1rc8: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1rc8.gif|left|200px]] | [[Image:1rc8.gif|left|200px]] | ||
'''T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA''' | {{Structure | ||
|PDB= 1rc8 |SIZE=350|CAPTION= <scene name='initialview01'>1rc8</scene>, resolution 2.75Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene> and <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Polynucleotide_5'-hydroxy-kinase Polynucleotide 5'-hydroxy-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] | |||
|GENE= PSET ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4]) | |||
}} | |||
'''T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1RC8 is a [ | 1RC8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RC8 OCA]. | ||
==Reference== | ==Reference== | ||
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:[http:// | Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14754987 14754987] | ||
[[Category: Bacteriophage t4]] | [[Category: Bacteriophage t4]] | ||
[[Category: Polynucleotide 5'-hydroxy-kinase]] | [[Category: Polynucleotide 5'-hydroxy-kinase]] | ||
| Line 26: | Line 35: | ||
[[Category: ssdna]] | [[Category: ssdna]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:49:36 2008'' | ||
Revision as of 14:49, 20 March 2008
| |||||||
| , resolution 2.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | PSET (Bacteriophage T4) | ||||||
| Activity: | Polynucleotide 5'-hydroxy-kinase, with EC number 2.7.1.78 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA
OverviewOverview
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.
About this StructureAbout this Structure
1RC8 is a Single protein structure of sequence from Bacteriophage t4. Full crystallographic information is available from OCA.
ReferenceReference
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase., Eastberg JH, Pelletier J, Stoddard BL, Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:14754987
Page seeded by OCA on Thu Mar 20 13:49:36 2008