.Snow, T.L.Poulos, and F.H.Arnold (2008).
Evolutionary history of a specialized p450 propane monooxygenase.
  J Mol Biol, 383, 1069-1080.
PDB code: 3cbd
15720389 B.Sielaff, and J.R.Andreesen (2005).
Kinetic and binding studies with purified recombinant proteins ferredoxin reductase, ferredoxin and cytochrome P450 comprising the morpholine mono-oxygenase from Mycobacterium sp. strain HE5.
  FEBS J, 272, 1148-1159.  
15912546 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.  
15651036 S.B.Kirton, C.W.Murray, M.L.Verdonk, and R.D.Taylor (2005).
Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins.
  Proteins, 58, 836-844.  
15146488 D.L.Harris, J.Y.Park, L.Gruenke, and L.Waskell (2004).
Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state.
  Proteins, 55, 895-914.  
15139037 M.Almlöf, B.O.Brandsdal, and J.Aqvist (2004).
Binding affinity prediction with different force fields: examination of the linear interaction energy method.
  J Comput Chem, 25, 1242-1254.  
15597203 M.H.Seifert, F.Schmitt, T.Herz, and B.Kramer (2004).
ProPose: a docking engine based on a fully configurable protein-ligand interaction model.
  J Mol Model, 10, 342-357.  
12831319 D.F.Lewis (2003).
P450 structures and oxidative metabolism of xenobiotics.
  Pharmacogenomics, 4, 387-395.  
12842870 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.  
11087371 C.Tetreau, M.Tourbez, and D.Lavalette (2000).
Conformational relaxation in hemoproteins: the cytochrome P-450cam case.
  Biochemistry, 39, 14219-14231.  
11050228 M.Schalk, and R.Croteau (2000).
A single amino acid substitution (F363I) converts the regiochemistry of the spearmint (-)-limonene hydroxylase from a C6- to a C3-hydroxylase.
  Proc Natl Acad Sci U S A, 97, 11948-11953.  
10336628 F.Cabello-Hurtado, M.Taton, N.Forthoffer, R.Kahn, S.Bak, A.Rahier, and D.Werck-Reichhart (1999).
Optimized expression and catalytic properties of a wheat obtusifoliol 14alpha-demethylase (CYP51) expressed in yeast. Complementation of erg11Delta yeast mutants by plant CYP51.
  Eur J Biochem, 262, 435-446.  
10320335 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.  
10480907 T.Shimanuki, H.Sato, S.Daff, I.Sagami, and T.Shimizu (1999).
Crucial role of Lys(423) in the electron transfer of neuronal nitric-oxide synthase.
  J Biol Chem, 274, 26956-26961.  
9928089 L.P.Wackett (1998).
Directed evolution of new enzymes and pathways for environmental biocatalysis.
  Ann N Y Acad Sci, 864, 142-152.  
9315848 B.R.Crane, L.M.Siegel, and E.D.Getzoff (1997).
Structures of the siroheme- and Fe4S4-containing active center of sulfite reductase in different states of oxidation: heme activation via reduction-gated exogenous ligand exchange.
  Biochemistry, 36, 12101-12119.
PDB codes: 2aop 3aop 4aop 5aop
8993324 C.Di Primo, E.Deprez, S.G.Sligar, and G.Hui Bon Hoa (1997).
Origin of the photoacoustic signal in cytochrome P-450cam: role of the Arg186-Asp251-Lys178 bifurcated salt bridge.
  Biochemistry, 36, 112-118.  
8993326 D.M.Hoover, J.T.Jarrett, R.H.Sands, W.R.Dunham, M.L.Ludwig, and R.G.Matthews (1997).
Interaction of Escherichia coli cobalamin-dependent methionine synthase and its physiological partner flavodoxin: binding of flavodoxin leads to axial ligand dissociation from the cobalamin cofactor.
  Biochemistry, 36, 127-138.  
  9512922 M.D.Segall, M.C.Payne, S.W.Ellis, G.T.Tucker, and R.N.Boyes (1997).
Ab initio molecular modeling in the study of drug metabolism.
  Eur J Drug Metab Pharmacokinet, 22, 283-289.  
9122160 T.I.Oprea, G.Hummer, and A.E.Garcia (1997).
Identification of a functional water channel in cytochrome P450 enzymes.
