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1yj5

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(New page: 200px<br /><applet load="1yj5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yj5, resolution 2.80&Aring;" /> '''Molecular architectu...)
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[[Image:1yj5.gif|left|200px]]<br /><applet load="1yj5" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yj5, resolution 2.80&Aring;" />
 
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'''Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme'''<br />
 
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==Overview==
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==Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme==
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Mammalian polynucleotide kinase (PNK) is a key component of both the base, excision repair (BER) and nonhomologous end-joining (NHEJ) DNA repair, pathways. PNK acts as a 5'-kinase/3'-phosphatase to create, 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for, ligation during repair. PNK is recruited to repair complexes through, interactions between its N-terminal FHA domain and phosphorylated, components of either pathway. Here, we describe the crystal structure of, intact mammalian PNK and a structure of the PNK FHA bound to a cognate, phosphopeptide. The kinase domain has a broad substrate binding pocket, which preferentially recognizes double-stranded substrates with recessed, 5' termini. In contrast, the phosphatase domain efficiently, dephosphorylates single-stranded 3'-phospho termini as well as, double-stranded substrates. The FHA domain is linked to the, kinase/phosphatase catalytic domain by a flexible tether, and it exhibits, a mode of target selection based on electrostatic complementarity between, the binding surface and the phosphothreonine peptide.
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<StructureSection load='1yj5' size='340' side='right'caption='[[1yj5]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yj5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YJ5 FirstGlance]. <br>
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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]] 2.8&#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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=1yj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yj5 OCA], [https://pdbe.org/1yj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1yj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yj5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PNKP_MOUSE PNKP_MOUSE] Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yj/1yj5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1yj5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mammalian polynucleotide kinase (PNK) is a key component of both the base excision repair (BER) and nonhomologous end-joining (NHEJ) DNA repair pathways. PNK acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. PNK is recruited to repair complexes through interactions between its N-terminal FHA domain and phosphorylated components of either pathway. Here, we describe the crystal structure of intact mammalian PNK and a structure of the PNK FHA bound to a cognate phosphopeptide. The kinase domain has a broad substrate binding pocket, which preferentially recognizes double-stranded substrates with recessed 5' termini. In contrast, the phosphatase domain efficiently dephosphorylates single-stranded 3'-phospho termini as well as double-stranded substrates. The FHA domain is linked to the kinase/phosphatase catalytic domain by a flexible tether, and it exhibits a mode of target selection based on electrostatic complementarity between the binding surface and the phosphothreonine peptide.
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==About this Structure==
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The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.,Bernstein NK, Williams RS, Rakovszky ML, Cui D, Green R, Karimi-Busheri F, Mani RS, Galicia S, Koch CA, Cass CE, Durocher D, Weinfeld M, Glover JN Mol Cell. 2005 Mar 4;17(5):657-70. PMID:15749016<ref>PMID:15749016</ref>
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1YJ5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=1YJ5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase., Bernstein NK, Williams RS, Rakovszky ML, Cui D, Green R, Karimi-Busheri F, Mani RS, Galicia S, Koch CA, Cass CE, Durocher D, Weinfeld M, Glover JN, Mol Cell. 2005 Mar 4;17(5):657-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15749016 15749016]
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</div>
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<div class="pdbe-citations 1yj5" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Polynucleotide 5'-hydroxy-kinase]]
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[[Category: Bernstein NK]]
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[[Category: Protein complex]]
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[[Category: Cass CE]]
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[[Category: Bernstein, N.K.]]
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[[Category: Cui D]]
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[[Category: Cass, C.E.]]
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[[Category: Durocher D]]
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[[Category: Cui, D.]]
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[[Category: Galicia S]]
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[[Category: Durocher, D.]]
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[[Category: Glover JNM]]
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[[Category: Galicia, S.]]
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[[Category: Green R]]
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[[Category: Glover, J.N.M.]]
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[[Category: Karimi-Busheri F]]
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[[Category: Green, R.]]
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[[Category: Koch CA]]
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[[Category: Karimi-Busheri, F.]]
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[[Category: Mani RS]]
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[[Category: Koch, C.A.]]
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[[Category: Rakovszky ML]]
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[[Category: Mani, R.S.]]
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[[Category: Weinfeld M]]
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[[Category: Rakovszky, M.L.]]
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[[Category: Williams RS]]
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[[Category: Weinfeld, M.]]
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[[Category: Williams, R.S.]]
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[[Category: SO4]]
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[[Category: beta sandwich]]
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[[Category: p-loop]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:49:34 2007''
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Current revision

Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme

PDB ID 1yj5

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