8XK7 | pdb_00008xk7

binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

• PDB DOI: https://doi.org/10.2210/pdb8XK7/pdb
• NAKB: 8XK7

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermus aquaticus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-22 Released: 2024-11-27 
• Deposition Author(s): Wen, C., Liu, H., Yang, L., Gong, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for C2'-methoxy Recognition by DNA Polymerases and Function Improvement.

Wen, C., Wang, G., Yang, L., Chen, T., Liu, H., Gong, W.

(2024) J Mol Biology 436: 168744-168744

• PubMed: 39147125 
• DOI: https://doi.org/10.1016/j.jmb.2024.168744
• Primary Citation Related Structures: 
  8XJR, 8XK7, 8XK9


• PubMed Abstract: 
  

  DNA modified with C2'-methoxy (C2'-OMe) greatly enhances its resistance to nucleases, which is beneficial for the half-life of aptamers and DNA nanomaterials. Although the unnatural DNA polymerases capable of incorporating C2'-OMe modified nucleoside monophosphates (C2'-OMe-NMPs) were engineered via directed evolution, the detailed molecular mechanism by which an evolved DNA polymerase recognizes C2'-OMe-NTPs remains poorly understood. Here, we present the crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing the C2'-OMe-GTP in different states. Our results reveal the structural basis for recognition of C2'-methoxy by SFM4-3. Based on the analysis of other mutated residues in SFM4-3, a new Stoffel fragment variant with faster catalytic rate and stronger inhibitor-resistance was obtained. In addition, the capture of a novel pre-insertion co-existing with template 5'-overhang stacking conformation provides insight into the catalytic mechanism of Taq DNA polymerase.

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Organizational Affiliation: 
• Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China.
MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China. Electronic address: [e-mail].
Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China. Electronic address: [e-mail].
Division of Biological Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, PR China. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.33 kDa 
• Atom Count: 5,330 
• Modeled Residue Count: 576 
• Deposited Residue Count: 584 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	554	Thermus aquaticus	Mutation(s): 0  Gene Names: polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821  Go to UniProtKB:  P19821

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA(5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP*OMG)-3')	B	17	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA(5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*CP*OMG)-3')	C	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.61	α = 90
b = 65.628	β = 103.51
c = 107.378	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Wen, C., Liu, H., Yang, L., Gong, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release