4UBS

The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


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Literature

Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.

Xu, L.H.Ikeda, H.Liu, L.Arakawa, T.Wakagi, T.Shoun, H.Fushinobu, S.

(2015) Appl.Microbiol.Biotechnol. 99: 3081-3091

  • DOI: 10.1007/s00253-014-6148-y

  • PubMed Abstract: 
  • Diclofenac is a nonsteroidal anti-inflammatory drug. It undergoes hydroxylation by mammalian cytochrome P450 enzymes at 4'- and/or 5'-positions. A bacterial P450 enzyme, CYP105D7 from Streptomyces avermitilis, has been shown to catalyze hydroxylation ...

    Diclofenac is a nonsteroidal anti-inflammatory drug. It undergoes hydroxylation by mammalian cytochrome P450 enzymes at 4'- and/or 5'-positions. A bacterial P450 enzyme, CYP105D7 from Streptomyces avermitilis, has been shown to catalyze hydroxylation of 1-deoxypentalenic acid and an isoflavone daidzein. Here, we demonstrated that CYP105D7 also catalyzes hydroxylation of diclofenac at the C4'-position. A spectroscopic analysis showed that CYP105D7 binds diclofenac in a slightly cooperative manner with an affinity of 65 μM and a Hill coefficient of 1.16. The crystal structure of CYP105D7 in complex with diclofenac was determined at 2.2 Å resolution. The distal pocket of CYP105D7 contains two diclofenac molecules, illustrating drug recognition with a double-ligand-binding mode. The C3' and C4' atoms of the dichlorophenyl ring of one diclofenac molecule are positioned near the heme iron, suggesting that it is positioned appropriately for aromatic hydroxylation to yield the 4'-hydroxylated product. However, recognition of diclofenac by CYP105D7 was completely different from that of rabbit CYP2C5, which binds one diclofenac molecule with a cluster of water molecules. The distal pocket of CYP105D7 contains four arginine residues, forming a wall of the substrate-binding pocket, and the arginine residues are conserved in bacterial P450s in the CYP105 family.


    Organizational Affiliation

    Ocean College, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China, lianhuaxu@zju.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pentalenic acid synthase
A
393Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)Mutation(s): 0 
Gene Names: cyp28 (cyp105d7)
EC: 1.14.15.11
Find proteins for Q825I8 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Go to UniProtKB:  Q825I8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DIF
Query on DIF

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A
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
DICLOFENAC
C14 H11 Cl2 N O2
DCOPUUMXTXDBNB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DIFKd: 65000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.897α = 90.00
b = 139.897β = 90.00
c = 65.268γ = 120.00
Software Package:
Software NamePurpose
HKLdata reduction
MOLREPmodel building
ADSCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the fundamental research funds for the central universitiesChina2013QNA4042

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references