9YTQ | pdb_00009ytq

Computationally Designed Tetramer of Apo-HC4 (C1 symmetry)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Computational Design of a Highly Stable Dicopper Catechol Oxidase.

Eng, V.H.Narehood, S.M.Li, Y.Gascon, M.Hoffnagle, A.M.Shiau, A.A.Semonis, M.Green, M.T.Britt, R.D.Tezcan, F.A.

(2026) J Am Chem Soc 148: 8361-8373

  • DOI: https://doi.org/10.1021/jacs.5c18979
  • Primary Citation Related Structures: 
    9YTQ

  • PubMed Abstract: 

    Type 3 (T3) Cu proteins play essential roles in binding and activating molecular oxygen (O 2 ) and are prevalent across all domains of life. Despite sharing the same coordination motif, T3 Cu proteins display divergent functions: hemocyanin transports O 2 , while tyrosinase catalyzes the hydroxylation of monophenols and the subsequent oxidation of diphenols and catechol oxidase oxidizes only diphenols. Here, we report the design and characterization of a di-Cu protein (Cu-HC4) inspired by the active sites of natural T3 Cu proteins to investigate the structural features that facilitate catalytic oxidase activity. Cu-HC4 is roughly 1/5th the size of the commercially available mushroom tyrosinase and shares only around 20% sequence identity with the T3 Cu protein templates. Notably, Cu-HC4 displays high thermostability and exhibits diphenol oxidation activity at ambient and elevated temperatures (≥60 °C). Cu-HC4 also initiates the formation of melanin polymers, mimicking melanin biosynthesis of natural tyrosinases. Mechanistic investigations demonstrate that Cu-HC4 utilizes both Cu centers cooperatively for diphenol oxidation and requires O 2 for catalysis like natural Cu oxidases but follows a distinct catalytic pathway compared to those enzymes. Cryo-EM characterization of a tetrameric form of HC4 reveals slight deviations in the relative positions of the active site His residues that may account for differences in reactivity between Cu-HC4 and natural T3 Cu enzymes.


  • Organizational Affiliation
    • Department of Chemistry, University of California, San Diego, La Jolla, California 92093, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed tetrameric HC4 protein.
A, B, C, D
138synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-2038238
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R24GM154186
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM138884

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Data collection, Database references
  • Version 1.2: 2026-03-18
    Changes: Data collection, Database references