9PGZ | pdb_00009pgz

X-ray crystal structure of SRD42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Enhancing enzymatic bioconjugation efficiency via installation of a substrate recruitment domain.

Shelby, C.Kuzelka, K.P.Ellis, J.M.Yao, Z.McCue, A.C.Park, R.Nair, S.K.Bowers, A.Kuhlman, B.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.10.27.684804
  • Primary Citation Related Structures: 
    9PGZ

  • PubMed Abstract: 

    Enzyme mediated bioconjugation provides a method for easy and rapid formation of protein-protein and protein-small molecule conjugates under mild conditions. Promiscuous enzymes are of particular interest because they can catalyze conjugation reactions on a broad set of substrates. However, this promiscuity carries the risk of undesirable off-target modifications. To mitigate this effect, we used computational design to install a substrate recruitment domain (SRD) onto the promiscuous enzyme, tyrosinase. The redesigned tyrosinase, called D42, preferentially modifies tyrosine residues within the peptide core (core) linked to a 6-amino acid recognition motif/sequence (RS) specific for the SRD. Incorporation of the recognition sequence along with a neighboring tyrosine in peptides or proteins allows for rapid D42-mediated conversion of the tyrosine to an orthoquinone, which can be selectively modified with a variety of nucleophiles. We demonstrate the utility of our design system by rapidly installing cytotoxic molecules on a monoclonal antibody.

Macromolecule Content 

  • Total Structure Weight: 40.52 kDa 
  • Atom Count: 2,918 
  • Modeled Residue Count: 348 
  • Deposited Residue Count: 353 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosinase,Tyrosine-protein kinase Fyn353Priestia megateriumHomo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for B2ZB02 (Priestia megaterium)
Explore B2ZB02 
Go to UniProtKB:  B2ZB02
Find proteins for P06241 (Homo sapiens)
Explore P06241 
Go to UniProtKB:  P06241
PHAROS:  P06241
GTEx:  ENSG00000010810 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP06241B2ZB02
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.264α = 90
b = 150.264β = 90
c = 150.264γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Database references