9DF9 | pdb_00009df9

Thermococcus gammatolerans DNA Ligase

• PDB DOI: https://doi.org/10.2210/pdb9DF9/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermococcus gammatolerans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-08-29 Released: 2026-03-18 
• Deposition Author(s): Quintana-Armas, A.X., Rudino-Pinera, E., Cardona-Felix, C., Flores-Hernandez, E.
• Funding Organization(s): Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT), Consejo Nacional de Ciencia y Tecnologia (CONACYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Snapshots of Motion: A Novel Structural Intermediate Reveals Conserved Dynamics in Archaeal DNA Ligases.

Quintana-Armas, A.X., Flores-Hernandez, E., Cardona-Felix, C., Rudino-Pinera, E.

(2026) Proteins 94: 1245-1258

• PubMed: 41560473 
• DOI: https://doi.org/10.1002/prot.70116
• Primary Citation Related Structures: 
  9DF9, 9DFA


• PubMed Abstract: 
  

  We present the first x-ray crystallographic structural evidence of an archaeal DNA ligase showing the AMP covalent adduct together with further cofactor hydrolysis, capturing a transient intermediary in the first step of the ligation reaction, triggered by the pyrophosphate hydrolysis. Our crystallographic models of Thermococcus gammatolerans DNA ligase (LigTgam), coupled with bioinformatic analysis of at least 28 crystallographic structures from ATP- and NAD ⁺ -dependent DNA ligases, highlight the central role of domain mobility. Notably, elevated B-values are consistently observed in key catalytic and binding regions, suggesting a link between structural flexibility and enzymatic efficiency. Remarkably, this pattern of high B-values is conserved in replicative ligases, including bacterial Lig A, indicating a broader evolutionary relevance. These fluctuations emphasize the importance of conformational adaptability in accommodating substrate DNA and facilitating catalytic steps, including adenylation and phosphodiester bond formation. In this work, we delve deeper into this dynamic behavior, providing evidence of its critical role in ligase function.

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Organizational Affiliation: 
• Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
SECIHTI - Centro de Investigaciones Biológicas del Noroeste (CIBNOR-Unidad La Paz), La Paz, Baja California Sur, México.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.16 kDa 
• Atom Count: 4,366 
• Modeled Residue Count: 553 
• Deposited Residue Count: 553 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	553	Thermococcus gammatolerans	Mutation(s): 0  Gene Names: lig, TGAM_1718 EC: 6.5.1.6
UniProt
Find proteins for C5A7K8 (Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)) Explore C5A7K8  Go to UniProtKB:  C5A7K8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77	α = 90
b = 89.4	β = 90
c = 111.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Quintana-Armas, A.X., Rudino-Pinera, E., Cardona-Felix, C., Flores-Hernandez, E.

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Funding Organization	Location	Grant Number
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IN226523
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	--

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Database references