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PDBsum entry 6cpp
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Oxidoreductase(oxygenase) PDB id
6cpp

 

 

 

 

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Contents
Protein chain
405 a.a. *
Ligands
HEM
CAE
Waters ×204
* Residue conservation analysis
PDB id:
6cpp
Name: Oxidoreductase(oxygenase)
Title: Crystal structures of cytochrome p450-cam complexed with camphane, thiocamphor, and adamantane: factors controlling p450 substrate hydroxylation
Structure: Cytochrome p450-cam. Chain: a. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303
Resolution:
1.90Å     R-factor:   0.190    
Authors: R.Raag,T.L.Poulos
Key ref:
R.Raag and T.L.Poulos (1991). Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation. Biochemistry, 30, 2674-2684. PubMed id: 2001355 DOI: 10.1021/bi00224a016
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/bi00224a016 Biochemistry 30:2674-2684 (1991)
PubMed id: 2001355  
 
 
Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation.
R.Raag, T.L.Poulos.
 
  ABSTRACT  
 
X-ray crystal structures have been determined for complexes of cytochrome P-450CAM with the substrates camphane, adamantane, and thiocamphor. Unlike the natural substrate camphor, which hydrogen bonds to Tyr96 and is metabolized to a single product, camphane, adamantane and thiocamphor do not hydrogen bond to the enzyme and all are hydroxylated at multiple positions. Evidently the lack of a substrate-enzyme hydrogen bond allows substrates greater mobility in the active site, explaining this lower regiospecificity of metabolism as well as the inability of these substrates to displace the distal ligand to the heme iron. Tyr96 is a ligand, via its carbonyl oxygen atom, to a cation that is thought to stabilize the camphor-P-450CAM complex [Poulos, T. L., Finzel, B. C., & Howard, A. J. (1987) J. Mol. Biol. 195, 687-700]. The occupancy and temperature factor of the cationic site are lower and higher, respectively, in the presence of the non-hydrogen-bonding substrates investigated here than in the presence of camphor, underscoring the relationship between cation and substrate binding. Thiocamphor gave the most unexpected orientation in the active site of any of the substrates we have investigated to date. The orientation of thiocamphor is quite different from that of camphor. That is, carbons 5 and 6, at which thiocamphor is primarily hydroxylated [Atkins, W. M., & Sligar, S. G. (1988) J. Biol. Chem. 263, 18842-18849], are positioned near Tyr96 rather than near the heme iron. Therefore, the crystallographically observed thiocamphor-P-450CAM structure may correspond to a nonproductive complex. Disordered solvent has been identified in the active site in the presence of uncoupling substrates that channel reducing equivalents away from substrate hydroxylation toward hydrogen peroxide and/or "excess" water production. A buried solvent molecule has also been identified, which may promote uncoupling by moving from an internal location to the active site in the presence of highly mobile substrates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354674 J.Liu, D.Obando, V.Liao, T.Lifa, and R.Codd (2011).
The many faces of the adamantyl group in drug design.
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21171581 Y.T.Lee, E.C.Glazer, R.F.Wilson, C.D.Stout, and D.B.Goodin (2011).
Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel.
  Biochemistry, 50, 693-703.  
20223990 L.M.Jensen, R.Sanishvili, V.L.Davidson, and C.M.Wilmot (2010).
In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex.
  Science, 327, 1392-1394.
PDB codes: 3l4m 3l4o
19947890 N.Shakunthala (2010).
New cytochrome P450 mechanisms: implications for understanding molecular basis for drug toxicity at the level of the cytochrome.
  Expert Opin Drug Metab Toxicol, 6, 1.  
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.  
19222039 A.Seifert, S.Vomund, K.Grohmann, S.Kriening, V.B.Urlacher, S.Laschat, and J.Pleiss (2009).
Rational design of a minimal and highly enriched CYP102A1 mutant library with improved regio-, stereo- and chemoselectivity.
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19368882 D.L.Mobley, and K.A.Dill (2009).
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
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19060161 R.W.Eaton, and P.Sandusky (2009).
Biotransformations of 2-methylisoborneol by camphor-degrading bacteria.
  Appl Environ Microbiol, 75, 583-588.  
17526697 L.Gómez-Gil, P.Kumar, D.Barriault, J.T.Bolin, M.Sylvestre, and L.D.Eltis (2007).
Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme.
  J Bacteriol, 189, 5705-5715.  
16637647 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, 5786-5791.  
15489303 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.  
16080691 G.S.Koe, and V.L.Vilker (2005).
Effect of oxygen on the dehalogenation of 1,2-Dibromo-3-chloropropane by cytochrome P450cam (CYP101).
  Biotechnol Prog, 21, 1119-1127.  
16108714 R.H.Lilien, B.W.Stevens, A.C.Anderson, and B.R.Donald (2005).
A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.
  J Comput Biol, 12, 740-761.  
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.  
15020590 M.G.Joyce, H.M.Girvan, A.W.Munro, and D.Leys (2004).
A single mutation in cytochrome P450 BM3 induces the conformational rearrangement seen upon substrate binding in the wild-type enzyme.
  J Biol Chem, 279, 23287-23293.
PDB codes: 1smi 1smj
