3gde

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{{Seed}}
 
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[[Image:3gde.jpg|left|200px]]
 
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==The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus==
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The line below this paragraph, containing "STRUCTURE_3gde", creates the "Structure Box" on the page.
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<StructureSection load='3gde' size='340' side='right'caption='[[3gde]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3gde]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GDE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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{{STRUCTURE_3gde| PDB=3gde | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gde OCA], [https://pdbe.org/3gde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gde RCSB], [https://www.ebi.ac.uk/pdbsum/3gde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gde ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DNLI_ARCFU DNLI_ARCFU] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/3gde_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3gde ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA ligases join the breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 3'-hydroxyl and 5'-phosphate termini. They fall into two classes that require either ATP or NAD(+) as the source of an AMP group that is covalently attached to a strictly conserved lysine. Conformational flexibility is essential for the function of multi-domain DNA ligases because they must undergo large conformational changes involving domain rearrangements during the course of the reaction. In the absence of the nicked DNA substrate, both open and closed conformations have been observed for the ATP-dependent DNA ligases from Sulfolobus solfataricus and Pyrococcus furiosus. Here, the crystal structure of an ATP-dependent DNA ligase from Archaeoglobus fulgidus has been determined in the DNA-unbound unadenylated state. It resembles the closed conformation of P. furiosus DNA ligase but was even more closed, thus enhancing our understanding of the conformational variability of these enzymes.
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===The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus===
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ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation.,Kim do J, Kim O, Kim HW, Kim HS, Lee SJ, Suh SW Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt, 6):544-50. Epub 2009 May 22. PMID:19478428<ref>PMID:19478428</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3gde" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19478428}}, adds the Publication Abstract to the page
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*[[DNA ligase 3D structures|DNA ligase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19478428 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19478428}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3GDE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GDE OCA].
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==Reference==
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<ref group="xtra">PMID:19478428</ref><references group="xtra"/>
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[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Kim, D J.]]
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[[Category: Large Structures]]
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[[Category: Kim, H S.]]
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[[Category: Kim DJ]]
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[[Category: Kim, H W.]]
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[[Category: Kim H-W]]
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[[Category: Kim, O.]]
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[[Category: Kim HS]]
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[[Category: Lee, S J.]]
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[[Category: Kim O]]
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[[Category: Suh, S W.]]
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[[Category: Lee SJ]]
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[[Category: Adenylation domain]]
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[[Category: Suh SW]]
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[[Category: Atp-binding]]
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[[Category: Atp-dependent dna ligase]]
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[[Category: Cell cycle]]
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[[Category: Cell division]]
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[[Category: Dna damage]]
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[[Category: Dna recombination]]
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[[Category: Dna repair]]
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[[Category: Dna replication]]
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[[Category: Dna-binding domain]]
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[[Category: Ligase]]
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[[Category: Nucleotide-binding]]
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[[Category: Ob-fold domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 13:25:34 2009''
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Current revision

The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus

PDB ID 3gde

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