1rc8

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{{Seed}}
 
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[[Image:1rc8.png|left|200px]]
 
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==T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA==
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The line below this paragraph, containing "STRUCTURE_1rc8", creates the "Structure Box" on the page.
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<StructureSection load='1rc8' size='340' side='right'caption='[[1rc8]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1rc8]] is a 2 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=1RC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RC8 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.75&#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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_1rc8| PDB=1rc8 | SCENE= }}
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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=1rc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rc8 OCA], [https://pdbe.org/1rc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1rc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rc8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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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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[[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/rc/1rc8_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=1rc8 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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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.
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===T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_14754987}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1rc8" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 14754987 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_14754987}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus T4]]
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1RC8 is a 2 chains structure of sequences 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].
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[[Category: Large Structures]]
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[[Category: Eastberg JH]]
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==Reference==
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[[Category: Pelletier J]]
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<ref group="xtra">PMID:14754987</ref><references group="xtra"/>
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[[Category: Stoddard BL]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Polynucleotide 5'-hydroxy-kinase]]
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[[Category: Eastberg, J H.]]
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[[Category: Pelletier, J.]]
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[[Category: Stoddard, B L.]]
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[[Category: Alpha/beta]]
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[[Category: Kinase]]
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[[Category: P-loop]]
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[[Category: Phosphatase]]
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[[Category: Ssdna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:18:47 2009''
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Current revision

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

PDB ID 1rc8

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