9DTH | pdb_00009dth

Tyr-His linked F33Y CuBMb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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Literature

A Post-translational Histidine-Histidine Cross-Link Enhances Enzymatic Oxygen Reduction Activity with Greater pH Adaptability.

Liu, Y.Vilbert, A.C.Ghosh, B.Young, R.P.Merkley, E.D.Mukherjee, A.Phan, L.Van Stappen, C.Baghi-Damodaran, A.Miner, K.D.Adkins, J.Cort, J.Lu, Y.

(2025) J Am Chem Soc 147: 37688-37700

  • DOI: https://doi.org/10.1021/jacs.5c12710
  • Primary Citation of Related Structures:  
    9DTH, 9DTI

  • PubMed Abstract: 

    Cross-linked protein residues exist as enzyme cofactors to enable or enhance catalytic activities. Despite their importance in nature, the chemical identity of the cross-links is limited to certain amino acid combinations, whose function and the formation mechanism remain insufficiently understood due to the difficulty in isolating native enzymes without the cross-links. Herein, we report the formation and characterization of both His-Tyr and His-His cross-links under oxidative enzymatic turnover conditions in L29H/F33Y/F43H Mb, a structural and functional model of heme-copper oxidase (HCO). The connectivity of the cross-link was characterized as N ε2 (His29)-C δ2 (His43) by mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR). Interestingly, formation of the cross-link significantly enhances the oxygen reduction activity of the enzyme at neutral or basic pH with higher product specificity. X-ray crystallography has identified a novel Tyr-His cross-link through a Tyr-O-His linkage. Our mechanistic studies indicate the involvement of high-valent heme-iron and the neighboring tyrosine in an oxidative self-processing pathway to generate the cross-link. This work serves as a new example while providing insights into the enzyme cross-link formation, allowing the design of artificial biocatalysts containing these novel cross-links with higher activity and pH adaptability.


  • Organizational Affiliation
    • Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 0 
Gene Names: MB
EC: 1.7 (PDB Primary Data), 1.11.1 (PDB Primary Data)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.886α = 90
b = 31.407β = 102.54
c = 70.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-15 
  • Deposition Author(s): Lu, Y., Liu, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141931

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references