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| | <StructureSection load='6oeb' size='340' side='right'caption='[[6oeb]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='6oeb' size='340' side='right'caption='[[6oeb]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6oeb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6nld 6nld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OEB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OEB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6oeb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6nld 6nld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OEB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></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]] 2.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMCES, C3orf37, DC12, SRAPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6oeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oeb OCA], [http://pdbe.org/6oeb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oeb RCSB], [http://www.ebi.ac.uk/pdbsum/6oeb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oeb 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=6oeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oeb OCA], [https://pdbe.org/6oeb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oeb RCSB], [https://www.ebi.ac.uk/pdbsum/6oeb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oeb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN]] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref> | + | [https://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 23: |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arrowsmith, C H]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Bountra, C]] | + | [[Category: Arrowsmith CH]] |
| - | [[Category: Edwards, A M]] | + | [[Category: Bountra C]] |
| - | [[Category: Halabelian, L]] | + | [[Category: Edwards AM]] |
| - | [[Category: Li, Y]] | + | [[Category: Halabelian L]] |
| - | [[Category: Ravichandran, M]] | + | [[Category: Li Y]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Ravichandran M]] |
| - | [[Category: Zeng, H]] | + | [[Category: Zeng H]] |
| - | [[Category: 3' overhang]]
| + | |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Dna-damage protein]]
| + | |
| - | [[Category: Dna-protein complex]]
| + | |
| - | [[Category: Hmce]]
| + | |
| - | [[Category: Sgc]]
| + | |
| - | [[Category: Srap domain]]
| + | |
| Structural highlights
Function
HMCES_HUMAN Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).[1]
Publication Abstract from PubMed
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a variety of single-strand- and double-strand-containing DNA structures found in DNA-damage sites, including 5' and 3' overhang DNAs and gapped DNAs with short single-strand segments.
Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.,Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH Nat Struct Mol Biol. 2019 Jul;26(7):607-612. doi: 10.1038/s41594-019-0246-6. Epub, 2019 Jun 24. PMID:31235913[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Aravind L, Anand S, Iyer LM. Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. Biol Direct. 2013 Aug 15;8:20. doi: 10.1186/1745-6150-8-20. PMID:23945014 doi:http://dx.doi.org/10.1186/1745-6150-8-20
- ↑ Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH. Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition. Nat Struct Mol Biol. 2019 Jul;26(7):607-612. doi: 10.1038/s41594-019-0246-6. Epub, 2019 Jun 24. PMID:31235913 doi:http://dx.doi.org/10.1038/s41594-019-0246-6
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