1kdh: Difference between revisions
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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[[Image:1kdh.jpg|left|200px]]<br /><applet load="1kdh" size=" | [[Image:1kdh.jpg|left|200px]]<br /><applet load="1kdh" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1kdh, resolution 3.00Å" /> | caption="1kdh, resolution 3.00Å" /> | ||
'''Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA'''<br /> | '''Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA'''<br /> | ||
==Overview== | ==Overview== | ||
The crystal structure of the catalytic core of murine terminal | 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. | ||
==About this Structure== | ==About this Structure== | ||
1KDH 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 MG and NA 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:// | 1KDH 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 <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NA:'>NA</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1KDH OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Boule, J | [[Category: Boule, J B.]] | ||
[[Category: Delarue, M.]] | [[Category: Delarue, M.]] | ||
[[Category: Expert-Bezancon, N.]] | [[Category: Expert-Bezancon, N.]] | ||
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[[Category: polymerase]] | [[Category: polymerase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:32:57 2008'' | ||
Revision as of 14:33, 21 February 2008
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Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA
OverviewOverview
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.
About this StructureAbout this Structure
1KDH is a Single protein structure of sequence from Mus musculus with and as ligands. Active as DNA nucleotidylexotransferase, with EC number 2.7.7.31 Full crystallographic information is available from OCA.
ReferenceReference
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
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