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 9YTV | pdb_00009ytv

Cocrystal structure of P450BLT in complex with NleRYLH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.209 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Spectroscopic characterization and co-crystal structure of P450 Blt reveal the molecular basis for biarylitide formation.

Campbell, J., Li, B., Rutan, D., Nolan, K., Wang, Y.

(2026) J Inorg Biochem 286: 113465-113465

  • DOI: https://doi.org/10.1016/j.jinorgbio.2026.113465
  • Primary Citation Related Structures: 
    9YTV

  • PubMed Abstract: 

    P450 Blt is a cytochrome P450 enzyme (CYP) that forms crosslinked biarylitides by installing an intramolecular aromatic CN bond on a ribosomally synthesized pentapeptide. Closely related CYPs, such as the nitrating enzyme RufO, exhibit distinct catalytic selectivity on the same peptide scaffold. Although both P450 Blt and RufO have been characterized, direct mechanistic comparison has been limited by the lack of spectroscopic studies of P450 Blt and differences in their crystallization methods. Here, we performed spectroscopic and structural characterization of P450 Blt to establish a framework for understanding this emerging family of pentapeptide-modifying CYPs. P450 Blt efficiently catalyzed Tyr-3 and His-5 coupling of its peptide substrate using heterologous ferredoxin-dependent redox systems and remained active through the peroxide shunt pathway. Spectroscopies showed that peptide binding minimally perturbs the heme structure, closely resembling RufO. Transient kinetics identified a ferric superoxo intermediate that formed more slowly than in RufO and was markedly stabilized in the presence of the peptide. A 1.81 Å co-crystal structure of the binary complex complements the previously reported peptide-soaked structure by capturing a more catalytically relevant substrate-bound state, revealing a low-spin heme center, peptide side-chain movements, and peptide-induced active site rearrangements. Comparison with the co-crystal structure of RufO demonstrates that substrate recognition and the Tyr-3 binding site are highly conserved, whereas the positioning of His-5 and its associated hydrogen-bonding network remain the principal structural differences between the two enzymes. These findings suggest that subtle active site differences modulate substrate positioning, oxygen activation, and likely proton transfer for selective catalysis.


  • Organizational Affiliation: 
    • Department of Chemistry, University of Georgia, Athens, GA 30602, United States of America.

Macromolecule Content 

  • Total Structure Weight: 44.64 kDa 
  • Atom Count: 3,413 
  • Modeled Residue Count: 392 
  • Deposited Residue Count: 406 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P450BLT401Micromonospora sp. MW-13Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NLE-ARG-TYR-LEU-HIS5synthetic constructMutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
NLE
Query on NLE
LEUNorleucineC6 H13 N O2

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.209 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.722α = 90
b = 55.874β = 118.81
c = 85.385γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

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

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-21
    Type: Initial release