2fmq: Difference between revisions

Revision as of 04:04, 4 May 2008

Sodium in active site of DNA Polymerase Beta

OverviewOverview

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 StructureAbout this Structure

2FMQ is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

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 Sun May 4 04:04:45 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:2fmq.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2fmq |SIZE=350|CAPTION= <scene name='initialview01'>2fmq</scene>, resolution 2.20&Aring;
+The line below this paragraph, containing "STRUCTURE_2fmq", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DUP:2&#39;-DEOXYURIDINE+5&#39;-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+-->
-|DOMAIN=
+{{STRUCTURE_2fmq|  PDB=2fmq  |  SCENE=  }}
-|RELATEDENTRY=[[2fmp|2FMP]], [[2fms|2FMS]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fmq OCA], [http://www.ebi.ac.uk/pdbsum/2fmq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fmq RCSB]</span>
-}}
 '''Sodium in active site of DNA Polymerase Beta'''
@@ Line 32: / Line 29: @@
 [[Category: Shock, D D.]]
 [[Category: Wilson, S H.]]
-[[Category: nucleotidyl transferase]]
+[[Category: Nucleotidyl transferase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 04:04:45 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:04:57 2008''