4KPA

Crystal structure of cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Evidence: A Single Charged Residue Affects Substrate Binding in Cytochrome P450 BM-3.

Catalano, J.Sadre-Bazzaz, K.Amodeo, G.A.Tong, L.McDermott, A.

(2013) Biochemistry 52: 6807-6815

  • DOI: 10.1021/bi4000645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P4 ...

    Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPG's low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA , represents an initial binding step in the P450 cycle.


    Organizational Affiliation

    Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 BM-3
A
494Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)Mutation(s): 0 
Gene Names: cyp102A1 (cyp102)
Find proteins for P14779 (Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512))
Go to UniProtKB:  P14779
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
140
Query on 140

Download SDF File 
Download CCD File 
A
N-PALMITOYLGLYCINE
N-HEXADECANOYLGLYCINE
C18 H35 N O3
KVTFEOAKFFQCCX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
140Kd: 4 - 297 nM (99) BINDINGDB
140Kd: 370 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 188.700α = 90.00
b = 59.320β = 90.00
c = 56.240γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
COMOphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description