1x9n: Difference between revisions

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[[Image:1x9n.png|left|200px]]


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==Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA==
The line below this paragraph, containing "STRUCTURE_1x9n", creates the "Structure Box" on the page.
<StructureSection load='1x9n' size='340' side='right'caption='[[1x9n]], [[Resolution|resolution]] 3.00&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'>[[1x9n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X9N 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]] 3&#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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_1x9n|  PDB=1x9n  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1x9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x9n OCA], [https://pdbe.org/1x9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x9n RCSB], [https://www.ebi.ac.uk/pdbsum/1x9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x9n ProSAT]</span></td></tr>
</table>
== 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/x9/1x9n_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1x9n ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication. Here we report the crystal structure of human DNA ligase I (residues 233 to 919) in complex with a nicked, 5' adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein-protein interface that may coordinate the joining of Okazaki fragments.


===Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA===
Human DNA ligase I completely encircles and partially unwinds nicked DNA.,Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T Nature. 2004 Nov 25;432(7016):473-8. PMID:15565146<ref>PMID:15565146</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15565146}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1x9n" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15565146 is the PubMed ID number.
-->
{{ABSTRACT_PUBMED_15565146}}
 
==About this Structure==
[[1x9n]] is a 4 chain structure of [[DNA ligase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X9N OCA].


==See Also==
==See Also==
*[[DNA ligase|DNA ligase]]
*[[DNA ligase 3D structures|DNA ligase 3D structures]]
*[[Ligases|Ligases]]
== References ==
 
<references/>
==Reference==
__TOC__
<ref group="xtra">PMID:015565146</ref><references group="xtra"/>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Brien, P J.O.]]
[[Category: Large Structures]]
[[Category: Ellenberger, T.]]
[[Category: Ellenberger T]]
[[Category: Pascal, J M.]]
[[Category: O'Brien PJ]]
[[Category: Tomkinson, A E.]]
[[Category: Pascal JM]]
[[Category: 5'-adenylated nicked dna]]
[[Category: Tomkinson AE]]
[[Category: Dna ligase]]
[[Category: Ligase-dna complex]]
[[Category: Protein-dna complex]]

Latest revision as of 03:39, 21 November 2024

Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNACrystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA

Structural highlights

1x9n is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication. Here we report the crystal structure of human DNA ligase I (residues 233 to 919) in complex with a nicked, 5' adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein-protein interface that may coordinate the joining of Okazaki fragments.

Human DNA ligase I completely encircles and partially unwinds nicked DNA.,Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T Nature. 2004 Nov 25;432(7016):473-8. PMID:15565146[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature. 2004 Nov 25;432(7016):473-8. PMID:15565146 doi:10.1038/nature03082

1x9n, resolution 3.00Å

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