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.

3gpu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:10, 1 November 2017

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex

Structural highlights

3gpu is a 3 chain structure with sequence from Atcc 12980. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	3gpp, 3gpx, 3gpy, 3gq3, 3gq4, 3gq5
Gene:	MutM (ATCC 12980)
Activity:	DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.,Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL Nature. 2009 Dec 10;462(7274):762-6. PMID:20010681^[1]

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

References

↑ Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL. Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature. 2009 Dec 10;462(7274):762-6. PMID:20010681 doi:10.1038/nature08561

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==
 <StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
@@ Line 8: / Line 9: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://pdbe.org/3gpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu PDBsum]</span></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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://pdbe.org/3gpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 31: / Line 32: @@
 </div>
 <div class="pdbe-citations 3gpu" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
 == References ==
 <references/>

3gpu

From Proteopedia

Revision as of 07:10, 1 November 2017

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox