This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2ex3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2ex3" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ex3, resolution 3.000&Aring;" /> '''Bacteriophage phi29...)
Current revision (09:20, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ex3.gif|left|200px]]<br /><applet load="2ex3" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2ex3, resolution 3.000&Aring;" />
 
-
'''Bacteriophage phi29 DNA polymerase bound to terminal protein'''<br />
 
-
==Overview==
+
==Bacteriophage phi29 DNA polymerase bound to terminal protein==
-
The absolute requirement for primers in the initiation of DNA synthesis, poses a problem for replicating the ends of linear chromosomes. The DNA, polymerase of bacteriophage phi29 solves this problem by using a serine, hydroxyl of terminal protein to prime replication. The 3.0 A resolution, structure shows one domain of terminal protein making no interactions, a, second binding the polymerase and a third domain containing the priming, serine occupying the same binding cleft in the polymerase as duplex DNA, does during elongation. Thus, the progressively elongating DNA duplex, product must displace this priming domain. Further, this heterodimer of, polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at, the ends of the bacteriophage genome. We propose a model for the, transition from the initiation to the elongation phases in which the, priming domain of terminal protein moves out of the active site as, polymerase elongates the primer strand. The model indicates that terminal, protein should dissociate from polymerase after the incorporation of, approximately six nucleotides.
+
<StructureSection load='2ex3' size='340' side='right'caption='[[2ex3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2ex3]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EX3 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ex3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ex3 OCA], [https://pdbe.org/2ex3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ex3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ex3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ex3 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2ex3_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ex3 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2EX3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with PB as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2EX3 OCA].
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition., Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2006 Mar 22;25(6):1335-43. Epub 2006 Mar 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16511564 16511564]
+
[[Category: Bacillus virus phi29]]
-
[[Category: DNA-directed DNA polymerase]]
+
[[Category: Large Structures]]
-
[[Category: Protein complex]]
+
[[Category: Berman AJ]]
-
[[Category: Vibrio phage f237]]
+
[[Category: Blanco L]]
-
[[Category: Berman, A.J.]]
+
[[Category: Kamtekar S]]
-
[[Category: Blanco, L.]]
+
[[Category: Salas M]]
-
[[Category: Kamtekar, S.]]
+
[[Category: Steitz TA]]
-
[[Category: Salas, M.]]
+
[[Category: Wang J]]
-
[[Category: Steitz, T.A.]]
+
[[Category: De Vega M]]
-
[[Category: Vega, M.de.]]
+
-
[[Category: Wang, J.]]
+
-
[[Category: PB]]
+
-
[[Category: dna polymerase: protein primer complex]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:11:56 2007''
+

Current revision

Bacteriophage phi29 DNA polymerase bound to terminal protein

PDB ID 2ex3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ex3"
Personal tools