1kdh: Difference between revisions
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New page: left|200px<br /><applet load="1kdh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kdh, resolution 3.00Å" /> '''Binary Complex of Mu... |
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== | ==Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA== | ||
The crystal structure of the catalytic core of murine terminal | <StructureSection load='1kdh' size='340' side='right'caption='[[1kdh]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1kdh]] is a 2 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=1KDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDH FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdh OCA], [https://pdbe.org/1kdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdh RCSB], [https://www.ebi.ac.uk/pdbsum/1kdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdh ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kdh_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=1kdh ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
[[Category: | <div class="pdbe-citations 1kdh" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Boule JB]] | |||
[[Category: Boule | [[Category: Delarue M]] | ||
[[Category: Delarue | [[Category: Expert-Bezancon N]] | ||
[[Category: Expert-Bezancon | [[Category: Jourdan N]] | ||
[[Category: Jourdan | [[Category: Lescar J]] | ||
[[Category: Lescar | [[Category: Papanicolaou C]] | ||
[[Category: Papanicolaou | [[Category: Rougeon F]] | ||
[[Category: Rougeon | [[Category: Sukumar N]] | ||
[[Category: Sukumar | |||
Latest revision as of 08:56, 16 August 2023
Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA
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