PDBsum entry 1zo9

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
458 a.a. *
HEM ×2
EPM ×2
GOL ×14
MES ×2
Waters ×1072
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the wild type heme domain of p450bm-3 w palmitoylmethionine
Structure: Bifunctional p-450:nadph-p450 reductase. Chain: a, b. Fragment: cytochrome p450. Engineered: yes
Source: Bacillus megaterium. Organism_taxid: 1404. Gene: cyp102a1, cyp102. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.70Å     R-factor:   0.164     R-free:   0.199
Authors: A.Hegda,B.Chen,D.R.Tomchick,M.Bondlela,D.C.Haines,N.Schaffer M.Machius,S.E.Graham,J.A.Peterson
Key ref: A.Hegde et al. (2007). Interactions of substrates at the surface of P450s can greatly enhance substrate potency. Biochemistry, 46, 14010-14017. PubMed id: 18004886 DOI: 10.1021/bi701667m
12-May-05     Release date:   01-Aug-06    
Go to PROCHECK summary

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

 Enzyme reactions 
   Enzyme class 2: E.C.  - Unspecific monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RH + reduced flavoprotein + O2 = ROH + oxidized flavoprotein + H2O
+ reduced flavoprotein
+ O(2)
+ oxidized flavoprotein
+ H(2)O
      Cofactor: Heme-thiolate
   Enzyme class 3: E.C.  - NADPH--hemoprotein reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + n oxidized hemoprotein = NADP+ + n reduced hemoprotein
+ n oxidized hemoprotein
= NADP(+)
+ n reduced hemoprotein
      Cofactor: 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  


DOI no: 10.1021/bi701667m Biochemistry 46:14010-14017 (2007)
PubMed id: 18004886  
Interactions of substrates at the surface of P450s can greatly enhance substrate potency.
A.Hegde, D.C.Haines, M.Bondlela, B.Chen, N.Schaffer, D.R.Tomchick, M.Machius, H.Nguyen, P.K.Chowdhary, L.Stewart, C.Lopez, J.A.Peterson.
Cytochrome P450s are a superfamily of heme containing enzymes that use molecular oxygen and electrons from reduced nicotinamide cofactors to monooxygenate organic substrates. The fatty acid hydroxylase P450BM-3 has been particularly widely studied due to its stability, high activity, similarity to mammalian P450s, and presence of a cytochrome P450 reductase domain that allows the enzyme to directly receive electrons from NADPH without a requirement for additional redox proteins. We previously characterized the substrate N-palmitoylglycine, which found extensive use in studies of P450BM-3 due to its high affinity, high turnover number, and increased solubility as compared to fatty acid substrates. Here, we report that even higher affinity substrates can be designed by acylation of other amino acids, resulting in P450BM-3 substrates with dissociation constants below 100 nM. N-Palmitoyl-l-leucine and N-palmitoyl-l-methionine were found to have the highest affinity, with dissociation constants of less than 8 nM and turnover numbers similar to palmitic acid and N-palmitoylglycine. The interactions of the amino acid side chains with a hydrophobic pocket near R47, as revealed by our crystal structure determination of N-palmitoyl-l-methionine bound to the heme domain of P450BM-3, appears to be responsible for increasing the affinity of substrates. The side chain of R47, previously shown to be important in interactions with negatively charged substrates, does not interact strongly with N-palmitoyl-l-methionine and is found positioned at the enzyme-solvent interface. These are the tightest binding substrates for P450BM-3 reported to date, and the affinity likely approaches the maximum attainable affinity for the binding of substrates of this size to P450BM-3.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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