1dgs

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CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

Structural highlights

1dgs is a 2 chain structure with sequence from Thermus filiformis. The July 2004 RCSB PDB Molecule of the Month feature on DNA Ligase by David S. Goodsell is 10.2210/rcsb_pdb/mom_2004_7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:AMP, ZN
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNLJ_THEFI DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.,Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
18 reviews cite this structure
Eukaryotic DNA ligases: structural and functional insights.
Ellenberger et al. (2008)
17 more
83 other articles
No citations found

See Also

References

  1. ↑ Jeon HJ, Shin HJ, Choi JJ, Hoe HS, Kim HK, Suh SW, Kwon ST. Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis. FEMS Microbiol Lett. 2004 Aug 1;237(1):111-8. PMID:15268945 doi:http://dx.doi.org/10.1016/j.femsle.2004.06.018
  2. ↑ Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 2000 Mar 1;19(5):1119-29. PMID:10698952 doi:http://dx.doi.org/10.1093/emboj/19.5.1119

Contents


PDB ID 1dgs

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OCA

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