2fms

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|PDB= 2fms |SIZE=350|CAPTION= <scene name='initialview01'>2fms</scene>, resolution 2.00&Aring;
|PDB= 2fms |SIZE=350|CAPTION= <scene name='initialview01'>2fms</scene>, resolution 2.00&Aring;
|SITE=
|SITE=
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=DUP:2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>
+
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=DUP:2&#39;-DEOXYURIDINE 5&#39;-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>
|ACTIVITY=
|ACTIVITY=
|GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
|GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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[[Category: nucleotidyl transferase]]
[[Category: nucleotidyl transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:54:26 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:06:27 2008''

Revision as of 13:06, 23 March 2008

Image:2fms.gif


PDB ID 2fms

Drag the structure with the mouse to rotate
, resolution 2.00Å
Ligands: , , and
Gene: POLB (Homo sapiens)
Coordinates: save as pdb, mmCIF, xml



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. 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

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