  Proc Natl Acad Sci U S A, 94, 2133-2138.  
9010605 K.Wakasugi, K.Ishimori, and I.Morishima (1996).
NMR studies of recombinant cytochrome P450cam mutants.
  Biochimie, 78, 763-770.  
8612070 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.  
8639665 S.Narasimhulu (1996).
Interactions of substrate and product with cytochrome P450 2B4.
  Biochemistry, 35, 1840-1847.  
9010607 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.  
8634279 V.Helms, E.Deprez, E.Gill, C.Barret, G.Hui Bon Hoa, and R.C.Wade (1996).
Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket.
  Biochemistry, 35, 1485-1499.  
7743131 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.  
7612848 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.  
  7645302 D.F.Lewis (1995).
Three-dimensional models of human and other mammalian microsomal P450s constructed from an alignment with P450102 (P450bm3).
  Xenobiotica, 25, 333-366.  
7492620 M.Tsubaki, K.Morimoto, S.Tomita, S.Miura, Y.Ichikawa, A.Miyatake, F.Masuya, and H.Hori (1995).
Electron paramagnetic resonance investigation of cytochrome P-450c21 from bovine adrenocortical microsomes: a new enzymatic activity.
  Biochim Biophys Acta, 1259, 89-98.  
7890644 P.J.Loida, S.G.Sligar, M.D.Paulsen, G.E.Arnold, and R.L.Ornstein (1995).
Stereoselective hydroxylation of norcamphor by cytochrome P450cam. Experimental verification of molecular dynamics simulations.
  J Biol Chem, 270, 5326-5330.  
7499289 S.Kadkhodayan, E.D.Coulter, D.M.Maryniak, T.A.Bryson, and J.H.Dawson (1995).
Uncoupling oxygen transfer and electron transfer in the oxygenation of camphor analogues by cytochrome P450-CAM. Direct observation of an intermolecular isotope effect for substrate C-H activation.
  J Biol Chem, 270, 28042-28048.  
8519982 V.Helms, and R.C.Wade (1995).
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study.
  Biophys J, 69, 810-824.  
7876903 J.A.Braatz, M.B.Bass, and R.L.Ornstein (1994).
An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2.
  J Comput Aided Mol Des, 8, 607-622.  
7925408 M.A.Pierrel, Y.Batard, M.Kazmaier, C.Mignotte-Vieux, F.Durst, and D.Werck-Reichhart (1994).
Catalytic properties of the plant cytochrome P450 CYP73 expressed in yeast. Substrate specificity of a cinnamate hydroxylase.
  Eur J Biochem, 224, 835-844.  
7815091 M.D.Paulsen, and R.L.Ornstein (1994).
Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam.
  J Comput Aided Mol Des, 8, 389-404.  
  8453374 M.D.Paulsen, D.Filipovic, S.G.Sligar, and R.L.Ornstein (1993).
Controlling the regiospecificity and coupling of cytochrome P450cam: T185F mutant increases coupling and abolishes 3-hydroxynorcamphor product.
  Protein Sci, 2, 357-365.  
7763853 M.S.Logan, L.M.Newman, C.A.Schanke, and L.P.Wackett (1993).
Cosubstrate effects in reductive dehalogenation by Pseudomonas putida G786 expressing cytochrome P-450CAM.
  Biodegradation, 4, 39-50.  
1425665 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.  
1517776 D.F.Lewis, and H.Moereels (1992).
The sequence homologies of cytochromes P-450 and active-site geometries.
  J Comput Aided Mol Des, 6, 235-252.  
1372979 M.B.Bass, D.F.Hopkins, W.A.Jaquysh, and R.L.Ornstein (1992).
A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding.
  Proteins, 12, 266-277.  
1594575 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.  
1474394 M.D.Paulsen, and R.L.Ornstein (1992).
Predicting the product specificity and coupling of cytochrome P450cam.
  J Comput Aided Mol Des, 6, 449-460.  
1608967 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.  
1749772 M.D.Paulsen, and R.L.Ornstein (1991).
A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam.
  Proteins, 11, 184-204.  
2226459 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.
  Eur J Biochem, 193, 383-386.  
2213064 R.C.Wade (1990).
Solvation of the active site of cytochrome P450-cam.
  J Comput Aided Mol Des, 4, 199-204.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer
spacer