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PDBsum entry 2bdm

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Oxidoreductase PDB id
2bdm
Jmol
Contents
Protein chain
465 a.a. *
Ligands
HEM-TMI
TMI ×2
CM5 ×4
Waters ×131
* Residue conservation analysis
PDB id:
2bdm
Name: Oxidoreductase
Title: Structure of cytochrome p450 2b4 with bound bifonazole
Structure: Cytochrome p450 2b4. Chain: a. Fragment: residues 28-491. Synonym: cypiib4, p450-lm2, isozyme 2, p450 types b0 and b1 engineered: yes
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Gene: cyp2b4. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.196     R-free:   0.215
Authors: Y.Zhao,M.A.White,B.K.Muralidhara,L.Sun,J.R.Halpert,C.D.Stout
Key ref:
Y.Zhao et al. (2006). Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. J Biol Chem, 281, 5973-5981. PubMed id: 16373351 DOI: 10.1074/jbc.M511464200
Date:
20-Oct-05     Release date:   27-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00178  (CP2B4_RABIT) -  Cytochrome P450 2B4
Seq:
Struc:
491 a.a.
465 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.14.14.1  - Unspecific monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RH + reduced flavoprotein + O2 = ROH + oxidized flavoprotein + H2O
RH
+ reduced flavoprotein
+ O(2)
= ROH
+ oxidized flavoprotein
+ H(2)O
      Cofactor: Heme-thiolate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     8 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M511464200 J Biol Chem 281:5973-5981 (2006)
PubMed id: 16373351  
 
 
Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.
Y.Zhao, M.A.White, B.K.Muralidhara, L.Sun, J.R.Halpert, C.D.Stout.
 
  ABSTRACT  
 
To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a type II binding spectrum in 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and tryptophan fluorescence quenching indicate no significant burial of protein apolar surface nor altered accessibility of Trp-121 upon bifonazole binding, in contrast to recent results with CPI. A 2.3 A crystal structure of 2B4-bifonazole reveals a novel open conformation with ligand bound in the active site, which is significantly different from either the U-shaped cleft of ligand-free 2B4 or the small active site pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is widely open in the middle but narrow at the top. A bifonazole molecule occupies the bottom of the active site cleft, where helix I is bent approximately 15 degrees to accommodate the bulky ligand. The structure also defines unanticipated interactions between helix C residues and bifonazole, suggesting an important role of helix C in azole recognition by mammalian P450s. Comparison of the ligand-free 2B4 structure, the 2B4-CPI structure, and the 2B4-bifonazole structure identifies structurally plastic regions that undergo correlated conformational changes in response to ligand binding. The most plastic regions are putative membrane-binding motifs involved in substrate access or substrate binding. The results allow us to model the membrane-associated state of P450 and provide insight into how lipophilic substrates access the buried active site.
 
  Selected figure(s)  
 
