5w2m

From Proteopedia

(Difference between revisions)

Current revision

APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA

Structural highlights

5w2m is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ABC3F_HUMAN DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. 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] ^[13]

Publication Abstract from PubMed

The single-stranded DNA (ssDNA) cytidine deaminase APOBEC3F (A3F) deaminates cytosine (C) to uracil (U) and is a known restriction factor of HIV-1. Its C-terminal catalytic domain (CD2) alone is capable of binding single-stranded nucleic acids and is important for deamination. However, little is known about how the CD2 interacts with ssDNA. Here we report a crystal structure of A3F-CD2 in complex with a 10-nucleotide ssDNA composed of poly-thymine, which reveals a novel positively charged nucleic acid binding site distal to the active center that plays a key role in substrate DNA binding and catalytic activity. Lysine and tyrosine residues within this binding site interact with the ssDNA, and mutating these residues dramatically impairs both ssDNA binding and catalytic activity. This binding site is not conserved in APOBEC3G (A3G), which may explain differences in ssDNA-binding characteristics between A3F-CD2 and A3G-CD2. In addition, we observed an alternative Zn-coordination conformation around the active center. These findings reveal the structural relationships between nucleic acid interactions and catalytic activity of A3F.

Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA.,Fang Y, Xiao X, Li SX, Wolfe A, Chen XS J Mol Biol. 2017 Nov 27. pii: S0022-2836(17)30557-0. doi:, 10.1016/j.jmb.2017.11.007. PMID:29191651^[14]

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

References

↑ Wiegand HL, Doehle BP, Bogerd HP, Cullen BR. A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins. EMBO J. 2004 Jun 16;23(12):2451-8. Epub 2004 May 20. PMID:15152192 doi:10.1038/sj.emboj.7600246
↑ 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
↑ Delebecque F, Suspene R, Calattini S, Casartelli N, Saib A, Froment A, Wain-Hobson S, Gessain A, Vartanian JP, Schwartz O. Restriction of foamy viruses by APOBEC cytidine deaminases. J Virol. 2006 Jan;80(2):605-14. PMID:16378963 doi:10.1128/JVI.80.2.605-614.2006
↑ Zielonka J, Bravo IG, Marino D, Conrad E, Perkovic M, Battenberg M, Cichutek K, Munk C. Restriction of equine infectious anemia virus by equine APOBEC3 cytidine deaminases. J Virol. 2009 Aug;83(15):7547-59. doi: 10.1128/JVI.00015-09. Epub 2009 May 20. PMID:19458006 doi:10.1128/JVI.00015-09
↑ Mbisa JL, Bu W, Pathak VK. APOBEC3F and APOBEC3G inhibit HIV-1 DNA integration by different mechanisms. J Virol. 2010 May;84(10):5250-9. doi: 10.1128/JVI.02358-09. Epub 2010 Mar 10. PMID:20219927 doi:10.1128/JVI.02358-09
↑ Paprotka T, Venkatachari NJ, Chaipan C, Burdick R, Delviks-Frankenberry KA, Hu WS, Pathak VK. Inhibition of xenotropic murine leukemia virus-related virus by APOBEC3 proteins and antiviral drugs. J Virol. 2010 Jun;84(11):5719-29. doi: 10.1128/JVI.00134-10. Epub 2010 Mar 24. PMID:20335265 doi:10.1128/JVI.00134-10
↑ 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
↑ 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
↑ Hultquist JF, Lengyel JA, Refsland EW, LaRue RS, Lackey L, Brown WL, Harris RS. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. J Virol. 2011 Nov;85(21):11220-34. doi: 10.1128/JVI.05238-11. Epub 2011 Aug 10. PMID:21835787 doi:10.1128/JVI.05238-11
↑ Phalora PK, Sherer NM, Wolinsky SM, Swanson CM, Malim MH. HIV-1 replication and APOBEC3 antiviral activity are not regulated by P bodies. J Virol. 2012 Nov;86(21):11712-24. doi: 10.1128/JVI.00595-12. Epub 2012 Aug 22. PMID:22915799 doi:10.1128/JVI.00595-12
↑ Refsland EW, Hultquist JF, Harris RS. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. PLoS Pathog. 2012;8(7):e1002800. doi: 10.1371/journal.ppat.1002800. Epub 2012 Jul, 12. PMID:22807680 doi:10.1371/journal.ppat.1002800
↑ Chaipan C, Smith JL, Hu WS, Pathak VK. APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages. J Virol. 2013 Jan;87(1):444-53. doi: 10.1128/JVI.00676-12. Epub 2012 Oct 24. PMID:23097438 doi:10.1128/JVI.00676-12
↑ Gillick K, Pollpeter D, Phalora P, Kim EY, Wolinsky SM, Malim MH. Suppression of HIV-1 infection by APOBEC3 proteins in primary human CD4(+) T cells is associated with inhibition of processive reverse transcription as well as excessive cytidine deamination. J Virol. 2013 Feb;87(3):1508-17. doi: 10.1128/JVI.02587-12. Epub 2012 Nov 14. PMID:23152537 doi:10.1128/JVI.02587-12
↑ Fang Y, Xiao X, Li SX, Wolfe A, Chen XS. Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA. J Mol Biol. 2017 Nov 27. pii: S0022-2836(17)30557-0. doi:, 10.1016/j.jmb.2017.11.007. PMID:29191651 doi:http://dx.doi.org/10.1016/j.jmb.2017.11.007

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5w2m"

@@ Line 1: / Line 1: @@
 ==APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA==
-<StructureSection load='5w2m' size='340' side='right' caption='[[5w2m]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+<StructureSection load='5w2m' size='340' side='right'caption='[[5w2m]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5w2m]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W2M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5w2m]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W2M 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">X-ray diffraction, [[Resolution|Resolution]] 3.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APOBEC3F ([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=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=5w2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w2m OCA], [http://pdbe.org/5w2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w2m RCSB], [http://www.ebi.ac.uk/pdbsum/5w2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w2m 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=5w2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w2m OCA], [https://pdbe.org/5w2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w2m RCSB], [https://www.ebi.ac.uk/pdbsum/5w2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w2m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ABC3F_HUMAN ABC3F_HUMAN]] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:15152192</ref> <ref>PMID:16527742</ref> <ref>PMID:16378963</ref> <ref>PMID:19458006</ref> <ref>PMID:20219927</ref> <ref>PMID:20335265</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21835787</ref> <ref>PMID:22915799</ref> <ref>PMID:22807680</ref> <ref>PMID:23097438</ref> <ref>PMID:23152537</ref>
+[https://www.uniprot.org/uniprot/ABC3F_HUMAN ABC3F_HUMAN] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:15152192</ref> <ref>PMID:16527742</ref> <ref>PMID:16378963</ref> <ref>PMID:19458006</ref> <ref>PMID:20219927</ref> <ref>PMID:20335265</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21835787</ref> <ref>PMID:22915799</ref> <ref>PMID:22807680</ref> <ref>PMID:23097438</ref> <ref>PMID:23152537</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Chen, X J]]
+[[Category: Large Structures]]
-[[Category: Fang, Y]]
+[[Category: Chen XS]]
-[[Category: Li, S X]]
+[[Category: Fang Y]]
-[[Category: Wolfe, A]]
+[[Category: Li S-X]]
-[[Category: Xiao, X]]
+[[Category: Wolfe A]]
-[[Category: Apobec]]
+[[Category: Xiao X]]
-[[Category: Dna binding protein]]

5w2m

From Proteopedia

Current revision

APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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