spacer
spacer

PDBsum entry 1jpz

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1jpz
Jmol
Contents
Protein chains
456 a.a. *
Ligands
HEM ×2
140 ×2
Waters ×955
* Residue conservation analysis
PDB id:
1jpz
Name: Oxidoreductase
Title: Crystal structure of a complex of the heme domain of p450bm- 3 with n-palmitoylglycine
Structure: Bifunctional p-450:nadph-p450 reductase. Chain: a, b. Fragment: cytochrome p450 102 domain. Synonym: p450bm-3. Cytochrome p450(bm-3) [includes: cytochrome p450 102, NADPH-cytochrome p450 reductase. Cytochrome p450 bm-3/NADPH--ferrihemoprotein reductase. Cytochrome p-450:nadph-p-450 reductase. Engineered: yes
Source: Bacillus megaterium. Organism_taxid: 1404. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.65Å     R-factor:   0.177     R-free:   0.193
Authors: D.C.Haines,D.R.Tomchick,M.Machius,J.A.Peterson
Key ref:
D.C.Haines et al. (2001). Pivotal role of water in the mechanism of P450BM-3. Biochemistry, 40, 13456-13465. PubMed id: 11695892 DOI: 10.1021/bi011197q
Date:
03-Aug-01     Release date:   09-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14779  (CPXB_BACME) -  Bifunctional P-450/NADPH-P450 reductase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1049 a.a.
456 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: 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
   Enzyme class 3: E.C.1.6.2.4  - NADPH--hemoprotein reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + n oxidized hemoprotein = NADP+ + n reduced hemoprotein
NADPH
+ n oxidized hemoprotein
= NADP(+)
+ n reduced hemoprotein
      Cofactor: FAD; FMN
FAD
FMN
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi011197q Biochemistry 40:13456-13465 (2001)
PubMed id: 11695892  
 
 
Pivotal role of water in the mechanism of P450BM-3.
D.C.Haines, D.R.Tomchick, M.Machius, J.A.Peterson.
 
  ABSTRACT  
 
Cytochrome P450s constitute a superfamily of enzymes that catalyze the oxidation of a vast number of structurally and chemically diverse hydrophobic substrates. Herein, we describe the crystal structure of a complex between the bacterial P450BM-3 and the novel substrate N-palmitoylglycine at a resolution of 1.65 A, which reveals previously unrecognizable features of active site reorganization upon substrate binding. N-palmitoylglycine binds with higher affinity than any other known substrate and reacts with a higher turnover number than palmitic acid but with unaltered regiospecificity along the fatty acid moiety. Substrate binding induces conformational changes in distinct regions of the enzyme including part of the I-helix adjacent to the active site. These changes cause the displacement by about 1 A of the pivotal water molecule that ligands the heme iron, resulting in the low-spin to high-spin conversion of the iron. The water molecule is trapped close to the heme group, which allows it to partition between the iron and the new binding site. This partitioning explains the existence of a high-spin-low-spin equilibrium after substrate binding. The close proximity of the water molecule to the heme iron indicates that it may also participate in the proton-transfer cascade that leads to heterolytic bond scission of oxygen in P450BM-3.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21395496 D.R.Davydov (2011).
Microsomal monooxygenase as a multienzyme system: the role of P450-P450 interactions.
  Expert Opin Drug Metab Toxicol, 7, 543-558.  
21400620 L.L.Wu, C.L.Yang, F.C.Lo, C.H.Chiang, C.W.Chang, K.Y.Ng, H.H.Chou, H.Y.Hung, S.I.Chan, and S.S.Yu (2011).
Tuning the Regio- and Stereoselectivity of CH Activation in n-Octanes by Cytochrome P450 BM-3 with Fluorine Substituents: Evidence for Interactions Between a CF Bond and Aromatic π Systems.
  Chemistry, 17, 4774-4787.  
21243168 M.J.Cryle (2011).
Carrier protein substrates in cytochrome P450-catalysed oxidation.
  Metallomics, 3, 323-326.  
21303163 T.R.Guizado, S.R.Louro, and C.Anteneodo (2011).
Hydration of hydrophobic biological porphyrins.
