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.


1mpg

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:47, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1mpg.gif|left|200px]]<br /><applet load="1mpg" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1mpg, resolution 1.80&Aring;" />
 
-
'''3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI'''<br />
 
-
==Overview==
+
==3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI==
-
Base-excision DNA repair proteins that target alkylation damage act on a variety of seemingly dissimilar adducts, yet fail to recognize other closely related lesions. The 1.8 A crystal structure of the monofunctional DNA glycosylase AlkA (E. coli 3-methyladenine-DNA glycosylase II) reveals a large hydrophobic cleft unusually rich in aromatic residues. An Asp residue projecting into this cleft is essential for catalysis, and it governs binding specificity for mechanism-based inhibitors. We propose that AlkA recognizes electron-deficient methylated bases through pi-donor/acceptor interactions involving the electron-rich aromatic cleft. Remarkably, AlkA is similar in fold and active site location to the bifunctional glycosylase/lyase endonuclease III, suggesting the two may employ fundamentally related mechanisms for base excision.
+
<StructureSection load='1mpg' size='340' side='right'caption='[[1mpg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1mpg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MPG FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mpg OCA], [https://pdbe.org/1mpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mpg RCSB], [https://www.ebi.ac.uk/pdbsum/1mpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mpg ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/3MG2_ECOLI 3MG2_ECOLI] Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine, 3-methylguanine, 7-methylguanine, O2-methylthymine, and O2-methylcytosine from the damaged DNA polymer formed by alkylation lesions.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mp/1mpg_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1mpg ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1MPG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-3-methyladenine_glycosylase_II DNA-3-methyladenine glycosylase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.21 3.2.2.21] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MPG OCA].
+
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Structural basis for the excision repair of alkylation-damaged DNA., Labahn J, Scharer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE, Cell. 1996 Jul 26;86(2):321-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8706136 8706136]
+
-
[[Category: DNA-3-methyladenine glycosylase II]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Ellenberger, T E.]]
+
[[Category: Ellenberger TE]]
-
[[Category: Ezaz-Nikpay, K.]]
+
[[Category: Ezaz-Nikpay K]]
-
[[Category: Labahn, J.]]
+
[[Category: Labahn J]]
-
[[Category: Long, A.]]
+
[[Category: Long A]]
-
[[Category: Schaerer, O D.]]
+
[[Category: Schaerer OD]]
-
[[Category: Verdine, G L.]]
+
[[Category: Verdine GL]]
-
[[Category: GOL]]
+
-
[[Category: alka]]
+
-
[[Category: base excision]]
+
-
[[Category: dna glycosylase]]
+
-
[[Category: dna repair]]
+
-
[[Category: hydrolase]]
+
-
[[Category: methylation]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:57:39 2008''
+

Current revision

3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI

PDB ID 1mpg

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/1mpg"
Personal tools