9MYE | pdb_00009mye

C28 Polymerase Incorporating RNA, n+1

• PDB DOI: https://doi.org/10.2210/pdb9MYE/pdb
• NAKB: 9MYE

• Classification: TRANSFERASE
• Organism(s): Thermococcus gorgonarius, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-21 Released: 2025-12-17 
• Deposition Author(s): Hajjar, M., Ko, G.K., Ho, E.J., Chim, N., Chaput, J.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.272 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Rapid evolution of a highly efficient RNA polymerase by homologous recombination.

Medina, E.L., Maola, V.A., Hajjar, M., Ko, G.K., Ho, E.J., Horton, A.R., Chim, N., Chaput, J.C.

(2026) Nat Chem Biol 

• PubMed: 41501182 
• DOI: https://doi.org/10.1038/s41589-025-02124-7
• Primary Citation of Related Structures:  
  9MYE


• PubMed Abstract: 
  

  Engineering DNA polymerases to efficiently synthesize artificial or noncognate nucleic acids remains an essential challenge in synthetic biology. Here we describe an evolutionary campaign designed to convert a family of highly selective DNA polymerases into an unnatural homolog with strong RNA synthesis activity. Starting from a homologous recombination library, a short evolutionary path was achieved using a single-cell droplet-based microfluidic selection strategy to produce C28, a newly engineered polymerase that can synthesize RNA with a rate of ~3 nt s ^-1 and of >99% fidelity. C28 is capable of long-range RNA synthesis, reverse transcription and chimeric DNA-RNA amplification using the PCR. Despite strong discrimination against other genetic systems, C28 readily accepts several 2'F and base-modified RNA analogs. Together, these findings highlight the power of directed evolution as an approach for reprogramming DNA polymerases with activities that could help drive future applications in biotechnology and medicine.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Chemistry, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 99.13 kDa 
• Atom Count: 6,715 
• Modeled Residue Count: 771 
• Deposited Residue Count: 804 
• Unique protein chains: 1
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	774	Thermococcus gorgonarius	Mutation(s): 0  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for P56689 (Thermococcus gorgonarius) Explore P56689  Go to UniProtKB:  P56689

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template	B [auth T]	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Primer	C [auth P]	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.272 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.97	α = 90
b = 102.34	β = 90
c = 112.23	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
iMOSFLM	data reduction
Aimless	data scaling
pointless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Hajjar, M., Ko, G.K., Ho, E.J., Chim, N., Chaput, J.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-01-14
  Changes: Database references
• Version 1.2: 2026-01-21
  Changes: Database references