1ly1

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(New page: 200px<br /><applet load="1ly1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ly1, resolution 2.00&Aring;" /> '''Structure and Mechan...)
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[[Image:1ly1.jpg|left|200px]]<br /><applet load="1ly1" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ly1, resolution 2.00&Aring;" />
 
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'''Structure and Mechanism of T4 Polynucleotide Kinase'''<br />
 
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==Overview==
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==Structure and Mechanism of T4 Polynucleotide Kinase==
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T4 polynucleotide kinase (Pnk), in addition to being an invaluable, research tool, exemplifies a family of bifunctional enzymes with 5'-kinase, and 3'-phosphatase activities that play key roles in RNA and DNA repair., T4 Pnk is a homotetramer composed of a C-terminal phosphatase domain and, an N-terminal kinase domain. The 2.0 A crystal structure of the isolated, kinase domain highlights a tunnel-like active site through the heart of, the enzyme, with an entrance on the 5' OH acceptor side that can, accommodate a single-stranded polynucleotide. The active site is composed, of essential side chains that coordinate the beta phosphate of the NTP, donor and the 3' phosphate of the 5' OH acceptor, plus a putative general, acid that activates the 5' OH. The structure rationalizes the different, specificities of T4 and eukaryotic Pnk and suggests a model for the, assembly of the tetramer.
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<StructureSection load='1ly1' size='340' side='right'caption='[[1ly1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1ly1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LY1 FirstGlance]. <br>
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1LY1 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 SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LY1 OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ly1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ly1 OCA], [https://pdbe.org/1ly1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ly1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ly1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ly1 ProSAT]</span></td></tr>
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Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme., Wang LK, Lima CD, Shuman S, EMBO J. 2002 Jul 15;21(14):3873-80. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12110598 12110598]
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</table>
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[[Category: Bacteriophage t4]]
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== Function ==
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[[Category: Polynucleotide 5'-hydroxy-kinase]]
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[https://www.uniprot.org/uniprot/KIPN_BPT4 KIPN_BPT4] Acts as a 5'-hydroxyl kinase, a 3'-phosphatase and a 2',3'-cyclic phosphodiesterase. Catalyzes the transfer of the terminal phosphate of ATP to the 5'-hydroxyl termini of ribo- and deoxyribonucleotides. In the presence of ADP the enzyme also catalyzes an exchange reaction. In the exchange reaction, an excess ADP causes the enzyme to transfer the 5' terminal phosphate from phosphorylated DNA to ADP. These activities modify the ends of nicked tRNA generated by a bacterial response to infection and facilitate repair by T4 RNA ligase.
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Lima, C.D.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Shuman, S.]]
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Check<jmol>
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[[Category: Wang, L.K.]]
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<jmolCheckbox>
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[[Category: SO4]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ly/1ly1_consurf.spt"</scriptWhenChecked>
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[[Category: kinase]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: phage]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: phosphatase]]
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</jmolCheckbox>
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[[Category: pnk]]
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</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/main_output.php?pdb_ID=1ly1 ConSurf].
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[[Category: polynucleotide]]
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<div style="clear:both"></div>
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[[Category: t4]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:58:25 2007''
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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[[Category: Lima CD]]
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[[Category: Shuman S]]
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[[Category: Wang LK]]

Current revision

Structure and Mechanism of T4 Polynucleotide Kinase

PDB ID 1ly1

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