Summary information and primary citation

PDB-id
1rrc; SNAP-derived features in text and JSON formats; DNAproDB
Class
transferase-DNA
Method
X-ray (2.46 Å)
Summary
T4 polynucleotide kinase bound to 5'-gtc-3' ssDNA
Reference
Eastberg JH, Pelletier J, Stoddard BL (2004): "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212.
Abstract
T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme phosphorylates the 5' hydroxyl termini of a wide variety of nucleic acid substrates, a behavior studied here through the determination of a series of crystal structures with single-stranded (ss)DNA oligonucleotide substrates of various lengths and sequences. In these structures, the 5' ribose hydroxyl is buried in the kinase active site in proper alignment for phosphoryl transfer. Depending on the ssDNA length, the first two or three nucleotide bases are well ordered. Numerous contacts are made both to the phosphoribosyl backbone and to the ordered bases. The position, side chain contacts and internucleotide stacking interactions of the ordered bases are strikingly different for a 5'-GT DNA end than for a 5'-TG end. The base preferences displayed at those positions by PNK are attributable to differences in the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js