2fms
From Proteopedia
(New page: 200px<br /> <applet load="2fms" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fms, resolution 2.00Å" /> '''DNA Polymerase beta...) |
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| - | [[Image:2fms.gif|left|200px]]<br /> | + | [[Image:2fms.gif|left|200px]]<br /><applet load="2fms" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="2fms" size=" | + | |
caption="2fms, resolution 2.00Å" /> | caption="2fms, resolution 2.00Å" /> | ||
'''DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site'''<br /> | '''DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The molecular details of the nucleotidyl transferase reaction have | + | The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide. |
==About this Structure== | ==About this Structure== | ||
| - | 2FMS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, NA, CL and DUP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 2FMS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=DUP:'>DUP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FMS OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Batra, V | + | [[Category: Batra, V K.]] |
| - | [[Category: Beard, W | + | [[Category: Beard, W A.]] |
| - | [[Category: Krahn, J | + | [[Category: Krahn, J M.]] |
| - | [[Category: Pedersen, L | + | [[Category: Pedersen, L C.]] |
| - | [[Category: Shock, D | + | [[Category: Shock, D D.]] |
| - | [[Category: Wilson, S | + | [[Category: Wilson, S H.]] |
[[Category: CL]] | [[Category: CL]] | ||
[[Category: DUP]] | [[Category: DUP]] | ||
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[[Category: nucleotidyl transferase]] | [[Category: nucleotidyl transferase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:23:00 2008'' |
Revision as of 15:23, 21 February 2008
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DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site
Overview
The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.
About this Structure
2FMS is a Single protein structure of sequence from Homo sapiens with , , and as ligands. Full crystallographic information is available from OCA.
Reference
Magnesium-induced assembly of a complete DNA polymerase catalytic complex., Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH, Structure. 2006 Apr;14(4):757-66. PMID:16615916
Page seeded by OCA on Thu Feb 21 17:23:00 2008
Categories: Homo sapiens | Single protein | Batra, V K. | Beard, W A. | Krahn, J M. | Pedersen, L C. | Shock, D D. | Wilson, S H. | CL | DUP | MG | NA | Nucleotidyl transferase
