5t5c: Difference between revisions

Latest revision as of 12:54, 4 October 2023

A Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme

Structural highlights

5t5c is a 6 chain structure with sequence from DNA launch vector pDE-GFP2 and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.851Å
Ligands:	MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EXOG_HUMAN Endo/exonuclease with nicking activity towards supercoiled DNA, a preference for single-stranded DNA and 5'-3' exonuclease activity.^[1]

Publication Abstract from PubMed

Human EXOG (hEXOG) is a 5'-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 A resolution, respectively. A Wing domain, absent in other betabetaalpha-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5'-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic 'tape-measure'. The symmetrical apo hEXOG homodimer becomes asymmetrical upon binding to DNA, providing a structural basis for how substrate DNA bound to one active site allosterically regulates the activity of the other. These properties of hEXOG suggest a pathway for mitochondrial BER that provides an optimal substrate for subsequent gap-filling synthesis by DNA polymerase gamma.

A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease.,Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW Nat Commun. 2017 May 3;8:14959. doi: 10.1038/ncomms14959. PMID:28466855^[2]

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

References

↑ Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G. EXOG, a novel paralog of Endonuclease G in higher eukaryotes. Nucleic Acids Res. 2008 Mar;36(4):1369-79. doi: 10.1093/nar/gkm1169. Epub 2008, Jan 10. PMID:18187503 doi:https://dx.doi.org/10.1093/nar/gkm1169
↑ Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW. A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease. Nat Commun. 2017 May 3;8:14959. doi: 10.1038/ncomms14959. PMID:28466855 doi:https://dx.doi.org/10.1038/ncomms14959

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G. EXOG, a novel paralog of Endonuclease G in higher eukaryotes. Nucleic Acids Res. 2008 Mar;36(4):1369-79. doi: 10.1093/nar/gkm1169. Epub 2008, Jan 10. PMID:18187503 doi:https://dx.doi.org/10.1093/nar/gkm1169

[2] Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW. A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease. Nat Commun. 2017 May 3;8:14959. doi: 10.1038/ncomms14959. PMID:28466855 doi:https://dx.doi.org/10.1038/ncomms14959

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='5t5c' size='340' side='right'caption='[[5t5c]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t5c]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5C OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T5C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t5c]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/DNA_launch_vector_pDE-GFP2 DNA launch vector pDE-GFP2] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T5C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.851&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t3v|5t3v]], [[5t40|5t40]], [[5t4i|5t4i]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EXOG, ENDOGL1, ENDOGL2, ENGL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5t5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5c OCA], [https://pdbe.org/5t5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t5c RCSB], [https://www.ebi.ac.uk/pdbsum/5t5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5c ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5t5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5c OCA], [http://pdbe.org/5t5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5c RCSB], [http://www.ebi.ac.uk/pdbsum/5t5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/EXOG_HUMAN EXOG_HUMAN]] Endo/exonuclease with nicking activity towards supercoiled DNA, a preference for single-stranded DNA and 5'-3' exonuclease activity.<ref>PMID:18187503</ref>
+[https://www.uniprot.org/uniprot/EXOG_HUMAN EXOG_HUMAN] Endo/exonuclease with nicking activity towards supercoiled DNA, a preference for single-stranded DNA and 5'-3' exonuclease activity.<ref>PMID:18187503</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: DNA launch vector pDE-GFP2]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Szymanski, M R]]
+[[Category: Szymanski MR]]
-[[Category: Yin, W Y]]
+[[Category: Yin WY]]
-[[Category: Complex]]
-[[Category: Dna-repair]]
-[[Category: Exonuclease]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Mitochondria]]

5t5c: Difference between revisions

Latest revision as of 12:54, 4 October 2023

A Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme

Structural highlights

Function

Publication Abstract from PubMed

References

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