This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3f0z

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:21, 23 February 2022

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in its apo-form

Structural highlights

3f0z is a 1 chain structure with sequence from "clostridium_acetobutyricum"_prevot_1940 "clostridium acetobutyricum" prevot 1940. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	3f10
Gene:	CAC2707, CA_C2707 ("Clostridium acetobutyricum" Prevot 1940)
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

DNA is subject to a multitude of oxidative damages generated by oxidizing agents from metabolism and exogenous sources and by ionizing radiation. Guanine is particularly vulnerable to oxidation, and the most common oxidative product 8-oxoguanine (8-oxoG) is the most prevalent lesion observed in DNA molecules. 8-OxoG can form a normal Watson-Crick pair with cytosine (8-oxoG:C), but it can also form a stable Hoogsteen pair with adenine (8-oxoG:A), leading to a G:C-->T:A transversion after replication. Fortunately, 8-oxoG is recognized and excised by either of two DNA glycosylases of the base excision repair pathway: formamidopyrimidine-DNA glycosylase and 8-oxoguanine DNA glycosylase (Ogg). While Clostridium acetobutylicum Ogg (CacOgg) DNA glycosylase can specifically recognize and remove 8-oxoG, it displays little preference for the base opposite the lesion, which is unusual for a member of the Ogg1 family. This work describes the crystal structures of CacOgg in its apo form and in complex with 8-oxo-2'-deoxyguanosine. A structural comparison between the apo form and the liganded form of the enzyme reveals a structural reorganization of the C-terminal domain upon binding of 8-oxoG, similar to that reported for human OGG1. A structural comparison of CacOgg with human OGG1, in complex with 8-oxoG containing DNA, provides a structural rationale for the lack of opposite base specificity displayed by CacOgg.

Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine.,Faucher F, Robey-Bond SM, Wallace SS, Doublie S J Mol Biol. 2009 Apr 3;387(3):669-79. Epub 2009 Feb 9. PMID:19361427^[1]

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

References

↑ Faucher F, Robey-Bond SM, Wallace SS, Doublie S. Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine. J Mol Biol. 2009 Apr 3;387(3):669-79. Epub 2009 Feb 9. PMID:19361427 doi:10.1016/j.jmb.2009.01.067

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f0z"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in its apo-form==
-<StructureSection load='3f0z' size='340' side='right' caption='[[3f0z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3f0z' size='340' side='right'caption='[[3f0z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_acetobutyricum"_prevot_1940 "clostridium acetobutyricum" prevot 1940]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"clostridium_acetobutyricum"_prevot_1940 "clostridium acetobutyricum" prevot 1940]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f10|3f10]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f10|3f10]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAC2707, CA_C2707 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1488 "Clostridium acetobutyricum" Prevot 1940])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAC2707, CA_C2707 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1488 "Clostridium acetobutyricum" Prevot 1940])</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=3f0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0z OCA], [http://pdbe.org/3f0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f0z RCSB], [http://www.ebi.ac.uk/pdbsum/3f0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0z ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3f0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0z OCA], [https://pdbe.org/3f0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0z RCSB], [https://www.ebi.ac.uk/pdbsum/3f0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0z ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Clostridium acetobutyricum prevot 1940]]
+[[Category: Large Structures]]
 [[Category: Doublie, S]]
 [[Category: Faucher, F]]

3f0z

From Proteopedia

Revision as of 09:21, 23 February 2022

Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in its apo-form

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox