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PDBsum entry 2bmh

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protein ligands Protein-protein interface(s) links
Oxidoreductase(oxygenase) PDB id
2bmh
Jmol
Contents
Protein chains
455 a.a. *
Ligands
HEM ×2
Waters ×390
* Residue conservation analysis
PDB id:
2bmh
Name: Oxidoreductase(oxygenase)
Title: Modeling protein-substrate interactions in the heme domain of cytochrome p450bm-3
Structure: Cytochrome p450 bm-3. Chain: a, b. Engineered: yes
Source: Bacillus megaterium. Organism_taxid: 1404
Resolution:
2.00Å     R-factor:   0.184    
Authors: H.Li,T.L.Poulos
Key ref:
H.Li and T.L.Poulos (1995). Modeling protein-substrate interactions in the heme domain of cytochrome P450(BM-3). Acta Crystallogr D Biol Crystallogr, 51, 21-32. PubMed id: 15299332 DOI: 10.1107/S0907444994009194
Date:
17-May-94     Release date:   31-Jul-94    
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.
455 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: 10.1107/S0907444994009194 Acta Crystallogr D Biol Crystallogr 51:21-32 (1995)
PubMed id: 15299332  
 
 
Modeling protein-substrate interactions in the heme domain of cytochrome P450(BM-3).
H.Li, T.L.Poulos.
 