  J Chem Phys, 134, 055103.  
21240430 W.C.Huang, P.M.Cullis, E.L.Raven, and G.C.Roberts (2011).
Control of the stereo-selectivity of styrene epoxidation by cytochrome P450 BM3 using structure-based mutagenesis.
  Metallomics, 3, 410-416.  
21110374 C.J.Whitehouse, W.Yang, J.A.Yorke, B.C.Rowlatt, A.J.Strong, C.F.Blanford, S.G.Bell, M.Bartlam, L.L.Wong, and Z.Rao (2010).
Structural basis for the properties of two single-site proline mutants of CYP102A1 (P450BM3).
  Chembiochem, 11, 2549-2556.
PDB code: 3m4v
20387782 D.Fishelovitch, S.Shaik, H.J.Wolfson, and R.Nussinov (2010).
How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?
  J Phys Chem B, 114, 5964-5970.  
20180779 H.M.Girvan, C.W.Levy, P.Williams, K.Fisher, M.R.Cheesman, S.E.Rigby, D.Leys, and A.W.Munro (2010).
Glutamate-haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3.
  Biochem J, 427, 455-466.
PDB codes: 3kx3 3kx4 3kx5
  21048857 I.Axarli, A.Prigipaki, and N.E.Labrou (2010).
Cytochrome P450 102A2 Catalyzes Efficient Oxidation of Sodium Dodecyl Sulphate: A Molecular Tool for Remediation.
  Enzyme Res, 2010, 125429.  
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.  
19492389 C.J.Whitehouse, S.G.Bell, W.Yang, J.A.Yorke, C.F.Blanford, A.J.Strong, E.J.Morse, M.Bartlam, Z.Rao, and L.L.Wong (2009).
A highly active single-mutation variant of P450BM3 (CYP102A1).
  Chembiochem, 10, 1654-1656.
PDB code: 3hf2
19865780 C.S.Porro, D.Kumar, and S.P.de Visser (2009).
Electronic properties of pentacoordinated heme complexes in cytochrome P450 enzymes: search for an Fe(i) oxidation state.
  Phys Chem Chem Phys, 11, 10219-10226.  
19728720 D.Fishelovitch, S.Shaik, H.J.Wolfson, and R.Nussinov (2009).
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism.
  J Phys Chem B, 113, 13018-13025.  
19526348 E.Bailo, L.Fruk, C.M.Niemeyer, and V.Deckert (2009).
Surface-enhanced Raman scattering as a tool to probe cytochrome P450-catalysed substrate oxidation.
  Anal Bioanal Chem, 394, 1797-1801.  
  19234632 E.Campos-Mollo, M.P.López-Garrido, C.Blanco-Marchite, J.Garcia-Feijoo, J.Peralta, J.Belmonte-Martínez, C.Ayuso, and J.Escribano (2009).
CYP1B1 mutations in Spanish patients with primary congenital glaucoma: phenotypic and functional variability.
  Mol Vis, 15, 417-431.  
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.  
20046929 L.Tian, and R.A.Friesner (2009).
QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism.
  J Chem Theory Comput, 5, 1421-1431.  
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
19347895 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, 5577-5587.  
18392864 C.K.Chen, T.K.h.Shokhireva, R.E.Berry, H.Zhang, and F.A.Walker (2008).
The effect of mutation of F87 on the properties of CYP102A1-CYP4C7 chimeras: altered regiospecificity and substrate selectivity.
  J Biol Inorg Chem, 13, 813-824.  
18831537 D.R.Davydov, N.Y.Davydova, and J.R.Halpert (2008).
Allosteric transitions in cytochrome P450eryF explored with pressure-perturbation spectroscopy, lifetime FRET, and a novel fluorescent substrate, Fluorol-7GA.
  Biochemistry, 47, 11348-11359.  
17957765 E.Stjernschantz, B.M.van Vugt-Lussenburg, A.Bonifacio, S.B.de Beer, G.van der Zwan, C.Gooijer, J.N.Commandeur, N.P.Vermeulen, and C.Oostenbrink (2008).
Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3.
