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4z3a

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Revision as of 06:18, 6 October 2017

Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch

Structural highlights

4z3a is a 3 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	4xeg, 4z47, 4z7b, 4z7z, 5cys
Activity:	Thymine-DNA glycosylase, with EC number 3.2.2.29
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TDG_HUMAN] In the DNA of higher eukaryotes, hydrolytic deamination of 5-methylcytosine to thymine leads to the formation of G/T mismatches. This enzyme corrects G/T mispairs to G/C pairs. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, it can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA. It can also remove uracil and 5-bromouracil from mispairs with guanine.

Publication Abstract from PubMed

Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G .: T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten-eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 A) structures of TDG enzyme-product complexes generated from substrates including G.U, G.T, G.hmU, G.fC and G.caC. The structures reveal many new features, including key water-mediated enzyme-substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme-product complex.

Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.,Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC Nucleic Acids Res. 2015 Sep 10. pii: gkv890. PMID:26358812^[1]

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

References

↑ Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC. Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA. Nucleic Acids Res. 2015 Sep 10. pii: gkv890. PMID:26358812 doi:http://dx.doi.org/10.1093/nar/gkv890

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4z3a"

@@ Line 1: / Line 1: @@
 ==Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch==
 <StructureSection load='4z3a' size='340' side='right' caption='[[4z3a]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xeg|4xeg]], [[4z47|4z47]], [[4z7b|4z7b]], [[4z7z|4z7z]], [[5cys|5cys]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymine-DNA_glycosylase Thymine-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.29 3.2.2.29] </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=4z3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z3a OCA], [http://pdbe.org/4z3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z3a RCSB], [http://www.ebi.ac.uk/pdbsum/4z3a 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=4z3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z3a OCA], [http://pdbe.org/4z3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z3a RCSB], [http://www.ebi.ac.uk/pdbsum/4z3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z3a ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 21: @@
 </div>
 <div class="pdbe-citations 4z3a" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA glycosylase|DNA glycosylase]]
 == References ==
 <references/>

4z3a

From Proteopedia

Revision as of 06:18, 6 October 2017

Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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