7d3w
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A== |
<StructureSection load='7d3w' size='340' side='right'caption='[[7d3w]]' scene=''> | <StructureSection load='7d3w' size='340' side='right'caption='[[7d3w]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full | + | <table><tr><td colspan='2'>[[7d3w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D3W 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=7d3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d3w OCA], [https://pdbe.org/7d3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d3w RCSB], [https://www.ebi.ac.uk/pdbsum/7d3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d3w ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7d3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d3w OCA], [https://pdbe.org/7d3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d3w RCSB], [https://www.ebi.ac.uk/pdbsum/7d3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d3w ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/ABC3A_HUMAN ABC3A_HUMAN] DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:10469298</ref> <ref>PMID:12859895</ref> <ref>PMID:16527742</ref> <ref>PMID:19461882</ref> <ref>PMID:20615867</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21460793</ref> <ref>PMID:21123384</ref> <ref>PMID:21368204</ref> <ref>PMID:22896697</ref> <ref>PMID:22457529</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | APOBEC3A (A3A) deaminates deoxycytidine in target motif TC in a single-stranded DNA (we termed it as TC DNA), which mortally mutates viral pathogens and immunoglobulins, and leads to the diversification and lethality of cancers. The crystal structure of A3A-DNA revealed a unique U-shaped recognition mode of target base dC(0) . However, when TC DNA was titrated into (15) N-labeled A3A solution, we observed two sets of (1) H-(15) N cross-peaks of A3A in HSQC spectra, and two sets of (1) H-(1) H cross-peaks of DNA in two-dimensional (13) C,(15) N-filtered TOCSY spectra, indicating two different kinds of conformers of either A3A or TC DNA existing in solution. Here, mainly by NMR, we demonstrated that one DNA conformer interacted with one A3A conformer, forming a specific complex A3A(S) -DNA(S) in a way almost similar to that observed in the reported crystal A3A-DNA structure, where dC(0) inserted into zinc ion binding center. While the other DNA conformer bound with another A3A conformer, but dC(0) did not extend into the zinc-binding pocket, forming a nonspecific A3A(NS) -DNA(NS) complex. The NMR solution structure implied three sites Asn(61) , His(182) and Arg(189) were necessary to DNA recognition. These observations indicate a distinctive way from that reported in X-ray crystal structure, suggesting an unexpected mode of deaminase APOBEC3A to identify target motif TC in DNA in solution. | ||
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| + | Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance.,Liu Y, Lan W, Wang C, Cao C Protein Sci. 2022 Feb;31(2):443-453. doi: 10.1002/pro.4242. Epub 2021 Nov 26. PMID:34792260<ref>PMID:34792260</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7d3w" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Synthetic construct]] |
| + | [[Category: Cao C]] | ||
| + | [[Category: Lan W]] | ||
| + | [[Category: Liu Y]] | ||
Current revision
Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3A
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