  ABSTRACT  
 
The crystal structure of heme domain of the fatty acid monooxygenase, cytochrome P450(BM-3), consisting of residues 1-455 has been independently solved to R = 0.18 at 2.0 A. The crystal form used, space group P2(1) with two molecules per asymmetric unit, is isomorphous with that form with residues 1-471 first described by Boddupalli et al. [Boddupalli, Hasemann, Ravinchandran, Lu, Goldsmith, Deisenhofer & Peterson (1992). Proc. Natl Acad. Sci. USA, 89, 5567-5571] and used by Ravichandran, Boddupalli, Hasemann, Peterson & Deisenhofer [(1993). Science, 261, 731-736] to determine the crystal structure. The substrate-access channel consists of a large, hydrophobic cleft that appears to be the most likely route taken by fatty acid substrates. Attempts to soak crystals in mother liquor containing a variety of fatty acid substrates yielded featureless difference Fouriers even though fatty acid substrates are known to bind with dissociation constants in the micro M range. Modeling substrate-enzyme interactions reveals few contacts between the enzyme and substrate. More detailed modeling was carried out by subjecting both molecules in the asymmetric unit to extensive energy minimization. These studies reveal that the heme-domain active-site cleft can undergo a large conformational change that closes the access channel thereby providing enhanced protein-substrate interactions. These conformational changes are prevented from occurring by intermolecular contacts in the crystal lattice which lock the protein in the 'open' conformation.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Space-filled diagrams of (a) P450cam and (b) molecule B of P450BM_3, viewed along their respective substrate-access channels. The heme groups are shaded. Although this is a comparison between substrate- bound (P450cam) and substrate- free (P450BM.3) enzymes, there is no significant change in struc- ture of the substrate-free form of P450~m (Poulos, Finzel & Howard, 1986). Panel (c) shows the same region of P450BM. 3 (molecule B) after the energy minimization. The heme is deeply buried due to the 'closing down' of the substrate-access channel.
Figure 5.
Fig. 5. The 2Fo - Fc omit maps (contoured at ltr) calculated with X-PLOR by running 100 cycles of positional refinement with the appropriate residues excluded. (a)/3-turn and 3~o helix region with residues 9-23 omitted. (b)/3-l pair with residues 40-50 omitted. (c) C-terminal portion of F helix and the F/G loop region with residues 180-200 omitted. (d) F/G loop and N-terminal portion of G helix with residues 190-214 omitted.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 21-32) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21156025 I.N.Van Bogaert, S.Groeneboer, K.Saerens, and W.Soetaert (2011).
The role of cytochrome P450 monooxygenases in microbial fatty acid metabolism.
  FEBS J, 278, 206-221.  
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
20947800 M.E.Ener, Y.T.Lee, J.R.Winkler, H.B.Gray, and L.Cheruzel (2010).
Photooxidation of cytochrome P450-BM3.
  Proc Natl Acad Sci U S A, 107, 18783-18786.  
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.  
19625248 C.Savino, L.C.Montemiglio, G.Sciara, A.E.Miele, S.G.Kendrew, P.Jemth, S.Gianni, and B.Vallone (2009).
Investigating the structural plasticity of a cytochrome P450: three-dimensional structures of P450 EryK and binding to its physiological substrate.
  J Biol Chem, 284, 29170-29179.
PDB codes: 2jjn 2jjo 2wio
19265398 S.Balaz (2009).
Modeling kinetics of subcellular disposition of chemicals.
  Chem Rev, 109, 1793-1899.  
17964298 B.L.Hilker, H.Fukushige, C.Hou, and D.Hildebrand (2008).
Comparison of Bacillus monooxygenase genes for unique fatty acid production.
  Prog Lipid Res, 47, 1.  
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.  
16163453 E.Hazai, Z.Bikádi, M.Simonyi, and D.Kupfer (2005).
Association of cytochrome P450 enzymes is a determining factor in their catalytic activity.
  J Comput Aided Mol Des, 19, 271-285.  
15617063 J.Mestres (2005).
Structure conservation in cytochromes P450.
  Proteins, 58, 596-609.  
15664991 T.D.Pfister, T.Ohki, T.Ueno, I.Hara, S.Adachi, Y.Makino, N.Ueyama, Y.Lu, and Y.Watanabe (2005).
Monooxygenation of an aromatic ring by F43W/H64D/V68I myoglobin mutant and hydrogen peroxide. Myoglobin mutants as a model for P450 hydroxylation chemistry.
  J Biol Chem, 280, 12858-12866.  
15256703 T.Tanaka, T.Okuda, and Y.Yamamoto (2004).
Characterization of the CYP3A4 active site by homology modeling.
  Chem Pharm Bull (Tokyo), 52, 830-835.  
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
10051560 I.F.Sevrioukova, H.Li, H.Zhang, J.A.Peterson, and T.L.Poulos (1999).
Structure of a cytochrome P450-redox partner electron-transfer complex.
  Proc Natl Acad Sci U S A, 96, 1863-1868.
PDB codes: 1bu7 1bvy
10593892 I.F.Sevrioukova, J.T.Hazzard, G.Tollin, and T.L.Poulos (1999).
The FMN to heme electron transfer in cytochrome P450BM-3. Effect of chemical modification of cysteines engineered at the FMN-heme domain interaction site.
  J Biol Chem, 274, 36097-36106.  
10584064 V.A.Payne, Y.T.Chang, and G.H.Loew (1999).
Homology modeling and substrate binding study of human CYP2C9 enzyme.
  Proteins, 37, 176-190.  
10584066 V.A.Payne, Y.T.Chang, and G.H.Loew (1999).
Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes.
  Proteins, 37, 204-217.  
10024026 Y.T.Chang, and G.H.Loew (1999).
Homology modeling and substrate binding study of human CYP4A11 enzyme.
  Proteins, 34, 403-415.  
9738009 S.Vasudevan, T.Tsuruo, and D.R.Rose (1998).
Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
  J Biol Chem, 273, 25413-25419.
PDB code: 1bln
9533688 W.Jentzen, J.G.Ma, and J.A.Shelnutt (1998).
Conservation of the conformation of the porphyrin macrocycle in hemoproteins.
  Biophys J, 74, 753-763.  
9065459 S.Govindaraj, and T.L.Poulos (1997).
The domain architecture of cytochrome P450BM-3.
  J Biol Chem, 272, 7915-7921.  
8995391 S.K.Grant, B.G.Green, R.Wang, S.G.Pacholok, and J.W.Kozarich (1997).
Characterization of inducible nitric-oxide synthase by cytochrome P-450 substrates and inhibitors. Inhibition by chlorzoxazone.
  J Biol Chem, 272, 977-983.  
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.  
8673608 J.R.Cupp-Vickery, O.Han, C.R.Hutchinson, and T.L.Poulos (1996).
Substrate-assisted catalysis in cytochrome P450eryF.
  Nat Struct Biol, 3, 632-637.  
8612066 T.L.Poulos (1996).
Ligands and electrons and haem proteins.
  Nat Struct Biol, 3, 401-403.  
8747463 M.Sundaramoorthy, J.Terner, and T.L.Poulos (1995).
The crystal structure of chloroperoxidase: a heme peroxidase--cytochrome P450 functional hybrid.
  Structure, 3, 1367-1377.
PDB codes: 1cpo 2cpo
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.