1rc8: Difference between revisions

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[[Image:1rc8.png|left|200px]]
==T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA==
<StructureSection load='1rc8' size='340' side='right' caption='[[1rc8]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rc8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RC8 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rpz|1rpz]], [[1rrc|1rrc]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSET ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_5'-hydroxyl-kinase Polynucleotide 5'-hydroxyl-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.78 2.7.1.78] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1rc8 RCSB], [http://www.ebi.ac.uk/pdbsum/1rc8 PDBsum]</span></td></tr>
<table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rc/1rc8_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


{{STRUCTURE_1rc8|  PDB=1rc8  |  SCENE=  }}
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<ref>PMID:14754987</ref>


===T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_14754987}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[1rc8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RC8 OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:014754987</ref><references group="xtra"/>
[[Category: Enterobacteria phage t4]]
[[Category: Enterobacteria phage t4]]
[[Category: Polynucleotide 5'-hydroxyl-kinase]]
[[Category: Polynucleotide 5'-hydroxyl-kinase]]

Revision as of 18:52, 29 September 2014

T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNAT4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA

Structural highlights

1rc8 is a 2 chain structure with sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
NonStd Res:
Related:1rpz, 1rrc
Gene:PSET (Enterobacteria phage T4)
Activity:Polynucleotide 5'-hydroxyl-kinase, with EC number 2.7.1.78
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Eastberg JH, Pelletier J, Stoddard BL. Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase. Nucleic Acids Res. 2004 Jan 30;32(2):653-60. Print 2004. PMID:14754987 doi:10.1093/nar/gkh212

1rc8, resolution 2.75Å

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