1RC8

T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA

Summary for 1RC8

• Entry DOI: 10.2210/pdb1rc8/pdb
• Related: 1RPZ 1RRC
• Descriptor: 5'-D(*GP*TP*CP*AP*C)-3', Polynucleotide kinase, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: kinase, phosphatase, alpha/beta, p-loop, ssdna, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage T4
• Total number of polymer chains: 2
• Total formula weight: 37260.02

Authors

Eastberg, J.H.,Pelletier, J.,Stoddard, B.L. (deposition date: 2003-11-03, release date: 2004-02-17, Last modification date: 2024-11-13)

Primary citation

Eastberg, J.H.,Pelletier, J.,Stoddard, B.L.
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
Nucleic Acids Res., 32:653-660, 2004

PubMed 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.

PubMed: 14754987
DOI: 10.1093/nar/gkh212

Experimental method

X-RAY DIFFRACTION (2.75 Å)