1kej

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(New page: 200px<br /><applet load="1kej" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kej, resolution 3.00&Aring;" /> '''Crystal Structure of...)
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[[Image:1kej.jpg|left|200px]]<br /><applet load="1kej" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kej, resolution 3.00&Aring;" />
 
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'''Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase complexed with ddATP'''<br />
 
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==Overview==
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==Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase complexed with ddATP==
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The crystal structure of the catalytic core of murine terminal, deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical, DNA polymerase beta-like fold locked in a closed form. In addition, the, structures of two different binary complexes, one with an oligonucleotide, primer and the other with an incoming ddATP-Co(2+) complex, show that the, substrates and the two divalent ions in the catalytic site are positioned, in TdT in a manner similar to that described for the human DNA polymerase, beta ternary complex, suggesting a common two metal ions mechanism of, nucleotidyl transfer in these two proteins. The inability of TdT to, accommodate a template strand can be explained by steric hindrance at the, catalytic site caused by a long lariat-like loop, which is absent in DNA, polymerase beta. However, displacement of this discriminating loop would, be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present, structure can be used to model the recently discovered human polymerase, mu, with which it shares 43% sequence identity.
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<StructureSection load='1kej' size='340' side='right'caption='[[1kej]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kej]] is a 1 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=1KEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEJ 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]] 3&#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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DAD:2,3-DIDEOXYADENOSINE-5-TRIPHOSPHATE'>DAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kej OCA], [https://pdbe.org/1kej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kej RCSB], [https://www.ebi.ac.uk/pdbsum/1kej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kej ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TDT_MOUSE TDT_MOUSE] Template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. One of the in vivo functions of this enzyme is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells.
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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/ke/1kej_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=1kej 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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The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.
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==About this Structure==
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Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.,Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C EMBO J. 2002 Feb 1;21(3):427-39. PMID:11823435<ref>PMID:11823435</ref>
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1KEJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with CO, NA and DAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_nucleotidylexotransferase DNA nucleotidylexotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.31 2.7.7.31] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KEJ 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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Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase., Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C, EMBO J. 2002 Feb 1;21(3):427-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11823435 11823435]
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</div>
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[[Category: DNA nucleotidylexotransferase]]
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<div class="pdbe-citations 1kej" style="background-color:#fffaf0;"></div>
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[[Category: Mus musculus]]
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[[Category: Single protein]]
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[[Category: Boule, J.B.]]
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[[Category: Delarue, M.]]
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[[Category: Expert-Bezancon, N.]]
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[[Category: Jourdan, N.]]
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[[Category: Lescar, J.]]
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[[Category: Papanicolaou, C.]]
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[[Category: Rougeon, F.]]
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[[Category: Sukumar, N.]]
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[[Category: CO]]
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[[Category: DAD]]
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[[Category: NA]]
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[[Category: nucleotidyl transferase]]
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[[Category: pol x family]]
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[[Category: polymerase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:07:57 2007''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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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]]
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[[Category: Mus musculus]]
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[[Category: Boule JB]]
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[[Category: Delarue M]]
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[[Category: Expert-Bezancon N]]
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[[Category: Jourdan N]]
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[[Category: Lescar J]]
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[[Category: Papanicolaou C]]
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[[Category: Rougeon F]]
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[[Category: Sukumar N]]

Current revision

Crystal Structure of Murine Terminal Deoxynucleotidyl Transferase complexed with ddATP

PDB ID 1kej

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