1rc8: Difference between revisions

Revision as of 07:19, 3 May 2008

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 Enterobacteria phage 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 Sat May 3 07:19:29 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:1rc8.gif|left|200px]]
- {{Structure
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-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= PSET ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
+-->
-|DOMAIN=
+{{STRUCTURE_1rc8|  PDB=1rc8  |  SCENE=  }}
-|RELATEDENTRY=[[1rpz|1RPZ]], [[1rrc|1RRC]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rc8 OCA], [http://www.ebi.ac.uk/pdbsum/1rc8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rc8 RCSB]</span>
-}}
 '''T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA'''
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 [[Category: Pelletier, J.]]
 [[Category: Stoddard, B L.]]
-[[Category: alpha/beta]]
+[[Category: Alpha/beta]]
-[[Category: kinase]]
+[[Category: Kinase]]
-[[Category: p-loop]]
+[[Category: P-loop]]
-[[Category: phosphatase]]
+[[Category: Phosphatase]]
-[[Category: ssdna]]
+[[Category: Ssdna]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:19:29 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:08 2008''