The enzyme consists of a larger N-terminal nucleotidyltransferase NTase domain and a smaller C-terminal OB domain with a cleft between them. Thus, we have the structure of a genuine catalytic intermediate. The OB domain consists of a five-stranded antiparallel beta barrel plus an alpha helix. Although ChVLig lacks the large N- or C-terminal flanking domains found in eukaryotic cellular DNA ligases, it can sustain mitotic growth, DNA repair, and nonhomologous end joining in budding yeast when it is the only source of ligase in the cell.
The OB domain binds across the minor groove on the face of the duplex behind the nick. The latch is critical for clamp closure and is a key determinant of nick sensing. Comparison of the crystal structures of the free and nick-bound ChVLig-AMP reveals a large domain rearrangements accompanying nick recognition.
The peptide segment that is destined to become the latch is disordered in the free ligase and sensitive to proteolysis. Addition of a divalent cation triggered nick sealing in crystallo , thereby establishing that the nick complex is a bona fide intermediate in the DNA repair pathway. LigA has a modular architecture built around a central ligase core composed of a NTase domain and an OB domain. Each step of the ligation pathway depends upon a different subset of the LigA domains, with only the NTase domain being required for all steps.
Subsequent studies in collaboration with Maria Jasin showed that E. Our crystal structure of E. The NTase domain binds to the broken DNA strands at and flanking the nick, the OB domain contacts the continuous template strand surrounding the nick, and the HhH domain binds both strands across the minor groove at the periphery of the footprint. Based on available structural data, it is clear that DNA ligases have evolved at least three different means of encircling DNA.
Comparisons of the E. The NTase domain includes defining peptide motifs that form the nucleotide-binding pocket. In principle, ligase might employ a general base to deprotonate the lysine. Several crystal structures of ligases absent metals provided scant support for either explanation. In these structures, the motif I lysine nucleophile is located next to a motif IV glutamate or aspartate side chain. The lysine and the motif IV carboxylate form an ion pair, the anticipated effect of which is to increase the pKa of lysine by virtue of surrounding negative charge.
It is unlikely that a glutamate or aspartate anion could serve as general base to abstract a proton from the lysine cation. A metal-driven mechanism was revealed by our recent crystal structure of Naegleria gruberi RNA ligase NgrRnl as a step 1 Michaelis complex with ATP and manganese its preferred metal cofactor. The key to capturing the Michaelis-like complex was the replacement of the lysine nucleophile by an isosteric methionine.
The 1. We solved a 1. Research Overview. Featured News. Phylogenetic Distribution Living organisms comprise 3 domains: eubacteria, archaeabacteria, and eukaryotes. A steady state kinetic analysis of the reaction-catalyzed E. A strain of E. Although able to grow at 30 degrees C, the mutant is still defective at this temperature in its ability to repair damage to its DNA caused by ultraviolet irradiation and by alkylating agents. Try to answer the quiz below to check what you have learned so far about ligases.
Genes are expressed through the process of protein synthesis. This elaborate tutorial provides an in-depth review of the different steps of the biological production of protein starting from the gene up to the process of secretion. Also included are topics on DNA replication during interphase of the cell cycle, DNA mutation and repair mechanisms, gene pool, modification, and diseases Read More.
This tutorial presents the benefits and the possible adverse eventualities of genetic engineering. Know more about this topic in this tutorial to be able to articulate the advantages and disadvantages of artificially manipulating genes Skip to content Main Navigation Search. Dictionary Articles Tutorials Biology Forum. Table of Contents. Ligases are classified into six subclasses: 1 EC 6. Synonym: synthetase. To Email. Time is Up! Genetic Information and Protein Synthesis Genes are expressed through the process of protein synthesis.
Related Articles No related articles found See all Related Topics. Enzymes that bring about joining or binding of two biological macromolecules.
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