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.


4z3a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:12, 27 September 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU mismatch==
==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=''>
+
<StructureSection load='4z3a' size='340' side='right'caption='[[4z3a]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4z3a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z3A FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4z3a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z3A FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
-
<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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4z3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z3a OCA], [https://pdbe.org/4z3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z3a RCSB], [https://www.ebi.ac.uk/pdbsum/4z3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z3a ProSAT]</span></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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z3a ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/TDG_HUMAN 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.
+
[https://www.uniprot.org/uniprot/TDG_HUMAN 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.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 21: Line 19:
</div>
</div>
<div class="pdbe-citations 4z3a" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 4z3a" style="background-color:#fffaf0;"></div>
 +
 +
==See Also==
 +
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Thymine-DNA glycosylase]]
+
[[Category: Homo sapiens]]
-
[[Category: Drohat, A C]]
+
[[Category: Large Structures]]
-
[[Category: Malik, S S]]
+
[[Category: Synthetic construct]]
-
[[Category: Pozharski, E]]
+
[[Category: Drohat AC]]
-
[[Category: Hydrolase-dna complex]]
+
[[Category: Malik SS]]
-
[[Category: Protein-dna complex]]
+
[[Category: Pozharski E]]

Current revision

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

PDB ID 4z3a

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/4z3a"
Personal tools