2pyj: Difference between revisions

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[[Image:2pyj.gif|left|200px]]
[[Image:2pyj.gif|left|200px]]


{{Structure
<!--
|PDB= 2pyj |SIZE=350|CAPTION= <scene name='initialview01'>2pyj</scene>, resolution 2.03&Aring;
The line below this paragraph, containing "STRUCTURE_2pyj", 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=DGT:2&#39;-DEOXYGUANOSINE-5&#39;-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2&#39;,3&#39;-DIDEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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= 2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 Bacillus phage phi29])
-->
|DOMAIN=
{{STRUCTURE_2pyj| PDB=2pyj  | SCENE= }}  
|RELATEDENTRY=[[2py5|2PY5]], [[2pyl|2PYL]], [[2pzs|2PZS]]
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyj OCA], [http://www.ebi.ac.uk/pdbsum/2pyj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pyj RCSB]</span>
}}


'''Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)'''
'''Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)'''
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[[Category: Steitz, T A.]]
[[Category: Steitz, T A.]]
[[Category: Vega, M de.]]
[[Category: Vega, M de.]]
[[Category: protein-dna complex]]
[[Category: Protein-dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:01:15 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:42:21 2008''

Revision as of 11:01, 4 May 2008

File:2pyj.gif

Template:STRUCTURE 2pyj

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)


Overview

Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

About this Structure

2PYJ is a Single protein structure of sequence from Bacillus phage phi29. Full crystallographic information is available from OCA.

Reference

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604 Page seeded by OCA on Sun May 4 14:01:15 2008

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