Figure 1.
A, structure of ligand-free 2B4. B, structure of 2B4-CPI. The chemical formula of CPI is shown below the protein structure. C, structure of 2B4-bifonazole. The chemical formula of bifonazole is shown below the protein structure. The three structures are shown in the same orientation by aligning the most conserved tertiary structure (residues 61-98 and 306-465). Four regions around the active site (residues 100-140, 203-262, 276-290, and 474-479) are colored green in A, orange in B, and yellow in C, respectively, with the major helices labeled. Other parts of the protein are colored gray in all three structures. Heme, CPI, and bifonazole are shown as red, cyan, and forest green sticks, respectively. Images were generated using PyMol (www.pymol.org) unless otherwise credited.
Figure 2.
A, divergent stereo view of the 2B4-bifonazole monomer. Helices and strands are colored yellow and blue, respectively. The termini and major helices are labeled. Heme, bifonazole, and Cymal-5 molecules are shown as red, forest green, and cyan sticks, respectively. B, the dimer interface of 2B4-bifonazole is stabilized by interdigitating β-strands, and extra copies of detergent and substrate that associate with exposed hydrophobic regions. For clarity, only residues 98-117 and 204-230 are shown. Molecules A and B are colored yellow and gray, respectively. Heme is shown as red sticks. Bifonazole and Cymal-5 of molecule A are shown as forest green and cyan sticks, respectively. Bifonazole and Cymal-5 of molecule B are shown as green and pale cyan sticks, respectively. Helix F′ and β-strands 6-1, 7-1, 7-2, and 7-3 are labeled. The chemical formula of Cymal-5 is shown.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 5973-5981) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19961857 A.J.Annalora, D.B.Goodin, W.X.Hong, Q.Zhang, E.F.Johnson, and C.D.Stout (2010).
Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism.
  J Mol Biol, 396, 441-451.
PDB codes: 3k9v 3k9y
20697922 O.Shoji, T.Fujishiro, S.Nagano, S.Tanaka, T.Hirose, Y.Shiro, and Y.Watanabe (2010).
Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis.
  J Biol Inorg Chem, 15, 1331-1339.
PDB codes: 2zqj 2zqx
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.  
19700628 H.L.Lin, H.Zhang, K.R.Noon, and P.F.Hollenberg (2009).
Mechanism-based inactivation of CYP2B1 and its F-helix mutant by two tert-butyl acetylenic compounds: covalent modification of prosthetic heme versus apoprotein.
  J Pharmacol Exp Ther, 331, 392-403.  
19605359 H.Zhang, C.Kenaan, D.Hamdane, G.H.Hoa, and P.F.Hollenberg (2009).
Effect of conformational dynamics on substrate recognition and specificity as probed by the introduction of a de novo disulfide bond into cytochrome P450 2B1.
  J Biol Chem, 284, 25678-25686.  
19720728 H.Zhang, H.L.Lin, V.J.Walker, D.Hamdane, and P.F.Hollenberg (2009).
tert-Butylphenylacetylene is a potent mechanism-based inactivator of cytochrome P450 2B4: inhibition of cytochrome P450 catalysis by steric hindrance.
  Mol Pharmacol, 76, 1011-1018.  
19555717 I.G.Denisov, D.J.Frank, and S.G.Sligar (2009).
Cooperative properties of cytochromes P450.
  Pharmacol Ther, 124, 151-167.  
19074393 L.H.Xu, S.Fushinobu, H.Ikeda, T.Wakagi, and H.Shoun (2009).
Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state.
  J Bacteriol, 191, 1211-1219.
PDB codes: 3e5j 3e5k 3e5l
19104915 M.K.Leong, Y.M.Chen, H.B.Chen, and P.H.Chen (2009).
Development of a New Predictive Model for Interactions with Human Cytochrome P450 2A6 Using Pharmacophore Ensemble/Support Vector Machine (PhE/SVM) Approach.
  Pharm Res, 26, 987.  
19397311 S.C.Gay, L.Sun, K.Maekawa, J.R.Halpert, and C.D.Stout (2009).
Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.
  Biochemistry, 48, 4762-4771.
PDB codes: 3g5n 3g93
19053752 C.C.Peng, J.L.Cape, T.Rushmore, G.J.Crouch, and J.P.Jones (2008).
Cytochrome P450 2C9 type II binding studies on quinoline-4-carboxamide analogues.
  J Med Chem, 51, 8000-8011.  
18622598 E.M.Isin, and F.P.Guengerich (2008).
Substrate binding to cytochromes P450.
  Anal Bioanal Chem, 392, 1019-1030.  
18478283 J.E.Mendieta-Wejebe, M.C.Rosales-Hernández, H.Rios, J.Trujillo-Ferrara, G.López-Pérez, F.Tamay-Cach, R.Ramos-Morales, and J.Correa-Basurto (2008).
Comparing the electronic properties and docking calculations of heme derivatives on CYP2B4.