  Proteins, 71, 336-352.  
18818197 K.J.McLean, P.Carroll, D.G.Lewis, A.J.Dunford, H.E.Seward, R.Neeli, M.R.Cheesman, L.Marsollier, P.Douglas, W.E.Smith, I.Rosenkrands, S.T.Cole, D.Leys, T.Parish, and A.W.Munro (2008).
Characterization of Active Site Structure in CYP121: A CYTOCHROME P450 ESSENTIAL FOR VIABILITY OF MYCOBACTERIUM TUBERCULOSIS H37Rv.
  J Biol Chem, 283, 33406-33416.
PDB code: 3cxv
18483737 M.Dietrich, S.Eiben, C.Asta, T.A.Do, J.Pleiss, and V.B.Urlacher (2008).
Cloning, expression and characterisation of CYP102A7, a self-sufficient P450 monooxygenase from Bacillus licheniformis.
  Appl Microbiol Biotechnol, 79, 931-940.  
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
18473391 R.J.Branco, A.Seifert, M.Budde, V.B.Urlacher, M.J.Ramos, and J.Pleiss (2008).
Anchoring effects in a wide binding pocket: the molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium.
  Proteins, 73, 597-607.  
18512058 T.Kitazume, Y.Yamazaki, S.Matsuyama, H.Shoun, and N.Takaya (2008).
Production of hydroxy-fatty acid derivatives from waste oil by Escherichia coli cells producing fungal cytochrome P450foxy.
  Appl Microbiol Biotechnol, 79, 981-988.  
17318599 A.Bonifacio, A.R.Groenhof, P.H.Keizers, C.de Graaf, J.N.Commandeur, N.P.Vermeulen, A.W.Ehlers, K.Lammertsma, C.Gooijer, and G.van der Zwan (2007).
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.
  J Biol Inorg Chem, 12, 645-654.  
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.  
17077084 H.M.Girvan, H.E.Seward, H.S.Toogood, M.R.Cheesman, D.Leys, and A.W.Munro (2007).
Structural and spectroscopic characterization of P450 BM3 mutants with unprecedented P450 heme iron ligand sets. New heme ligation states influence conformational equilibria in P450 BM3.
  J Biol Chem, 282, 564-572.
PDB codes: 2ij2 2ij3 2ij4
17279501 H.Yuki, Y.Tanaka, M.Hata, H.Ishikawa, S.Neya, and T.Hoshino (2007).
Implementation of pi-pi interactions in molecular dynamics simulation.
  J Comput Chem, 28, 1091-1099.  
17598905 J.D.Bloom, P.A.Romero, Z.Lu, and F.H.Arnold (2007).
Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution.
  Biol Direct, 2, 17.  
17322527 K.A.Feenstra, E.B.Starikov, V.B.Urlacher, J.N.Commandeur, and N.P.Vermeulen (2007).
Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.
  Protein Sci, 16, 420-431.  
18028029 K.J.McLean, H.M.Girvan, and A.W.Munro (2007).
Cytochrome P450/redox partner fusion enzymes: biotechnological and toxicological prospects.
  Expert Opin Drug Metab Toxicol, 3, 847-863.  
16439365 B.K.Muralidhara, S.Negi, C.C.Chin, W.Braun, and J.R.Halpert (2006).
Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling.
  J Biol Chem, 281, 8051-8061.  
16224788 C.R.Otey, G.Bandara, J.Lalonde, K.Takahashi, and F.H.Arnold (2006).
Preparation of human metabolites of propranolol using laboratory-evolved bacterial cytochromes P450.
  Biotechnol Bioeng, 93, 494-499.  
16594730 C.R.Otey, M.Landwehr, J.B.Endelman, K.Hiraga, J.D.Bloom, and F.H.Arnold (2006).
Structure-guided recombination creates an artificial family of cytochromes P450.
  PLoS Biol, 4, e112.  
16862534 D.Roccatano, T.S.Wong, U.Schwaneberg, and M.Zacharias (2006).
Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study.
  Biopolymers, 83, 467-476.  
16581913 J.D.Bloom, S.T.Labthavikul, C.R.Otey, and F.H.Arnold (2006).
Protein stability promotes evolvability.
