3RR5

DNA ligase from the archaeon Thermococcus sp. 1519

Summary for 3RR5

• Entry DOI: 10.2210/pdb3rr5/pdb
• Related: 2CFM 2HIV 3GDE
• Descriptor: DNA ligase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: atp-dependent thermostable dna ligase, archaeon, ligase
• Biological source: Thermococcus sp. 1519
• Total number of polymer chains: 1
• Total formula weight: 64916.13

Authors

Petrova, T.,Bezsudnova, E.Y.,Boyko, K.M.,Mardanov, A.V.,Popov, V.O.,Polyakov, K.M.,Ravin, N.V.,Shabalin, I.G.,Skryabin, K.G.,Stekhanova, T.N.,Kovalchuk, M.V. (deposition date: 2011-04-29, release date: 2012-04-11, Last modification date: 2023-09-13)

Primary citation

Petrova, T.,Bezsudnova, E.Y.,Boyko, K.M.,Mardanov, A.V.,Polyakov, K.M.,Volkov, V.V.,Kozin, M.,Ravin, N.V.,Shabalin, I.G.,Skryabin, K.G.,Stekhanova, T.N.,Kovalchuk, M.V.,Popov, V.O.
ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.
Acta Crystallogr.,Sect.F, 68:1440-1447, 2012

PubMed Abstract: DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.

PubMed: 23192021
DOI: 10.1107/S1744309112043394

Experimental method

X-RAY DIFFRACTION (3.018 Å)