8ka3: Difference between revisions

Revision as of 08:55, 21 February 2024

Arabidopsis AP endonuclease APR complex with 22bp THF-containing DNA

Structural highlights

8ka3 is a 4 chain structure with sequence from Arabidopsis thaliana 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 3Å
Ligands:	3DR, NI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARP_ARATH Repairs oxidative DNA damages, seems also to act as a redox factor (PubMed:7512729). Is multifunctional and may be involved both in DNA repair and in the regulation of transcription (PubMed:7512729). Exhibits apurinic/apyrimidinic (AP) endonuclease activity (PubMed:25569774, PubMed:21781197, PubMed:25228464). Catalyzes the conversion of 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) to 3'-OH (PubMed:25228464). May be involved in base excision repair in chloroplasts (PubMed:19372224). According to a report, has a significant in vitro 3'-phosphatase activity (PubMed:25228464). According to another report, has no in vitro 3'-phosphatase activity (PubMed:25569774). Has a strong non-specific affinity to DNA (PubMed:25228464).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

References

↑ Gutman BL, Niyogi KK. Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. J Biol Chem. 2009 Jun 19;284(25):17006-17012. PMID:19372224 doi:10.1074/jbc.M109.008342
↑ Córdoba-Cañero D, Roldán-Arjona T, Ariza RR. Arabidopsis ARP endonuclease functions in a branched base excision DNA repair pathway completed by LIG1. Plant J. 2011 Nov;68(4):693-702. PMID:21781197 doi:10.1111/j.1365-313X.2011.04720.x
↑ Lee J, Jang H, Shin H, Choi WL, Mok YG, Huh JH. AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis. Nucleic Acids Res. 2014 Oct;42(18):11408-18. doi: 10.1093/nar/gku834. Epub 2014 , Sep 16. PMID:25228464 doi:https://dx.doi.org/10.1093/nar/gku834
↑ Li Y, Córdoba-Cañero D, Qian W, Zhu X, Tang K, Zhang H, Ariza RR, Roldán-Arjona T, Zhu JK. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected]. PLoS Genet. 2015 Jan 8;11(1):e1004905. PMID:25569774 doi:10.1371/journal.pgen.1004905
↑ Babiychuk E, Kushnir S, Van Montagu M, Inzé D. The Arabidopsis thaliana apurinic endonuclease Arp reduces human transcription factors Fos and Jun. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3299-303. PMID:7512729 doi:10.1073/pnas.91.8.3299
↑ Murphy TM, Belmonte M, Shu S, Britt AB, Hatteroth J. Requirement for abasic endonuclease gene homologues in Arabidopsis seed development. PLoS One. 2009;4(1):e4297. PMID:19172180 doi:10.1371/journal.pone.0004297

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OCA

[1] Gutman BL, Niyogi KK. Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. J Biol Chem. 2009 Jun 19;284(25):17006-17012. PMID:19372224 doi:10.1074/jbc.M109.008342

[2] Córdoba-Cañero D, Roldán-Arjona T, Ariza RR. Arabidopsis ARP endonuclease functions in a branched base excision DNA repair pathway completed by LIG1. Plant J. 2011 Nov;68(4):693-702. PMID:21781197 doi:10.1111/j.1365-313X.2011.04720.x

[3] Lee J, Jang H, Shin H, Choi WL, Mok YG, Huh JH. AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis. Nucleic Acids Res. 2014 Oct;42(18):11408-18. doi: 10.1093/nar/gku834. Epub 2014 , Sep 16. PMID:25228464 doi:https://dx.doi.org/10.1093/nar/gku834

[4] Li Y, Córdoba-Cañero D, Qian W, Zhu X, Tang K, Zhang H, Ariza RR, Roldán-Arjona T, Zhu JK. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected]. PLoS Genet. 2015 Jan 8;11(1):e1004905. PMID:25569774 doi:10.1371/journal.pgen.1004905

[5] Babiychuk E, Kushnir S, Van Montagu M, Inzé D. The Arabidopsis thaliana apurinic endonuclease Arp reduces human transcription factors Fos and Jun. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3299-303. PMID:7512729 doi:10.1073/pnas.91.8.3299

[6] Murphy TM, Belmonte M, Shu S, Britt AB, Hatteroth J. Requirement for abasic endonuclease gene homologues in Arabidopsis seed development. PLoS One. 2009;4(1):e4297. PMID:19172180 doi:10.1371/journal.pone.0004297

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8ka3 is ON HOLD  until Paper Publication
+==Arabidopsis AP endonuclease APR complex with 22bp THF-containing DNA==
+<StructureSection load='8ka3' size='340' side='right'caption='[[8ka3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8ka3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] 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=8KA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8KA3 FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<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>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=8ka3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ka3 OCA], [https://pdbe.org/8ka3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ka3 RCSB], [https://www.ebi.ac.uk/pdbsum/8ka3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ka3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARP_ARATH ARP_ARATH] Repairs oxidative DNA damages, seems also to act as a redox factor (PubMed:7512729). Is multifunctional and may be involved both in DNA repair and in the regulation of transcription (PubMed:7512729). Exhibits apurinic/apyrimidinic (AP) endonuclease activity (PubMed:25569774, PubMed:21781197, PubMed:25228464). Catalyzes the conversion of 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) to 3'-OH (PubMed:25228464). May be involved in base excision repair in chloroplasts (PubMed:19372224). According to a report, has a significant in vitro 3'-phosphatase activity (PubMed:25228464). According to another report, has no in vitro 3'-phosphatase activity (PubMed:25569774). Has a strong non-specific affinity to DNA (PubMed:25228464).<ref>PMID:19372224</ref> <ref>PMID:21781197</ref> <ref>PMID:25228464</ref> <ref>PMID:25569774</ref> <ref>PMID:7512729</ref> <ref>PMID:19172180</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Guo WT]]
+[[Category: Wu BX]]

8ka3: Difference between revisions

Revision as of 08:55, 21 February 2024

Arabidopsis AP endonuclease APR complex with 22bp THF-containing DNA

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