Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.81 kDa 
• Atom Count: 3,582 
• Modelled Residue Count: 393 
• Deposited Residue Count: 393 
• Unique protein chains: 1

 4UBS

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

• PDB DOI: 10.2210/pdb4UBS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces avermitilis MA-4680 = NBRC 14893
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-13 Released: 2014-11-05 
• Deposition Author(s): Xu, L.H., Ikeda, H., Arakawa, T., Wakagi, T., Shoun, H., Fushinobu, S.
• Funding Organization(s): the fundamental research funds for the central universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

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

• PubMed: 25341403 
• DOI: 10.1007/s00253-014-6148-y
• Primary Citation of Related Structures:  
  4UBS


• 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 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.

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Organizational Affiliation: 

Ocean College, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentalenic acid synthase	A	393	Streptomyces avermitilis MA-4680 = NBRC 14893	Mutation(s): 0  Gene Names: cyp105d7, cyp28, SAV_7469 EC: 1.14.15.11
UniProt
Find proteins for Q825I8 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q825I8  Go to UniProtKB:  Q825I8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DIF	C [auth A], D [auth A]	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID C14 H11 Cl2 N O2 DCOPUUMXTXDBNB-UHFFFAOYSA-N
PGE	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	X [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
DIF	Binding MOAD:  4UBS	Kd: 6.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.897	α = 90
b = 139.897	β = 90
c = 65.268	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	model building
HKL	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Xu, L.H., Ikeda, H., Arakawa, T., Wakagi, T., Shoun, H., Fushinobu, S.

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Funding Organization	Location	Grant Number
the fundamental research funds for the central universities	China	2013QNA4042

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2020-01-29
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy