3GDE
The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus
Summary for 3GDE
| Entry DOI | 10.2210/pdb3gde/pdb |
| Descriptor | DNA ligase, PHOSPHATE ION (3 entities in total) |
| Functional Keywords | atp-dependent dna ligase, dna-binding domain, adenylation domain, ob-fold domain, atp-binding, cell cycle, cell division, dna damage, dna recombination, dna repair, dna replication, ligase, nucleotide-binding |
| Biological source | Archaeoglobus fulgidus |
| Total number of polymer chains | 1 |
| Total formula weight | 64310.91 |
| Authors | |
| Primary citation | Kim, D.J.,Kim, O.,Kim, H.-W.,Kim, H.S.,Lee, S.J.,Suh, S.W. ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation Acta Crystallogr.,Sect.F, 65:544-550, 2009 Cited by PubMed Abstract: DNA ligases join the breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 3'-hydroxyl and 5'-phosphate termini. They fall into two classes that require either ATP or NAD(+) as the source of an AMP group that is covalently attached to a strictly conserved lysine. Conformational flexibility is essential for the function of multi-domain DNA ligases because they must undergo large conformational changes involving domain rearrangements during the course of the reaction. In the absence of the nicked DNA substrate, both open and closed conformations have been observed for the ATP-dependent DNA ligases from Sulfolobus solfataricus and Pyrococcus furiosus. Here, the crystal structure of an ATP-dependent DNA ligase from Archaeoglobus fulgidus has been determined in the DNA-unbound unadenylated state. It resembles the closed conformation of P. furiosus DNA ligase but was even more closed, thus enhancing our understanding of the conformational variability of these enzymes. PubMed: 19478428DOI: 10.1107/S1744309109017485 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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