3n9b

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[[Image:3n9b.jpg|left|200px]]
 
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==Crystal Structure of the P. aeruginosa LigD phosphoesterase domain==
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The line below this paragraph, containing "STRUCTURE_3n9b", creates the "Structure Box" on the page.
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<StructureSection load='3n9b' size='340' side='right'caption='[[3n9b]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
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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'>[[3n9b]] 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=3N9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N9B FirstGlance]. <br>
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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]] 1.92&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene></td></tr>
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{{STRUCTURE_3n9b| PDB=3n9b | 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=3n9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9b OCA], [https://pdbe.org/3n9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n9b RCSB], [https://www.ebi.ac.uk/pdbsum/3n9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n9b ProSAT]</span></td></tr>
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</table>
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===Phosphoesterase===
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== Function ==
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[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.
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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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(as it appears on PubMed at http://www.pubmed.gov), where 20616014 is the PubMed ID number.
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n9/3n9b_consurf.spt"</scriptWhenChecked>
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{{ABSTRACT_PUBMED_20616014}}
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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3N9B is a 2 chains structure with sequences 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=3N9B OCA].
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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=3n9b ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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<ref group="xtra">PMID:20616014</ref><references group="xtra"/>
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
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[[Category: Nair, P.]]
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[[Category: Nair P]]
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[[Category: Shuman, S.]]
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[[Category: Shuman S]]
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[[Category: Smith, P.]]
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[[Category: Smith P]]
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[[Category: Beta barrel]]
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[[Category: Ligase]]
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[[Category: Manganese]]
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[[Category: Metalloenzyme]]
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[[Category: Nhej]]
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[[Category: Phosphoesterase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 11 23:58:43 2010''
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Current revision

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

PDB ID 3n9b

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