9YVV | pdb_00009yvv

Cocrystallized structure of Bmp7 in complex with 2,4-dibromophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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Literature

Bacterial cytochrome P450 for oxidative halogenated biaryl coupling.

Petriti, V.Nolan, K.Xu, W.Tsai, S.Wang, X.Xie, W.J.Zheng, G.Wang, Y.Ding, Y.

(2026) ACS Catal 16: 2615-2627

  • DOI: https://doi.org/10.1021/acscatal.5c08060
  • Primary Citation Related Structures: 
    9MS3, 9YV5, 9YVV

  • PubMed Abstract: 

    Biaryl motifs are fundamental structural elements in many pharmaceuticals, agrochemicals, and advanced materials. Traditional synthetic approaches for biaryl bond formation often require harsh conditions, costly catalysts, and pre-functionalized starting materials, which limit their efficiency, sustainability, and substrate scope. Enzymatic catalysis offers a greener alternative. However, biocatalysts capable of directly coupling halogenated biaryl compounds remain largely underexplored. Here, we report the functional characterization of the marine-derived cytochrome P450 enzyme Bmp7, which catalyzes the formation of halogenated biaryls. We first characterized the product profile of recombinant Bmp7 using its native substrate 2,4-dibromophenol ( 1 ) and confirmed the dominant ortho - ortho C-C homocoupled product as MC21-A. Screening a halogenated aromatic substrate library revealed that Bmp7 binds and catalyzes the coupling of 17 halogenated phenols, as evidenced by spectral shift assays, LC-HRMS, HRMS/MS and GC-MS analyses. Two homocoupled products were structurally confirmed by NMR analysis to possess ortho-ortho C-C linkages. In addition to efficient homocoupling, Bmp7 catalyzed heterocoupling reactions between substrate 1 and 16 other substrates, producing mixtures of homocoupled and heterocoupled halogenated biphenols. X-ray crystallography revealed the binding of two substrate 1 molecules within the active site, while DFT calculations supported a single-radical reaction mechanism, shedding light on the mechanistic basis of the coupling reaction. Together, these findings lay the groundwork for these findings establish a foundation for future efforts in enzyme engineering and the development of biocatalytic strategies for synthetic applications.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610 USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polybrominated aromatic compounds synthase495Marinomonas mediterraneaMutation(s): 0 
Gene Names: bmp7Marme_4095
EC: 1.14.19
UniProt
Find proteins for F2K081 (Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1))
Explore F2K081 
Go to UniProtKB:  F2K081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2K081
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Y8I (Subject of Investigation/LOI)
Query on Y8I

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
2,4-bis(bromanyl)phenol
C6 H4 Br2 O
FAXWFCTVSHEODL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.22α = 90
b = 101.22β = 90
c = 159.924γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM147510
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128742

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Database references