6u7t

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "6u7t" [edit=sysop:move=sysop])
Line 3: Line 3:
<StructureSection load='6u7t' size='340' side='right'caption='[[6u7t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='6u7t' size='340' side='right'caption='[[6u7t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6u7t]] is a 3 chain structure. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5dpk 5dpk] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fsq 3fsq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U7T FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6u7t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5dpk 5dpk] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fsq 3fsq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U7T FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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>, <scene name='pdbligand=NR1:(3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM'>NR1</scene></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>, <scene name='pdbligand=NR1:(3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM'>NR1</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6q0c|6q0c]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6q0c|6q0c]]</td></tr>
 +
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mutY ([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/Adenine_glycosylase Adenine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.31 3.2.2.31] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_glycosylase Adenine glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.31 3.2.2.31] </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=6u7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u7t OCA], [http://pdbe.org/6u7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u7t RCSB], [http://www.ebi.ac.uk/pdbsum/6u7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u7t ProSAT]</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=6u7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u7t OCA], [http://pdbe.org/6u7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u7t RCSB], [http://www.ebi.ac.uk/pdbsum/6u7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u7t ProSAT]</span></td></tr>
Line 12: Line 13:
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/MUTY_GEOSE MUTY_GEOSE]] Base excision repair (BER) glycosylase that initiates repair of A:oxoG to C:G by removing the inappropriately paired adenine base from the DNA backbone, generating an abasic site product (PubMed:25995449) (PubMed:14961129). 8-oxoguanine (oxoG) is a genotoxic DNA lesion resulting from oxidation of guanine; this residue is misread by replicative DNA polymerases, that insert adenine instead of cytosine opposite the oxidized damaged base. Shows a powerful dicrimination of A versus C, since it does not cleave cytosine in oxoG:C pairs (PubMed:25995449). May also be able to remove adenine from A:G mispairs, although this activity may not be physiologically relevant (PubMed:14961129).<ref>PMID:25995449</ref> <ref>PMID:14961129</ref>
[[http://www.uniprot.org/uniprot/MUTY_GEOSE MUTY_GEOSE]] Base excision repair (BER) glycosylase that initiates repair of A:oxoG to C:G by removing the inappropriately paired adenine base from the DNA backbone, generating an abasic site product (PubMed:25995449) (PubMed:14961129). 8-oxoguanine (oxoG) is a genotoxic DNA lesion resulting from oxidation of guanine; this residue is misread by replicative DNA polymerases, that insert adenine instead of cytosine opposite the oxidized damaged base. Shows a powerful dicrimination of A versus C, since it does not cleave cytosine in oxoG:C pairs (PubMed:25995449). May also be able to remove adenine from A:G mispairs, although this activity may not be physiologically relevant (PubMed:14961129).<ref>PMID:25995449</ref> <ref>PMID:14961129</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indicate a catalytic role for Tyr126 and approach of the water nucleophile on the same side as the departing adenine base. The idea that Tyr126 participates in catalysis, recently predicted by modeling calculations, is strongly supported by mutagenesis and by seeing close contact between the hydroxyl group of this residue and the azaribose moiety of the transition state analog. NMR analysis of MutY methanolysis products corroborates a mechanism for adenine removal with retention of stereochemistry. Based on these results, we propose a revised mechanism for MutY that involves two nucleophilic displacement steps akin to the mechanisms accepted for 'retaining' O-glycosidases. This new-for-MutY yet familiar mechanism may also be operative in related base excision repair glycosylases and provides a critical framework for analysis of human MutY (MUTYH) variants associated with inherited colorectal cancer.
 +
 +
Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.,Woods RD, O'Shea VL, Chu A, Cao S, Richards JL, Horvath MP, David SS Nucleic Acids Res. 2015 Dec 15. pii: gkv1469. PMID:26673696<ref>PMID:26673696</ref>
 +
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 6u7t" style="background-color:#fffaf0;"></div>
 +
 +
==See Also==
 +
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 17: Line 30:
</StructureSection>
</StructureSection>
[[Category: Adenine glycosylase]]
[[Category: Adenine glycosylase]]
 +
[[Category: Atcc 12980]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cao, S]]
[[Category: Cao, S]]

Revision as of 11:52, 13 November 2019

MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)

PDB ID 6u7t

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/6u7t"
Personal tools