1rc8
From Proteopedia
(New page: 200px<br /><applet load="1rc8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rc8, resolution 2.75Å" /> '''T4 Polynucleotide Ki...) |
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| - | [[Image:1rc8.gif|left|200px]]<br /><applet load="1rc8" size=" | + | [[Image:1rc8.gif|left|200px]]<br /><applet load="1rc8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rc8, resolution 2.75Å" /> | caption="1rc8, resolution 2.75Å" /> | ||
'''T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA'''<br /> | '''T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme | + | 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 Structure== | ==About this Structure== | ||
| - | 1RC8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with CA, DMS and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | + | 1RC8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=DMS:'>DMS</scene> and <scene name='pdbligand=ADP:'>ADP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RC8 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Polynucleotide 5'-hydroxy-kinase]] | [[Category: Polynucleotide 5'-hydroxy-kinase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Eastberg, J | + | [[Category: Eastberg, J H.]] |
[[Category: Pelletier, J.]] | [[Category: Pelletier, J.]] | ||
| - | [[Category: Stoddard, B | + | [[Category: Stoddard, B L.]] |
[[Category: ADP]] | [[Category: ADP]] | ||
[[Category: CA]] | [[Category: CA]] | ||
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[[Category: ssdna]] | [[Category: ssdna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:18 2008'' |
Revision as of 12:49, 21 February 2008
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T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA
Overview
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 Structure
1RC8 is a Single protein structure of sequence from Bacteriophage t4 with , and as ligands. Active as Polynucleotide 5'-hydroxy-kinase, with EC number 2.7.1.78 Full crystallographic information is available from OCA.
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:14754987
Page seeded by OCA on Thu Feb 21 14:49:18 2008
Categories: Bacteriophage t4 | Polynucleotide 5'-hydroxy-kinase | Single protein | Eastberg, J H. | Pelletier, J. | Stoddard, B L. | ADP | CA | DMS | Alpha/beta | Kinase | P-loop | Phosphatase | Ssdna