  Proc Natl Acad Sci U S A, 103, 5869-5874.  
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.  
16240317 T.Kubo, M.W.Peters, P.Meinhold, and F.H.Arnold (2006).
Enantioselective epoxidation of terminal alkenes to (R)- and (S)-epoxides by engineered cytochromes P450 BM-3.
  Chemistry, 12, 1216-1220.  
16759725 V.B.Urlacher, and S.Eiben (2006).
Cytochrome P450 monooxygenases: perspectives for synthetic application.
  Trends Biotechnol, 24, 324-330.  
16028306 K.Schleinkofer, Sudarko, P.J.Winn, S.K.Lüdemann, and R.C.Wade (2005).
Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?
  EMBO Rep, 6, 584-589.  
16080215 P.Meinhold, M.W.Peters, M.M.Chen, K.Takahashi, and F.H.Arnold (2005).
Direct conversion of ethane to ethanol by engineered cytochrome P450 BM3.
  Chembiochem, 6, 1765-1768.  
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.  
15066989 D.Li, D.J.Stuehr, S.R.Yeh, and D.L.Rousseau (2004).
Heme distortion modulated by ligand-protein interactions in inducible nitric-oxide synthase.
  J Biol Chem, 279, 26489-26499.  
15100217 E.E.Scott, M.A.White, Y.A.He, E.F.Johnson, C.D.Stout, and J.R.Halpert (2004).
Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding.
  J Biol Chem, 279, 27294-27301.
PDB code: 1suo
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.  
15256616 P.A.Williams, J.Cosme, D.M.Vinkovic, A.Ward, H.C.Angove, P.J.Day, C.Vonrhein, I.J.Tickle, and H.Jhoti (2004).
Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone.
  Science, 305, 683-686.
PDB codes: 1w0e 1w0f 1w0g
12524265 A.Gorokhov, M.Negishi, E.F.Johnson, L.C.Pedersen, L.Perera, T.A.Darden, and L.G.Pedersen (2003).
Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4.
  Biophys J, 84, 57-68.  
12519760 D.S.Lee, A.Yamada, H.Sugimoto, I.Matsunaga, H.Ogura, K.Ichihara, S.Adachi, S.Y.Park, and Y.Shiro (2003).
Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies.
  J Biol Chem, 278, 9761-9767.
PDB code: 1izo
14529269 H.Zhang, L.Gruenke, D.Arscott, A.Shen, C.Kasper, D.L.Harris, M.Glavanovich, R.Johnson, and L.Waskell (2003).
Determination of the rate of reduction of oxyferrous cytochrome P450 2B4 by 5-deazariboflavin adenine dinucleotide T491V cytochrome P450 reductase.
  Biochemistry, 42, 11594-11603.  
12888556 O.Pylypenko, F.Vitali, K.Zerbe, J.A.Robinson, and I.Schlichting (2003).
Crystal structure of OxyC, a cytochrome P450 implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis.
  J Biol Chem, 278, 46727-46733.
PDB code: 1ued
12861225 P.A.Williams, J.Cosme, A.Ward, H.C.Angove, D.Matak Vinković, and H.Jhoti (2003).
Crystal structure of human cytochrome P450 2C9 with bound warfarin.
  Nature, 424, 464-468.
PDB codes: 1og2 1og5
14597705 T.L.Poulos (2003).
Cytochrome P450 flexibility.
  Proc Natl Acad Sci U S A, 100, 13121-13122.  
12207020 K.Zerbe, O.Pylypenko, F.Vitali, W.Zhang, S.Rouset, M.Heck, J.W.Vrijbloed, D.Bischoff, B.Bister, R.D.Süssmuth, S.Pelzer, W.Wohlleben, J.A.Robinson, and I.Schlichting (2002).
Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis.
  J Biol Chem, 277, 47476-47485.
PDB codes: 1lfk 1lg9 1lgf
12482514 V.Urlacher, and R.D.Schmid (2002).
Biotransformations using prokaryotic P450 monooxygenases.
  Curr Opin Biotechnol, 13, 557-564.  
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.