3s57: Difference between revisions

Latest revision as of 08:36, 20 March 2024

ABH2 cross-linked with undamaged dsDNA-1 containing cofactors

Structural highlights

3s57 is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	AKG, GOL, MN, XL3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALKB2_HUMAN Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Duncan T, Trewick SC, Koivisto P, Bates PA, Lindahl T, Sedgwick B. Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16660-5. Epub 2002 Dec 16. PMID:12486230 doi:10.1073/pnas.262589799
↑ Aas PA, Otterlei M, Falnes PO, Vagbo CB, Skorpen F, Akbari M, Sundheim O, Bjoras M, Slupphaug G, Seeberg E, Krokan HE. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature. 2003 Feb 20;421(6925):859-63. PMID:12594517 doi:10.1038/nature01363
↑ Lee DH, Jin SG, Cai S, Chen Y, Pfeifer GP, O'Connor TR. Repair of methylation damage in DNA and RNA by mammalian AlkB homologues. J Biol Chem. 2005 Nov 25;280(47):39448-59. Epub 2005 Sep 20. PMID:16174769 doi:M509881200
↑ Ringvoll J, Moen MN, Nordstrand LM, Meira LB, Pang B, Bekkelund A, Dedon PC, Bjelland S, Samson LD, Falnes PO, Klungland A. AlkB homologue 2-mediated repair of ethenoadenine lesions in mammalian DNA. Cancer Res. 2008 Jun 1;68(11):4142-9. doi: 10.1158/0008-5472.CAN-08-0796. PMID:18519673 doi:https://dx.doi.org/10.1158/0008-5472.CAN-08-0796
↑ Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238 doi:https://dx.doi.org/10.1038/nature06889

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Duncan T, Trewick SC, Koivisto P, Bates PA, Lindahl T, Sedgwick B. Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16660-5. Epub 2002 Dec 16. PMID:12486230 doi:10.1073/pnas.262589799

[2] Aas PA, Otterlei M, Falnes PO, Vagbo CB, Skorpen F, Akbari M, Sundheim O, Bjoras M, Slupphaug G, Seeberg E, Krokan HE. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature. 2003 Feb 20;421(6925):859-63. PMID:12594517 doi:10.1038/nature01363

[3] Lee DH, Jin SG, Cai S, Chen Y, Pfeifer GP, O'Connor TR. Repair of methylation damage in DNA and RNA by mammalian AlkB homologues. J Biol Chem. 2005 Nov 25;280(47):39448-59. Epub 2005 Sep 20. PMID:16174769 doi:M509881200

[4] Ringvoll J, Moen MN, Nordstrand LM, Meira LB, Pang B, Bekkelund A, Dedon PC, Bjelland S, Samson LD, Falnes PO, Klungland A. AlkB homologue 2-mediated repair of ethenoadenine lesions in mammalian DNA. Cancer Res. 2008 Jun 1;68(11):4142-9. doi: 10.1158/0008-5472.CAN-08-0796. PMID:18519673 doi:https://dx.doi.org/10.1158/0008-5472.CAN-08-0796

[5] Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238 doi:https://dx.doi.org/10.1038/nature06889

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[3]

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[5]

@@ Line 1: / Line 1: @@
-[[Image:3s57.jpg|left|200px]]
-<!--
+==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==
-The line below this paragraph, containing "STRUCTURE_3s57", creates the "Structure Box" on the page.
+<StructureSection load='3s57' size='340' side='right'caption='[[3s57]], [[Resolution|resolution]] 1.60&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'>[[3s57]] is a 3 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=3S57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S57 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
-{{STRUCTURE_3s57|  PDB=3s57  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [https://pdbe.org/3s57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [https://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
-===ABH2 cross-linked with undamaged dsDNA-1 containing cofactors===
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-[[3s57]] is a 3 chain structure with 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=3S57 OCA].
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Chen, B.]]
+[[Category: Large Structures]]
-[[Category: Dinner, A R.]]
+[[Category: Chen B]]
-[[Category: He, C.]]
+[[Category: Dinner AR]]
-[[Category: Jia, G.]]
+[[Category: He C]]
-[[Category: Li, C Q.]]
+[[Category: Jia G]]
-[[Category: Qi, B.]]
+[[Category: Li CQ]]
-[[Category: Ramirez, B.]]
+[[Category: Qi B]]
-[[Category: Yang, C G.]]
+[[Category: Ramirez B]]
-[[Category: Yi, C.]]
+[[Category: Yang C-G]]
-[[Category: Zhang, L.]]
+[[Category: Yi C]]
-[[Category: Zhang, W.]]
+[[Category: Zhang L]]
-[[Category: Dioxygenase]]
+[[Category: Zhang W]]
-[[Category: Dsdna binding]]
-[[Category: Jelly-roll fold]]
-[[Category: Oxidoreductase-dna complex]]
-[[Category: Plasma]]
-[[Category: Protein-dna complex]]

3s57: Difference between revisions

Latest revision as of 08:36, 20 March 2024

ABH2 cross-linked with undamaged dsDNA-1 containing cofactors

Structural highlights

Function

See Also

References

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