  J Mol Model, 14, 537-545.  
18976212 K.N.Myasoedova (2008).
New findings in studies of cytochromes P450.
  Biochemistry (Mosc), 73, 965-969.  
18453684 M.A.White, N.Mast, I.Bjorkhem, E.F.Johnson, C.D.Stout, and I.A.Pikuleva (2008).
Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1.
  Acta Crystallogr D Biol Crystallogr, 64, 487-495.  
18495666 N.Oezguen, S.Kumar, A.Hindupur, W.Braun, B.K.Muralidhara, and J.R.Halpert (2008).
Identification and analysis of conserved sequence motifs in cytochrome P450 family 2. Functional and structural role of a motif 187RFDYKD192 in CYP2B enzymes.
  J Biol Chem, 283, 21808-21816.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
18537573 S.Ekins, M.Iyer, M.D.Krasowski, and E.D.Kharasch (2008).
Molecular characterization of CYP2B6 substrates.
  Curr Drug Metab, 9, 363-373.  
18729327 U.M.Kent, C.Sridar, G.Spahlinger, and P.F.Hollenberg (2008).
Modification of serine 360 by a reactive intermediate of 17-alpha-ethynylestradiol results in mechanism-based inactivation of cytochrome P450s 2B1 and 2B6.
  Chem Res Toxicol, 21, 1956-1963.  
18366166 Y.Ding, W.H.Seufert, Z.Q.Beck, and D.H.Sherman (2008).
Analysis of the cryptophycin P450 epoxidase reveals substrate tolerance and cooperativity.
  J Am Chem Soc, 130, 5492-5498.  
17207766 A.J.Annalora, E.Bobrovnikov-Marjon, R.Serda, A.Pastuszyn, S.E.Graham, C.B.Marcus, and J.L.Omdahl (2007).
Hybrid homology modeling and mutational analysis of cytochrome P450C24A1 (CYP24A1) of the Vitamin D pathway: insights into substrate specificity and membrane bound structure-function.
  Arch Biochem Biophys, 460, 262-273.  
17534532 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, 585-609.  
17555301 D.R.Davydov, B.J.Baas, S.G.Sligar, and J.R.Halpert (2007).
Allosteric mechanisms in cytochrome P450 3A4 studied by high-pressure spectroscopy: pivotal role of substrate-induced changes in the accessibility and degree of hydration of the heme pocket.
  Biochemistry, 46, 7852-7864.  
17585868 G.I.Lepesheva, M.Seliskar, C.G.Knutson, N.V.Stourman, D.Rozman, and M.R.Waterman (2007).
Conformational dynamics in the F/G segment of CYP51 from Mycobacterium tuberculosis monitored by FRET.
  Arch Biochem Biophys, 464, 221-227.  
17274942 H.Fernando, D.R.Davydov, C.C.Chin, and J.R.Halpert (2007).
Role of subunit interactions in P450 oligomers in the loss of homotropic cooperativity in the cytochrome P450 3A4 mutant L211F/D214E/F304W.
  Arch Biochem Biophys, 460, 129-140.  
17254539 L.Sun, C.S.Chen, D.J.Waxman, H.Liu, J.R.Halpert, and S.Kumar (2007).
Re-engineering cytochrome P450 2B11dH for enhanced metabolism of several substrates including the anti-cancer prodrugs cyclophosphamide and ifosfamide.
  Arch Biochem Biophys, 458, 167-174.  
17705402 P.Lafite, F.André, D.C.Zeldin, P.M.Dansette, and D.Mansuy (2007).
Unusual regioselectivity and active site topology of human cytochrome P450 2J2.
  Biochemistry, 46, 10237-10247.  
17198380 T.N.Tsalkova, N.Y.Davydova, J.R.Halpert, and D.R.Davydov (2007).
Mechanism of interactions of alpha-naphthoflavone with cytochrome P450 3A4 explored with an engineered enzyme bearing a fluorescent probe.
  Biochemistry, 46, 106-119.  
18077893 V.O.Popov, R.A.Zvyagilskaya, and A.N.Bach (2007).
A.N.Bach--a revolutionary in politics and science. Commemorating 150th anniversary of academician A.N. Bach.
  Biochemistry (Mosc), 72, 1029-1038.  
17887776 Y.Zhao, L.Sun, B.K.Muralidhara, S.Kumar, M.A.White, C.D.Stout, and J.R.Halpert (2007).
Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
  Biochemistry, 46, 11559-11567.
PDB code: 2q6n
17027909 C.E.Hernandez, S.Kumar, H.Liu, and J.R.Halpert (2006).
Investigation of the role of cytochrome P450 2B4 active site residues in substrate metabolism based on crystal structures of the ligand-bound enzyme.
  Arch Biochem Biophys, 455, 61-67.  
16954191 M.Ekroos, and T.Sjögren (2006).
Structural basis for ligand promiscuity in cytochrome P450 3A4.
  Proc Natl Acad Sci U S A, 103, 13682-13687.
PDB codes: 2j0c 2j0d 2v0m
16793528 M.J.de Groot (2006).
Designing better drugs: predicting cytochrome P450 metabolism.
  Drug Discov Today, 11, 601-606.  
16859405 W.M.Atkins (2006).
Current views on the fundamental mechanisms of cytochrome P450 allosterism.
  Expert Opin Drug Metab Toxicol, 2, 573-579.  
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.