7yhp
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7yhp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] 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=7YHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YHP FirstGlance]. <br> | <table><tr><td colspan='2'>[[7yhp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] 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=7YHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YHP FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.1Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=7yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yhp OCA], [https://pdbe.org/7yhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yhp RCSB], [https://www.ebi.ac.uk/pdbsum/7yhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yhp 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=7yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yhp OCA], [https://pdbe.org/7yhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yhp RCSB], [https://www.ebi.ac.uk/pdbsum/7yhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yhp ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/SRY_HUMAN SRY_HUMAN] Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells (By similarity). In male adult brain involved in the maintenance of motor functions of dopaminergic neurons (By similarity). Involved in different aspects of gene regulation including promoter activation or repression (By similarity). Promotes DNA bending. SRY HMG box recognizes DNA by partial intercalation in the minor groove. Also involved in pre-mRNA splicing. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'.<ref>PMID:11818535</ref> <ref>PMID:15170344</ref> <ref>PMID:16762365</ref> <ref>PMID:11563911</ref> [https://www.uniprot.org/uniprot/ROS1_ARATH ROS1_ARATH] Bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity (PubMed:25240767). Generates 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) as a primary 5-meC excision intermediate (PubMed:25228464). Prevents DNA hypermethylation, specifically in the promoter of otherwise silenced loci. May be involved in DNA repair through its nicking activity on methylated DNA. Binds with similar affinity to both methylated and non-methylated DNA. Highly distributive behavior on DNA substrates containing multiple 5-meC residues. Involved with Pol IV in the remodeling of the 5S rDNA chromatin via DNA methylation modifications during the first days of development post-germination. Participates in UV-B induced- and oxidative DNA damage repair (PubMed:24155752).<ref>PMID:12526807</ref> <ref>PMID:16624880</ref> <ref>PMID:18845569</ref> <ref>PMID:19443451</ref> <ref>PMID:20489198</ref> <ref>PMID:24155752</ref> <ref>PMID:25228464</ref> <ref>PMID:25240767</ref> | [https://www.uniprot.org/uniprot/SRY_HUMAN SRY_HUMAN] Transcriptional regulator that controls a genetic switch in male development. It is necessary and sufficient for initiating male sex determination by directing the development of supporting cell precursors (pre-Sertoli cells) as Sertoli rather than granulosa cells (By similarity). In male adult brain involved in the maintenance of motor functions of dopaminergic neurons (By similarity). Involved in different aspects of gene regulation including promoter activation or repression (By similarity). Promotes DNA bending. SRY HMG box recognizes DNA by partial intercalation in the minor groove. Also involved in pre-mRNA splicing. Binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'.<ref>PMID:11818535</ref> <ref>PMID:15170344</ref> <ref>PMID:16762365</ref> <ref>PMID:11563911</ref> [https://www.uniprot.org/uniprot/ROS1_ARATH ROS1_ARATH] Bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity (PubMed:25240767). Generates 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) as a primary 5-meC excision intermediate (PubMed:25228464). Prevents DNA hypermethylation, specifically in the promoter of otherwise silenced loci. May be involved in DNA repair through its nicking activity on methylated DNA. Binds with similar affinity to both methylated and non-methylated DNA. Highly distributive behavior on DNA substrates containing multiple 5-meC residues. Involved with Pol IV in the remodeling of the 5S rDNA chromatin via DNA methylation modifications during the first days of development post-germination. Participates in UV-B induced- and oxidative DNA damage repair (PubMed:24155752).<ref>PMID:12526807</ref> <ref>PMID:16624880</ref> <ref>PMID:18845569</ref> <ref>PMID:19443451</ref> <ref>PMID:20489198</ref> <ref>PMID:24155752</ref> <ref>PMID:25228464</ref> <ref>PMID:25240767</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases. | ||
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| + | Molecular basis of the plant ROS1-mediated active DNA demethylation.,Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J Nat Plants. 2023 Feb;9(2):271-279. doi: 10.1038/s41477-022-01322-8. Epub 2023 Jan , 9. PMID:36624257<ref>PMID:36624257</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7yhp" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
CryoEM structure of Arabidopsis ROS1 in complex with 5mC-dsDNA at 3.1 Angstroms resolution
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