1xqo

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[[Image:1xqo.jpg|left|200px]]
 
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==Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum==
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The line below this paragraph, containing "STRUCTURE_1xqo", creates the "Structure Box" on the page.
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<StructureSection load='1xqo' size='340' side='right'caption='[[1xqo]], [[Resolution|resolution]] 1.03&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'>[[1xqo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XQO 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]] 1.03&#8491;</td></tr>
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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=1xqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqo OCA], [https://pdbe.org/1xqo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xqo RCSB], [https://www.ebi.ac.uk/pdbsum/1xqo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqo ProSAT]</span></td></tr>
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{{STRUCTURE_1xqo| PDB=1xqo | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AGOG_PYRAE AGOG_PYRAE] DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates.<ref>PMID:15604455</ref>
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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/xq/1xqo_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1xqo 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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Studies of DNA base excision repair (BER) pathways in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum identified an 8-oxoguanine-DNA glycosylase, Pa-AGOG (archaeal GO glycosylase), with distinct functional characteristics. Here, we describe its crystal structure and that of its complex with 8-oxoguanosine at 1.0 and 1.7 A resolution, respectively. Characteristic structural features are identified that confirm Pa-AGOG to be the founding member of a functional class within the helix-hairpin-helix (HhH) superfamily of DNA repair enzymes. Its hairpin structure differs substantially from that of other proteins containing an HhH motif, and we predict that it interacts with the DNA backbone in a distinct manner. Furthermore, the mode of 8-oxoguanine recognition, which involves several hydrogen-bonding and pi-stacking interactions, is unlike that observed in human OGG1, the prototypic 8-oxoguanine HhH-type DNA glycosylase. Despite these differences, the predicted kinked conformation of bound DNA and the catalytic mechanism are likely to resemble those of human OGG1.
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'''Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum'''
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A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.,Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK Structure. 2005 Jan;13(1):87-98. PMID:15642264<ref>PMID:15642264</ref>
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==Overview==
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Studies of DNA base excision repair (BER) pathways in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum identified an 8-oxoguanine-DNA glycosylase, Pa-AGOG (archaeal GO glycosylase), with distinct functional characteristics. Here, we describe its crystal structure and that of its complex with 8-oxoguanosine at 1.0 and 1.7 A resolution, respectively. Characteristic structural features are identified that confirm Pa-AGOG to be the founding member of a functional class within the helix-hairpin-helix (HhH) superfamily of DNA repair enzymes. Its hairpin structure differs substantially from that of other proteins containing an HhH motif, and we predict that it interacts with the DNA backbone in a distinct manner. Furthermore, the mode of 8-oxoguanine recognition, which involves several hydrogen-bonding and pi-stacking interactions, is unlike that observed in human OGG1, the prototypic 8-oxoguanine HhH-type DNA glycosylase. Despite these differences, the predicted kinked conformation of bound DNA and the catalytic mechanism are likely to resemble those of human OGG1.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1XQO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQO OCA].
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</div>
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<div class="pdbe-citations 1xqo" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure., Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK, Structure. 2005 Jan;13(1):87-98. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15642264 15642264]
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrobaculum aerophilum]]
[[Category: Pyrobaculum aerophilum]]
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[[Category: Single protein]]
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[[Category: Jiricny J]]
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[[Category: Jiricny, J.]]
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[[Category: Kostrewa D]]
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[[Category: Kostrewa, D.]]
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[[Category: Lingaraju GM]]
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[[Category: Lingaraju, G M.]]
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[[Category: Prota AE]]
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[[Category: Prota, A E.]]
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[[Category: Sartori AA]]
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[[Category: Sartori, A A.]]
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[[Category: Winkler FK]]
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[[Category: Winkler, F K.]]
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[[Category: 8-oxoguanine dna glycosylase]]
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[[Category: Archaea]]
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[[Category: Dna repair]]
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[[Category: Helix-hairpin-helix]]
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[[Category: P aerophilum]]
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[[Category: Pa-agog native]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:22:51 2008''
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Current revision

Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum

PDB ID 1xqo

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