7N5N

PCNA from Thermococcus gammatolerans: crystal III, collection 15, 2.20 A, 28.7 MGy

Summary for 7N5N

• Entry DOI: 10.2210/pdb7n5n/pdb
• Descriptor: DNA polymerase sliding clamp, GLYCEROL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: pcna, sliding clamp, radioresistance, radiation damage, ionizing radiation, dna binding protein
• Biological source: Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)
• Total number of polymer chains: 2
• Total formula weight: 61888.30

Authors

Marin-Tovar, Y.,Rudino-Pinera, E. (deposition date: 2021-06-05, release date: 2022-05-04, Last modification date: 2023-10-18)

Primary citation

Marin-Tovar, Y.,Serrano-Posada, H.,Diaz-Vilchis, A.,Rudino-Pinera, E.
PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation.
Proteins, 90:1684-1698, 2022

PubMed Abstract: Proliferating cell nuclear antigen (PCNA) is an essential protein for cell viability in archaea and eukarya, since it is involved in DNA replication and repair. In order to obtain insights regarding the characteristics that confer radioresistance, the structural study of the PCNA from Thermococcus gammatolerans (PCNA ) in a gradient of ionizing radiation by X-ray crystallography was carried out, together with a bioinformatic analysis of homotrimeric PCNA structures, their sequences, and their molecular interactions. The results obtained from the datasets and the accumulated radiation dose for the last collection from three crystals revealed moderate and localized damage, since even with the loss of resolution, the electron density map corresponding to the last collection allowed to build the whole structure. Attempting to understand this behavior, multiple sequence alignments, and structural superpositions were performed, revealing that PCNA is a protein with a poorly conserved sequence, but with a highly conserved structure. The PCNA presented the highest percentage of charged residues, mostly negatively charged, with a proportion of glutamate more than double aspartate, lack of cysteines and tryptophan, besides a high number of salt bridges. The structural study by X-ray crystallography reveals that the PCNA has the intrinsic ability to resist high levels of ionizing radiation, and the bioinformatic analysis suggests that molecular evolution selected a particular composition of amino acid residues, and their consequent network of synergistic interactions for extreme conditions, as a collateral effect, conferring radioresistance to a protein involved in the chromosomal DNA metabolism of a radioresistant microorganism.

PubMed: 35435259
DOI: 10.1002/prot.26346

Experimental method

X-RAY DIFFRACTION (2.2 Å)