ArticleNucleic acids research2003
Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
- Fidelity of DNA ligase I is sensitive to physiological MgThe Journal of biological chemistry · 2026Article
- Probing the mechanism of nick searching by LIG1 at the single-molecule level.Nucleic acids research · 2024Article
- Mismatch discrimination and sequence bias during end-joining by DNA ligases.Nucleic acids research · 2022Article
- Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase.Scientific reports · 2021Article
- Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins.Nucleic acids research · 2019Article
- DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.Nucleic acids research · 2018Article
- Article
- Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase.Nucleic acids research · 2014Article
- ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.Acta crystallographica. Section F, Structural biology and crystallization communications · 2012Article
- Kinetic analysis of DNA strand joining by Chlorella virus DNA ligase and the role of nucleotidyltransferase motif VI in ligase adenylylation.The Journal of biological chemistry · 2012Article
- Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase.The Journal of biological chemistry · 2011Article
- Structure-function analysis of the OB and latch domains of chlorella virus DNA ligase.The Journal of biological chemistry · 2011Article
- Functional dissection of the DNA interface of the nucleotidyltransferase domain of chlorella virus DNA ligase.The Journal of biological chemistry · 2011Article
- Solution NMR studies of Chlorella virus DNA ligase-adenylate.Journal of molecular biology · 2010Article
- Sequence-specific 1H N, 13C, and 15N backbone resonance assignments of the 34 kDa Paramecium bursaria Chlorella virus 1 (PBCV1) DNA ligase.Biomolecular NMR assignments · 2009Article
- The Phycodnaviridae: the story of how tiny giants rule the world.Current topics in microbiology and immunology · 2009Review
- The associative nature of adenylyl transfer catalyzed by T4 DNA ligase.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Dynamics of phosphodiester synthesis by DNA ligase.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Eukaryotic DNA ligases: structural and functional insights.Annual review of biochemistry · 2008Review
- Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides.Nucleic acids research · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent DNA ligase known; it suffices for yeast cell growth in lieu of the essential yeast DNA ligase Cdc9. The Chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its DNA footprint extends 8-9 nt on the 3'-hydroxyl (3'-OH) side of the nick and 11-12 nt on the 5'-phosphate (5'-PO4) side. Here we establish the minimal length requirements for ligatable 3'-OH and 5'-PO4 strands at the nick (6 nt) and describe a new crystal structure of the ligase-adenylate in a state construed to reflect the configuration of the active site prior to nick recognition. Comparison with a previous structure of the ligase-adenylate bound to sulfate (a mimetic of the nick 5'-PO4) suggests how the positions and contacts of the active site components and the bound adenylate are remodeled by DNA binding. We find that the minimal Chlorella virus ligase is capable of catalyzing non-homologous end-joining reactions in vivo in yeast, a process normally executed by the structurally more complex cellular Lig4 enzyme. Our results suggest a model of ligase evolution in which: (i) a small 'pluripotent' ligase is the progenitor of the much larger ligases found presently in eukaryotic cells and (ii) gene duplications, variations within the core ligase structure and the fusion of new domains to the core structure (affording new protein-protein interactions) led to the compartmentalization of eukaryotic ligase function, i.e. by enhancing some components of the functional repertoire of the ancestral ligase while disabling others.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.