1ngn
From Proteopedia
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==Mismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4== | ==Mismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4== | ||
| - | <StructureSection load='1ngn' size='340' side='right' caption='[[1ngn]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='1ngn' size='340' side='right'caption='[[1ngn]], [[Resolution|resolution]] 2.10Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1ngn]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1ngn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NGN FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ngn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ngn OCA], [https://pdbe.org/1ngn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ngn RCSB], [https://www.ebi.ac.uk/pdbsum/1ngn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ngn ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/MBD4_MOUSE MBD4_MOUSE] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein. |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ng/1ngn_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ng/1ngn_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</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=1ngn ConSurf]. | </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=1ngn ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | MBD4 is a member of the methyl-CpG-binding protein family. It contains two DNA binding domains, an amino-proximal methyl-CpG binding domain (MBD) and a C-terminal mismatch-specific glycosylase domain. Limited in vitro proteolysis of mouse MBD4 yields two stable fragments: a 139-residue fragment including the MBD, and the other 155-residue fragment including the glycosylase domain. Here we show that the latter fragment is active as a glycosylase on a DNA duplex containing a G:T mismatch within a CpG sequence context. The crystal structure confirmed the C-terminal domain is a member of the helix-hairpin-helix DNA glycosylase superfamily. The MBD4 active site is situated in a cleft that likely orients and binds DNA. Modeling studies suggest the mismatched target nucleotide will be flipped out into the active site where candidate residues for catalysis and substrate specificity are present. | ||
| - | + | ==See Also== | |
| - | + | *[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]] | |
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Bhagwat | + | [[Category: Mus musculus]] |
| - | [[Category: Cheng | + | [[Category: Bhagwat AS]] |
| - | [[Category: Qiu | + | [[Category: Cheng X]] |
| - | [[Category: Sohail | + | [[Category: Qiu C]] |
| - | [[Category: Wu | + | [[Category: Sohail A]] |
| - | [[Category: Zhang | + | [[Category: Wu P]] |
| - | + | [[Category: Zhang X]] | |
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Current revision
Mismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4
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Categories: Large Structures | Mus musculus | Bhagwat AS | Cheng X | Qiu C | Sohail A | Wu P | Zhang X