15189165 O.Pylypenko, and I.Schlichting (2004).
Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s.
  Annu Rev Biochem, 73, 991.  
12950252 G.A.Schoch, R.Attias, M.Le Ret, and D.Werck-Reichhart (2003).
Key substrate recognition residues in the active site of a plant cytochrome P450, CYP73A1. Homology guided site-directed mutagenesis.
  Eur J Biochem, 270, 3684-3695.  
14556625 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.
PDB codes: 1p2y 1p7r
12838268 S.J.Teague (2003).
Implications of protein flexibility for drug discovery.
  Nat Rev Drug Discov, 2, 527-541.  
12114516 X.Chen, A.Christopher, J.P.Jones, S.G.Bell, Q.Guo, F.Xu, Z.Rao, and L.L.Wong (2002).
Crystal structure of the F87W/Y96F/V247L mutant of cytochrome P-450cam with 1,3,5-trichlorobenzene bound and further protein engineering for the oxidation of pentachlorobenzene and hexachlorobenzene.
  J Biol Chem, 277, 37519-37526.
PDB code: 1j51
11606730 A.R.Dunn, I.J.Dmochowski, A.M.Bilwes, H.B.Gray, and B.R.Crane (2001).
Probing the open state of cytochrome P450cam with ruthenium-linker substrates.
  Proc Natl Acad Sci U S A, 98, 12420-12425.
PDB code: 1k2o
11114067 C.Jung (2000).
Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy.
  J Mol Recognit, 13, 325-351.  
11087371 C.Tetreau, M.Tourbez, and D.Lavalette (2000).
Conformational relaxation in hemoproteins: the cytochrome P-450cam case.
  Biochemistry, 39, 14219-14231.  
10777527 N.Y.Imbeault, J.B.Powlowski, C.L.Colbert, J.T.Bolin, and L.D.Eltis (2000).
Steady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase.
  J Biol Chem, 275, 12430-12437.  
10557259 I.J.Dmochowski, B.R.Crane, J.J.Wilker, J.R.Winkler, and H.B.Gray (1999).
Optical detection of cytochrome P450 by sensitizer-linked substrates.
  Proc Natl Acad Sci U S A, 96, 12987-12990.
PDB code: 1qmq
  10338024 R.Brem, and K.A.Dill (1999).
The effect of multiple binding modes on empirical modeling of ligand docking to proteins.
  Protein Sci, 8, 1134-1143.  
9556346 J.Contzen, and C.Jung (1998).
Step-scan time-resolved FTIR spectroscopy of cytochrome P-450cam carbon monoxide complex: a salt link involved in the ligand-rebinding process.
  Biochemistry, 37, 4317-4324.  
9343358 A.Archelas, and R.Furstoss (1997).
Synthesis of enantiopure epoxides through biocatalytic approaches.
  Annu Rev Microbiol, 51, 491-525.  
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.  
9283090 C.T.Migita, J.C.Salerno, B.S.Masters, P.Martasek, K.McMillan, and M.Ikeda-Saito (1997).
Substrate binding-induced changes in the EPR spectra of the ferrous nitric oxide complexes of neuronal nitric oxide synthase.
  Biochemistry, 36, 10987-10992.  
9428674 F.Bancel, N.Bec, C.Ebel, and R.Lange (1997).
A central role for water in the control of the spin state of cytochrome P-450scc.
  Eur J Biochem, 250, 276-285.  
9029508 G.Klebe, and H.J.Böhm (1997).
Energetic and entropic factors determining binding affinity in protein-ligand complexes.
  J Recept Signal Transduct Res, 17, 459-473.  
  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.  
9335524 S.Poli-Scaife, R.Attias, P.M.Dansette, and D.Mansuy (1997).
The substrate binding site of human liver cytochrome P450 2C9: an NMR study.
  Biochemistry, 36, 12672-12682.  
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.  
8809764 A.W.Munro, and J.G.Lindsay (1996).
Bacterial cytochromes P-450.
  Mol Microbiol, 20, 1115-1125.  
8942676 C.Jung, H.Schulze, and E.Deprez (1996).
Role of the polarity of the heme environment for the CO stretch modes in cytochrome P-450cam-CO.
  Biochemistry, 35, 15088-15094.  
9010597 H.Li, and T.L.Poulos (1996).
Conformational dynamics in cytochrome P450-substrate interactions.
  Biochimie, 78, 695-699.  
9010605 K.Wakasugi, K.Ishimori, and I.Morishima (1996).
NMR studies of recombinant cytochrome P450cam mutants.
  Biochimie, 78, 763-770.  
8798411 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.  
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.  
  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.  
7749919 J.R.Cupp-Vickery, and T.L.Poulos (1995).
Structure of cytochrome P450eryF involved in erythromycin biosynthesis.
  Nat Struct Biol, 2, 144-153.
PDB code: 1oxa
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.  
  8590980 T.Kinonen, M.Pasanen, J.Gynther, A.Poso, T.Järvinen, E.Alhava, and R.O.Juvonen (1995).
Competitive inhibition of coumarin 7-hydroxylation by pilocarpine and its interaction with mouse CYP 2A5 and human CYP 2A6.
  Br J Pharmacol, 116, 2625-2630.  
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.  
7925402 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.  
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.  
8026495 P.Urban, D.Werck-Reichhart, H.G.Teutsch, F.Durst, S.Regnier, M.Kazmaier, and D.Pompon (1994).
Characterization of recombinant plant cinnamate 4-hydroxylase produced in yeast. Kinetic and spectral properties of the major plant P450 of the phenylpropanoid pathway.
  Eur J Biochem, 222, 843-850.  
  8376348 J.D.Ropp, I.C.Gunsalus, and S.G.Sligar (1993).
Cloning and expression of a member of a new cytochrome P-450 family: cytochrome P-450lin (CYP111) from Pseudomonas incognita.
  J Bacteriol, 175, 6028-6037.  
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.  
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.  
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 codes are shown on the right.

 

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