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4pe8

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Crystal structure of TatD in complex with trinucleotide DNA

Structural highlights

4pe8 is a 2 chain structure with sequence from Escherichia coli K-12 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.894Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TATD_ECOLI Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Although TatD is not required for export activity, it is a central component of a quality control system that is linked to the Tat translocation system. May act by degrading wild-type pre-protein molecules that are misfolded. Shows magnesium-dependent DNase activity.^[1] ^[2]

Publication Abstract from PubMed

TatD is an evolutionarily conserved protein with thousands of homologues in all kingdoms of life. It has been suggested that TatD participates in DNA fragmentation during apoptosis in eukaryotic cells. However, the cellular functions and biochemical properties of TatD in bacterial and non-apoptotic eukaryotic cells remain elusive. Here we show that Escherichia coli TatD is a Mg2+-dependent 3'-5' exonuclease that prefers to digest single-stranded DNA and RNA. TatD-knockout cells are less resistant to the DNA damaging agent hydrogen peroxide, and TatD can remove damaged deaminated nucleotides from a DNA chain, suggesting that it may play a role in the H2O2-induced DNA repair. The crystal structure of the apo-form TatD and TatD bound to a single-stranded three-nucleotide DNA was determined by X-ray diffraction methods at a resolution of 2.0 and 2.9 A, respectively. TatD has a TIM-barrel fold and the single-stranded DNA is bound at the loop region on the top of the barrel. Mutational studies further identify important conserved metal ion-binding and catalytic residues in the TatD active site for DNA hydrolysis. We thus conclude that TatD is a new class of TIM-barrel 3'-5' exonuclease that not only degrades chromosomal DNA during apoptosis but also processes single-stranded DNA during DNA repair.

Structure and function of TatD exonuclease in DNA repair.,Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS Nucleic Acids Res. 2014 Aug 11. pii: gku732. PMID:25114049^[3]

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

References

↑ Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T. TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export. J Biol Chem. 2000 Jun 2;275(22):16717-22. PMID:10747959 doi:10.1074/jbc.M000800200
↑ Matos CF, Di Cola A, Robinson C. TatD is a central component of a Tat translocon-initiated quality control system for exported FeS proteins in Escherichia coli. EMBO Rep. 2009 May;10(5):474-9. doi: 10.1038/embor.2009.34. Epub 2009 Apr 3. PMID:19343049 doi:10.1038/embor.2009.34
↑ Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS. Structure and function of TatD exonuclease in DNA repair. Nucleic Acids Res. 2014 Aug 11. pii: gku732. PMID:25114049 doi:http://dx.doi.org/10.1093/nar/gku732

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4pe8"

@@ Line 1: / Line 1: @@
 ==Crystal structure of TatD in complex with trinucleotide DNA==
-<StructureSection load='4pe8' size='340' side='right' caption='[[4pe8]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
+<StructureSection load='4pe8' size='340' side='right'caption='[[4pe8]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pe8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PE8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PE8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pe8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] 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=4PE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PE8 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4p5u|4p5u]]</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]] 2.894&#8491;</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=4pe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pe8 OCA], [http://pdbe.org/4pe8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pe8 RCSB], [http://www.ebi.ac.uk/pdbsum/4pe8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pe8 ProSAT]</span></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=4pe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pe8 OCA], [https://pdbe.org/4pe8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pe8 RCSB], [https://www.ebi.ac.uk/pdbsum/4pe8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pe8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TATD_ECOLI TATD_ECOLI]] Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Although TatD is not required for export activity, it is a central component of a quality control system that is linked to the Tat translocation system. May act by degrading wild-type pre-protein molecules that are misfolded. Shows magnesium-dependent DNase activity.<ref>PMID:10747959</ref> <ref>PMID:19343049</ref>
+[https://www.uniprot.org/uniprot/TATD_ECOLI TATD_ECOLI] Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. Although TatD is not required for export activity, it is a central component of a quality control system that is linked to the Tat translocation system. May act by degrading wild-type pre-protein molecules that are misfolded. Shows magnesium-dependent DNase activity.<ref>PMID:10747959</ref> <ref>PMID:19343049</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Chen, Y]]
+[[Category: Escherichia coli K-12]]
-[[Category: Duh, Y]]
+[[Category: Large Structures]]
-[[Category: Hsiao, Y Y]]
+[[Category: Synthetic construct]]
-[[Category: Li, C L]]
+[[Category: Chen Y]]
-[[Category: Yuan, H S]]
+[[Category: Duh Y]]
-[[Category: Dna processing]]
+[[Category: Hsiao Y-Y]]
-[[Category: Dna repair]]
+[[Category: Li C-L]]
-[[Category: Exonuclease]]
+[[Category: Yuan HS]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Tim barrel]]

4pe8

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Current revision

Crystal structure of TatD in complex with trinucleotide DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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