1ly1

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[[Image:1ly1.jpg|left|200px]]
 
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{{Structure
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==Structure and Mechanism of T4 Polynucleotide Kinase==
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|PDB= 1ly1 |SIZE=350|CAPTION= <scene name='initialview01'>1ly1</scene>, resolution 2.00&Aring;
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<StructureSection load='1ly1' size='340' side='right'caption='[[1ly1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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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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|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>
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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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|GENE= PSET ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ly1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ly1 OCA], [http://www.ebi.ac.uk/pdbsum/1ly1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ly1 RCSB]</span>
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== Function ==
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}}
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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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== Evolutionary Conservation ==
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'''Structure and Mechanism of T4 Polynucleotide Kinase'''
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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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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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1LY1 is a [[Single protein]] structure of 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=1LY1 OCA].
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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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<div style="clear:both"></div>
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==Reference==
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__TOC__
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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://www.ncbi.nlm.nih.gov/pubmed/12110598 12110598]
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</StructureSection>
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[[Category: Enterobacteria phage t4]]
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[[Category: Escherichia virus T4]]
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[[Category: Polynucleotide 5'-hydroxy-kinase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Lima CD]]
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[[Category: Lima, C D.]]
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[[Category: Shuman S]]
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[[Category: Shuman, S.]]
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[[Category: Wang LK]]
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[[Category: Wang, L K.]]
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[[Category: kinase]]
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[[Category: phage]]
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[[Category: phosphatase]]
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[[Category: pnk]]
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[[Category: polynucleotide]]
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[[Category: t4]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:08:44 2008''
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Current revision

Structure and Mechanism of T4 Polynucleotide Kinase

PDB ID 1ly1

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