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.


1jx4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:55, 3 April 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jx4.gif|left|200px]]<br /><applet load="1jx4" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1jx4, resolution 1.70&Aring;" />
 
-
'''Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide'''<br />
 
-
==Overview==
+
==Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide==
-
Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions. Crystal structures of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, have been solved at 1.7 A and 2.1 A resolution, respectively. Despite a conserved active site and a hand-like configuration similar to all known polymerases, Dpo4 makes limited and nonspecific contacts with the replicating base pair, thus relaxing base selection. Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers.
+
<StructureSection load='1jx4' size='340' side='right'caption='[[1jx4]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1jx4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JX4 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]] 1.7&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADI:2,3-DIDEOXYADENOSINE-5-DIPHOSPHATE'>ADI</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1jx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jx4 OCA], [https://pdbe.org/1jx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jx4 RCSB], [https://www.ebi.ac.uk/pdbsum/1jx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jx4 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
 +
== 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/jx/1jx4_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=1jx4 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1JX4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ADI:'>ADI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1JX4 OCA].
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication., Ling H, Boudsocq F, Woodgate R, Yang W, Cell. 2001 Oct 5;107(1):91-102. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11595188 11595188]
+
[[Category: Large Structures]]
-
[[Category: DNA-directed DNA polymerase]]
+
[[Category: Saccharolobus solfataricus]]
-
[[Category: Single protein]]
+
[[Category: Boudsocq F]]
-
[[Category: Sulfolobus solfataricus]]
+
[[Category: Ling H]]
-
[[Category: Boudsocq, F.]]
+
[[Category: Woodgate R]]
-
[[Category: Ling, H.]]
+
[[Category: Yang W]]
-
[[Category: Woodgate, R.]]
+
-
[[Category: Yang, W.]]
+
-
[[Category: ADI]]
+
-
[[Category: CA]]
+
-
[[Category: MG]]
+
-
[[Category: dna polymerase]]
+
-
[[Category: protein-dna complex]]
+
-
[[Category: y-family]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:27:41 2008''
+

Current revision

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

PDB ID 1jx4

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/1jx4"
Personal tools