2fao: Difference between revisions

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{{Seed}}
[[Image:2fao.png|left|200px]]


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==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain==
The line below this paragraph, containing "STRUCTURE_2fao", creates the "Structure Box" on the page.
<StructureSection load='2fao' size='340' side='right'caption='[[2fao]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2fao]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAO FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_2fao| PDB=2fao |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fao OCA], [https://pdbe.org/2fao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fao RCSB], [https://www.ebi.ac.uk/pdbsum/2fao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fao ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LIGD_PSEAE LIGD_PSEAE] With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.<ref>PMID:15897197</ref> <ref>PMID:16046407</ref> <ref>PMID:20018881</ref>  The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.
== 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/fa/2fao_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=2fao ConSurf].
<div style="clear:both"></div>


===Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain===
==See Also==
 
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 
== References ==
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<references/>
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(as it appears on PubMed at http://www.pubmed.gov), where 16446439 is the PubMed ID number.
</StructureSection>
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[[Category: Large Structures]]
{{ABSTRACT_PUBMED_16446439}}
 
==About this Structure==
2FAO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAO OCA].
 
==Reference==
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D., Zhu H, Nandakumar J, Aniukwu J, Wang LK, Glickman MS, Lima CD, Shuman S, Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1711-6. Epub 2006 Jan 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16446439 16446439]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Single protein]]
[[Category: Aniukwu J]]
[[Category: Aniukwu, J.]]
[[Category: Glickman MS]]
[[Category: Glickman, M S.]]
[[Category: Lima CD]]
[[Category: Lima, C D.]]
[[Category: Nandakumar J]]
[[Category: Nandakumar, J.]]
[[Category: Shuman S]]
[[Category: Shuman, S.]]
[[Category: Wang LK]]
[[Category: Wang, L K.]]
[[Category: Zhu H]]
[[Category: Zhu, H.]]
[[Category: Ligase]]
[[Category: Nhej]]
[[Category: Polymerase]]
[[Category: Primase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:06:24 2008''
Retrieved from "https://proteopedia.org/2fao"