7cy5
From Proteopedia
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==Crystal Structure of CMD1 in complex with vitamin C== | ==Crystal Structure of CMD1 in complex with vitamin C== | ||
| - | <StructureSection load='7cy5' size='340' side='right'caption='[[7cy5]]' scene=''> | + | <StructureSection load='7cy5' size='340' side='right'caption='[[7cy5]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CY5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7cy5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CY5 FirstGlance]. <br> |
| - | </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=7cy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cy5 OCA], [https://pdbe.org/7cy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cy5 RCSB], [https://www.ebi.ac.uk/pdbsum/7cy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cy5 ProSAT]</span></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]] 2.2Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=7cy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cy5 OCA], [https://pdbe.org/7cy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cy5 RCSB], [https://www.ebi.ac.uk/pdbsum/7cy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cy5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.[https://www.uniprot.org/uniprot/CMD1_CHLRE CMD1_CHLRE] Dioxygenase that catalyzes DNA modification by mediating the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-glyceryl-methylcytosine (5gmC) (PubMed:31043749, PubMed:33531488). Catalyzes the conjugation of a glyceryl moiety from L-ascorbate (vitamin C) to the methyl group of 5mC through a carbon-carbon bond (PubMed:31043749, PubMed:33531488). 5gmC DNA modification may be required during photosynthesis as an epigenetic mark that couteracts DNA methylation (PubMed:31043749).<ref>PMID:31043749</ref> <ref>PMID:33531488</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | C(5)-glyceryl-methylcytosine (5gmC) is a novel DNA modification catalyzed by algal TET homologue CMD1 using vitamin C (VC) as co-substrate. Here, we report the structures of CMD1 in apo form and in complexes with VC or/and dsDNA. CMD1 exhibits comparable binding affinities for DNAs of different lengths, structures, and 5mC levels, and displays a moderate substrate preference for 5mCpG-containing DNA. CMD1 adopts the typical DSBH fold of Fe(2+)/2-OG-dependent dioxygenases. The lactone form of VC binds to the active site and mono-coordinates the Fe(2+) in a manner different from 2-OG. The dsDNA binds to a positively charged cleft of CMD1 and the 5mC/C is inserted into the active site and recognized by CMD1 in a similar manner as the TET proteins. The functions of key residues are validated by mutagenesis and activity assay. Our structural and biochemical data together reveal the molecular mechanism for the VC-derived 5gmC DNA modification by CMD1. | ||
| + | |||
| + | Molecular mechanism for vitamin C-derived C(5)-glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1.,Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J Nat Commun. 2021 Feb 2;12(1):744. doi: 10.1038/s41467-021-21061-2. PMID:33531488<ref>PMID:33531488</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7cy5" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Chlamydomonas reinhardtii]] | ||
| + | [[Category: Escherichia coli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ding J]] | [[Category: Ding J]] | ||
Current revision
Crystal Structure of CMD1 in complex with vitamin C
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