7B0H | pdb_00007b0h

TgoT_6G12 Ternary complex

• PDB DOI: https://doi.org/10.2210/pdb7B0H/pdb
• NAKB: 7B0H

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct, Thermococcus gorgonarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-19 Released: 2021-01-13 
• Deposition Author(s): Samson, C., Legrand, P., Tekpinar, M., Rozenski, J., Abramov, M., Holliger, P., Pinheiro, V., Herdewijn, P., Delarue, M.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.247 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.

Samson, C., Legrand, P., Tekpinar, M., Rozenski, J., Abramov, M., Holliger, P., Pinheiro, V.B., Herdwijn, P., Delarue, M.

(2020) Biomolecules 10

• PubMed: 33302546 
• DOI: https://doi.org/10.3390/biom10121647
• Primary Citation Related Structures: 
  7B06, 7B07, 7B08, 7B0F, 7B0G, 7B0H


• PubMed Abstract: 
  

  Archaeal DNA polymerases from the B-family (polB) have found essential applications in biotechnology. In addition, some of their variants can accept a wide range of modified nucleotides or xenobiotic nucleotides, such as 1,5-anhydrohexitol nucleic acid (HNA), which has the unique ability to selectively cross-pair with DNA and RNA. This capacity is essential to allow the transmission of information between different chemistries of nucleic acid molecules. Variants of the archaeal polymerase from Thermococcus gorgonarius, TgoT, that can either generate HNA from DNA (TgoT_6G12) or DNA from HNA (TgoT_RT521) have been previously identified. To understand how DNA and HNA are recognized and selected by these two laboratory-evolved polymerases, we report six X-ray structures of these variants, as well as an in silico model of a ternary complex with HNA. Structural comparisons of the apo form of TgoT_6G12 together with its binary and ternary complexes with a DNA duplex highlight an ensemble of interactions and conformational changes required to promote DNA or HNA synthesis. MD simulations of the ternary complex suggest that the HNA-DNA hybrid duplex remains stable in the A-DNA helical form and help explain the presence of mutations in regions that would normally not be in contact with the DNA if it were not in the A-helical form. One complex with two incorporated HNA nucleotides is surprisingly found in a one nucleotide-backtracked form, which is new for a DNA polymerase. This information can be used for engineering a new generation of more efficient HNA polymerase variants.

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Organizational Affiliation: 
• Unit of Structural Dynamics of Biological Macromolecules, UMR 3528 du CNRS, Institut Pasteur, 25-28 rue du Dr Roux, 75015 Paris, France.
Division of Biological Sciences, Synchrotron SOLEIL, 91190 Saint Aubin, France.
KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry Herestraat, 49-box 1041, 3000 Leuven, Belgium.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 192.59 kDa 
• Atom Count: 12,977 
• Modeled Residue Count: 1,513 
• Deposited Residue Count: 1,584 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	D [auth E], E [auth F]	773	Thermococcus gorgonarius	Mutation(s): 18  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for P56689 (Thermococcus gorgonarius) Explore P56689  Go to UniProtKB:  P56689

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*CP*GP*GP*CP*AP*AP*AP*TP*GP*CP*G)-3')	A, B [auth C]	13	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*CP*AP*TP*T)-3')	C [auth D], F [auth G]	6	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP (Subject of Investigation/LOI)	J [auth E], N [auth F]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MN (Subject of Investigation/LOI)	G [auth E], H [auth E], K [auth F], L [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	I [auth E], M [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.247 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.823	α = 90
b = 112.331	β = 90
c = 186.518	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Samson, C., Legrand, P., Tekpinar, M., Rozenski, J., Abramov, M., Holliger, P., Pinheiro, V., Herdewijn, P., Delarue, M.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	Belgium	G0H7618N

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary