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.


2f5q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:43, 23 August 2023) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='2f5q' size='340' side='right'caption='[[2f5q]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
<StructureSection load='2f5q' size='340' side='right'caption='[[2f5q]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2f5q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5Q FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[2f5q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F5Q FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r2y|1r2y]], [[1l1t|1l1t]], [[2f5n|2f5n]], [[2f5o|2f5o]], [[2f5p|2f5p]], [[2f5s|2f5s]]</div></td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-formamidopyrimidine_glycosylase DNA-formamidopyrimidine glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.23 3.2.2.23] </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=2f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5q OCA], [https://pdbe.org/2f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5q RCSB], [https://www.ebi.ac.uk/pdbsum/2f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5q 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=2f5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f5q OCA], [https://pdbe.org/2f5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f5q RCSB], [https://www.ebi.ac.uk/pdbsum/2f5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f5q ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
+
[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 38: Line 36:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 12980]]
+
[[Category: Geobacillus stearothermophilus]]
-
[[Category: DNA-formamidopyrimidine glycosylase]]
+
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Banerjee, A]]
+
[[Category: Banerjee A]]
-
[[Category: Santos, W L]]
+
[[Category: Santos WL]]
-
[[Category: Verdine, G L]]
+
[[Category: Verdine GL]]
-
[[Category: Control complex]]
+
-
[[Category: Damage search]]
+
-
[[Category: Disulfide crosslink]]
+
-
[[Category: Dna glycosylase]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Hydrolase-dna complex]]
+

Current revision

Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2

PDB ID 2f5q

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2f5q"
Personal tools