9BW8

Structure of P450Blt from Micromonospora sp. MW-13 in Complex with Fluorinated Biarylitide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Loss of fluorine during crosslinking by the biarylitide P450 Blt proceeds due to restricted peptide orientation.

Zhao, Y.Gullick, J.Hansen, M.H.Coe, L.Treisman, M.Schittenhelm, R.B.McKay, A.Murray, L.A.M.Tailhades, J.De Voss, J.J.Krenske, E.H.Cryle, M.J.

(2024) Chem Commun (Camb) 60: 13951-13954

  • DOI: https://doi.org/10.1039/d4cc04092a
  • Primary Citation of Related Structures:  
    9BW8

  • PubMed Abstract: 

    The biarylitide crosslinking enzyme P450 Blt can perform crosslinking between m -F-Tyr-3 and His-5 residues within peptide substrates with concomitant and specific loss of fluorine. Our investigations suggest that a small intrinsic preference for coupling ipso to fluorine is magnified by the binding of the peptide in a specific orientation that enforces the loss of fluorine during peptide crosslinking, likely via a two-step reaction mechanism involving the non-enzyme catalysed reductive elimination of fluoride.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. max.cryle@monash.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450-SU1
A, B, C
420Micromonospora sp. MW-13Mutation(s): 0 
Gene Names: C5N14_21030
EC: 1.14
UniProt
Find proteins for A0A3E2YLT4 (Micromonospora sp. MW-13)
Explore A0A3E2YLT4 
Go to UniProtKB:  A0A3E2YLT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3E2YLT4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fluorinated BiarylitideD [auth E]5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
M [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
TFA
Query on TFA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
L [auth C]
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YOF
Query on YOF
D [auth E]L-PEPTIDE LINKINGC9 H10 F N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.915α = 90
b = 94.152β = 91.77
c = 105.003γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP190101272
Australian Research Council (ARC)AustraliaDP210101752

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references