1xqp

From Proteopedia

(Difference between revisions)

Revision as of 10:15, 6 January 2021

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

Structural highlights

1xqp is a 1 chain structure with sequence from Atcc 51768. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1xqo
Gene:	Pa-AGOG (ATCC 51768)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1]

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

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.

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^[2]

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

References

↑ Sartori AA, Lingaraju GM, Hunziker P, Winkler FK, Jiricny J. Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases. Nucleic Acids Res. 2004 Dec 16;32(22):6531-9. Print 2004. PMID:15604455 doi:http://dx.doi.org/10.1093/nar/gkh995
↑ Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK. A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure. Structure. 2005 Jan;13(1):87-98. PMID:15642264 doi:10.1016/j.str.2004.10.011

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xqp"

@@ Line 1: / Line 1: @@
 ==Crystal structure of 8-oxoguanosine complexed Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum==
-<StructureSection load='1xqp' size='340' side='right' caption='[[1xqp]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
+<StructureSection load='1xqp' size='340' side='right'caption='[[1xqp]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xqp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xqp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XQP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8HG:2-DEOXY-8-OXOGUANOSINE'>8HG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8HG:2-DEOXY-8-OXOGUANOSINE'>8HG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xqo|1xqo]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xqo|1xqo]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pa-AGOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqp OCA], [http://pdbe.org/1xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqp RCSB], [http://www.ebi.ac.uk/pdbsum/1xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqp ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqp OCA], [http://pdbe.org/1xqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqp RCSB], [http://www.ebi.ac.uk/pdbsum/1xqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqp ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xq/1xqp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xq/1xqp_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 38: @@
 </StructureSection>
 [[Category: Atcc 51768]]
+[[Category: Large Structures]]
 [[Category: Jiricny, J]]
 [[Category: Kostrewa, D]]

1xqp

From Proteopedia

Revision as of 10:15, 6 January 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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