1de8: Difference between revisions

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-{{Seed}}
-[[Image:1de8.png|left|200px]]
-<!--
+==HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA==
-The line below this paragraph, containing "STRUCTURE_1de8", creates the "Structure Box" on the page.
+<StructureSection load='1de8' size='340' side='right'caption='[[1de8]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1de8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DE8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-{{STRUCTURE_1de8|  PDB=1de8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1de8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1de8 OCA], [https://pdbe.org/1de8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1de8 RCSB], [https://www.ebi.ac.uk/pdbsum/1de8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1de8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/APEX1_HUMAN APEX1_HUMAN] Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 in DNA repair and redox regulation of transcriptional factors. Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Does also incise at AP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of R-loop structures, and single-stranded RNA molecules. Has a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules during short-patch BER. Possesses a DNA 3' phosphodiesterase activity capable of removing lesions (such as phosphoglycolate) blocking the 3' side of DNA strand breaks. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Acts as a loading factor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role in the protection from granzymes-mediated cellular repair leading to cell death. Also involved in the DNA cleavage step of class switch recombination (CSR). On the other hand, APEX1 also exerts reversible nuclear redox activity to regulate DNA binding affinity and transcriptional activity of transcriptional factors by controlling the redox status of their DNA-binding domain, such as the FOS/JUN AP-1 complex after exposure to IR. Involved in calcium-dependent down-regulation of parathyroid hormone (PTH) expression by binding to negative calcium response elements (nCaREs). Together with HNRNPL or the dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator of transcriptional repression. Stimulates the YBX1-mediated MDR1 promoter activity, when acetylated at Lys-6 and Lys-7, leading to drug resistance. Acts also as an endoribonuclease involved in the control of single-stranded RNA metabolism. Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding region determinant (CRD). In association with NMD1, plays a role in the rRNA quality control process during cell cycle progression. Associates, together with YBX1, on the MDR1 promoter. Together with NPM1, associates with rRNA. Binds DNA and RNA.<ref>PMID:1719477</ref> <ref>PMID:12524539</ref> <ref>PMID:8355688</ref> <ref>PMID:8621488</ref> <ref>PMID:8932375</ref> <ref>PMID:9108029</ref> <ref>PMID:9207062</ref> <ref>PMID:9804799</ref> <ref>PMID:9560228</ref> <ref>PMID:10023679</ref> <ref>PMID:11118054</ref> <ref>PMID:11452037</ref> <ref>PMID:11832948</ref> <ref>PMID:11809897</ref> <ref>PMID:16617147</ref> <ref>PMID:18439621</ref> <ref>PMID:18809583</ref> <ref>PMID:18179823</ref> <ref>PMID:18579163</ref> <ref>PMID:19188445</ref> <ref>PMID:19401441</ref> <ref>PMID:19934257</ref> <ref>PMID:20699270</ref> <ref>PMID:21496894</ref> <ref>PMID:21762700</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/1de8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1de8 ConSurf].
+<div style="clear:both"></div>
-===HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA===
+==See Also==
+*[[Apurinic/apyrimidinic endonuclease 3D structures|Apurinic/apyrimidinic endonuclease 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_10667800}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 10667800 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_10667800}}
-==About this Structure==
-DE8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DE8 OCA].
-==Reference==
-DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected], Mol CD, Izumi T, Mitra S, Tainer JA, Nature. 2000 Jan 27;403(6768):451-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10667800 10667800]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Izumi, T.]]
+[[Category: Izumi T]]
-[[Category: Mitra, S.]]
+[[Category: Mitra S]]
-[[Category: Mol, C D.]]
+[[Category: Mol CD]]
-[[Category: Tainer, J A.]]
+[[Category: Tainer JA]]
-[[Category: Abasic site]]
-[[Category: Dna repair]]
-[[Category: Enzyme:dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:53:40 2008''