2m65: Difference between revisions

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==NMR structure of human restriction factor APOBEC3A==
==NMR structure of human restriction factor APOBEC3A==
<StructureSection load='2m65' size='340' side='right' caption='[[2m65]], [[NMR_Ensembles_of_Models | 30 NMR models]]' scene=''>
<StructureSection load='2m65' size='340' side='right'caption='[[2m65]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2m65]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M65 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M65 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2m65]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M65 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M65 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APOBEC3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2m65 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m65 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2m65 RCSB], [http://www.ebi.ac.uk/pdbsum/2m65 PDBsum]</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=2m65 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m65 OCA], [https://pdbe.org/2m65 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m65 RCSB], [https://www.ebi.ac.uk/pdbsum/2m65 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m65 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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>
[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;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 2m65" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Ahn, J]]
[[Category: Large Structures]]
[[Category: Byeon, C]]
[[Category: Ahn J]]
[[Category: Byeon, I L]]
[[Category: Byeon C]]
[[Category: Gronenborn, A M]]
[[Category: Byeon IL]]
[[Category: Antiviral defense]]
[[Category: Gronenborn AM]]
[[Category: Apobec3a]]
[[Category: Cytidine deaminase]]
[[Category: Host-virus interaction]]
[[Category: Hydrolase]]
[[Category: Zinc-binding]]

Latest revision as of 09:00, 15 May 2024

NMR structure of human restriction factor APOBEC3ANMR structure of human restriction factor APOBEC3A

Structural highlights

2m65 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]

Publication Abstract from PubMed

Human APOBEC3A is a single-stranded DNA cytidine deaminase that restricts viral pathogens and endogenous retrotransposons, and has a role in the innate immune response. Furthermore, its potential to act as a genomic DNA mutator has implications for a role in carcinogenesis. A deeper understanding of APOBEC3A's deaminase and nucleic acid-binding properties, which is central to its biological activities, has been limited by the lack of structural information. Here we report the nuclear magnetic resonance solution structure of APOBEC3A and show that the critical interface for interaction with single-stranded DNA substrates includes residues extending beyond the catalytic centre. Importantly, by monitoring deaminase activity in real time, we find that A3A displays similar catalytic activity on APOBEC3A-specific TTCA- or A3G-specific CCCA-containing substrates, involving key determinants immediately 5' of the reactive C. Our results afford novel mechanistic insights into APOBEC3A-mediated deamination and provide the structural basis for further molecular studies.

NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity.,Byeon IJ, Ahn J, Mitra M, Byeon CH, Hercik K, Hritz J, Charlton LM, Levin JG, Gronenborn AM Nat Commun. 2013;4:1890. doi: 10.1038/ncomms2883. PMID:23695684[13]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Madsen P, Anant S, Rasmussen HH, Gromov P, Vorum H, Dumanski JP, Tommerup N, Collins JE, Wright CL, Dunham I, MacGinnitie AJ, Davidson NO, Celis JE. Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1. J Invest Dermatol. 1999 Aug;113(2):162-9. PMID:10469298 doi:10.1046/j.1523-1747.1999.00682.x
  2. ↑ Mariani R, Chen D, Schrofelbauer B, Navarro F, Konig R, Bollman B, Munk C, Nymark-McMahon H, Landau NR. Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell. 2003 Jul 11;114(1):21-31. PMID:12859895
  3. ↑ Chen H, Lilley CE, Yu Q, Lee DV, Chou J, Narvaiza I, Landau NR, Weitzman MD. APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. Curr Biol. 2006 Mar 7;16(5):480-5. PMID:16527742 doi:10.1016/j.cub.2006.01.031
  4. ↑ Narvaiza I, Linfesty DC, Greener BN, Hakata Y, Pintel DJ, Logue E, Landau NR, Weitzman MD. Deaminase-independent inhibition of parvoviruses by the APOBEC3A cytidine deaminase. PLoS Pathog. 2009 May;5(5):e1000439. doi: 10.1371/journal.ppat.1000439. Epub 2009, May 22. PMID:19461882 doi:10.1371/journal.ppat.1000439
  5. ↑ Thielen BK, McNevin JP, McElrath MJ, Hunt BV, Klein KC, Lingappa JR. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem. 2010 Sep 3;285(36):27753-66. doi: 10.1074/jbc.M110.102822. Epub 2010, Jul 8. PMID:20615867 doi:10.1074/jbc.M110.102822
  6. ↑ Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol. 2010 Feb;17(2):222-9. doi: 10.1038/nsmb.1744. Epub 2010 Jan , 10. PMID:20062055 doi:10.1038/nsmb.1744
  7. ↑ Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011 Apr 29;145(3):423-34. doi: 10.1016/j.cell.2011.03.022. Epub 2011 Apr, 14. PMID:21496894 doi:10.1016/j.cell.2011.03.022
  8. ↑ Landry S, Narvaiza I, Linfesty DC, Weitzman MD. APOBEC3A can activate the DNA damage response and cause cell-cycle arrest. EMBO Rep. 2011 May;12(5):444-50. doi: 10.1038/embor.2011.46. Epub 2011 Apr 1. PMID:21460793 doi:10.1038/embor.2011.46
  9. ↑ Bulliard Y, Narvaiza I, Bertero A, Peddi S, Rohrig UF, Ortiz M, Zoete V, Castro-Diaz N, Turelli P, Telenti A, Michielin O, Weitzman MD, Trono D. Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities. J Virol. 2011 Feb;85(4):1765-76. doi: 10.1128/JVI.01651-10. Epub 2010 Dec 1. PMID:21123384 doi:10.1128/JVI.01651-10
  10. ↑ Suspene R, Aynaud MM, Guetard D, Henry M, Eckhoff G, Marchio A, Pineau P, Dejean A, Vartanian JP, Wain-Hobson S. Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4858-63. doi:, 10.1073/pnas.1009687108. Epub 2011 Mar 2. PMID:21368204 doi:10.1073/pnas.1009687108
  11. ↑ Carpenter MA, Li M, Rathore A, Lackey L, Law EK, Land AM, Leonard B, Shandilya SM, Bohn MF, Schiffer CA, Brown WL, Harris RS. Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J Biol Chem. 2012 Oct 5;287(41):34801-8. doi: 10.1074/jbc.M112.385161. Epub 2012 , Aug 15. PMID:22896697 doi:10.1074/jbc.M112.385161
  12. ↑ Ooms M, Krikoni A, Kress AK, Simon V, Munk C. APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T-lymphotropic virus type 1. J Virol. 2012 Jun;86(11):6097-108. doi: 10.1128/JVI.06570-11. Epub 2012 Mar 28. PMID:22457529 doi:10.1128/JVI.06570-11
  13. ↑ Byeon IJ, Ahn J, Mitra M, Byeon CH, Hercik K, Hritz J, Charlton LM, Levin JG, Gronenborn AM. NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat Commun. 2013;4:1890. doi: 10.1038/ncomms2883. PMID:23695684 doi:10.1038/ncomms2883
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