2kbo

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (19:11, 29 May 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2kbo.png|left|200px]]
 
-
{{STRUCTURE_2kbo| PDB=2kbo | SCENE= }}
+
==Structure, interaction, and real-time monitoring of the enzymatic reaction of wild type APOBEC3G==
 +
<StructureSection load='2kbo' size='340' side='right'caption='[[2kbo]]' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2kbo]] 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=2KBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KBO FirstGlance]. <br>
 +
</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='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=2kbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kbo OCA], [https://pdbe.org/2kbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kbo RCSB], [https://www.ebi.ac.uk/pdbsum/2kbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kbo ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ABC3G_HUMAN ABC3G_HUMAN] DNA deaminase (cytidine deaminase) that mediates a form of innate resistance to retroviral infections (at least to HIV-1 infection) by triggering G-to-A hypermutation in the newly synthesized viral DNA. The replacements C-to-U in the minus strand DNA of HIV-1 during reverse transcription, leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. Modification of both DNA strands is not excluded. This antiviral activity is neutralized by the virion infectivity factor (VIF), that prevents the incorporation of APOBEC3G into progeny HIV-1 virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome. May also prevent the transposition of a subset of retroelements. Binds a variety of RNAs, but does not display detectable APOB, NF1 and NAT1 mRNA editing.<ref>PMID:14557625</ref> <ref>PMID:12167863</ref> <ref>PMID:12808466</ref> <ref>PMID:12809610</ref> <ref>PMID:12808465</ref> <ref>PMID:12859895</ref> <ref>PMID:12970355</ref> <ref>PMID:14528300</ref> <ref>PMID:15031497</ref> <ref>PMID:16527742</ref> <ref>PMID:21123384</ref> <ref>PMID:18288108</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/2kbo_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2kbo ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Human APOBEC3G exhibits anti-human immunodeficiency virus-1 (HIV-1) activity by deaminating cytidines of the minus strand of HIV-1. Here, we report a solution structure of the C-terminal deaminase domain of wild-type APOBEC3G. The interaction with DNA was examined. Many differences in the interaction were found between the wild type and recently studied mutant APOBEC3Gs. The position of the substrate cytidine, together with that of a DNA chain, in the complex, was deduced. Interestingly, the deamination reaction of APOBEC3G was successfully monitored using NMR signals in real time. Real-time monitoring has revealed that the third cytidine of the d(CCCA) segment is deaminated at an early stage and that then the second one is deaminated at a late stage, the first one not being deaminated at all. This indicates that the deamination is carried out in a strict 3' --&gt; 5' order. Virus infectivity factor (Vif) of HIV-1 counteracts the anti-HIV-1 activity of APOBEC3G. The structure of the N-terminal domain of APOBEC3G, with which Vif interacts, was constructed with homology modelling. The structure implies the mechanism of species-specific sensitivity of APOBEC3G to Vif action.
-
===Structure, interaction, and real-time monitoring of the enzymatic reaction of wild type APOBEC3G===
+
Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G.,Furukawa A, Nagata T, Matsugami A, Habu Y, Sugiyama R, Hayashi F, Kobayashi N, Yokoyama S, Takaku H, Katahira M EMBO J. 2009 Feb 18;28(4):440-51. Epub 2009 Jan 15. PMID:19153609<ref>PMID:19153609</ref>
-
{{ABSTRACT_PUBMED_19153609}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2kbo" style="background-color:#fffaf0;"></div>
-
[[2kbo]] 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=2KBO OCA].
+
== References ==
-
 
+
<references/>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:019153609</ref><references group="xtra"/>
+
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Furukawa, A.]]
+
[[Category: Large Structures]]
-
[[Category: Habu, Y.]]
+
[[Category: Furukawa A]]
-
[[Category: Hayashi, F.]]
+
[[Category: Habu Y]]
-
[[Category: Katahira, M.]]
+
[[Category: Hayashi F]]
-
[[Category: Kobayashi, N.]]
+
[[Category: Katahira M]]
-
[[Category: Matsugami, A.]]
+
[[Category: Kobayashi N]]
-
[[Category: Nagata, T.]]
+
[[Category: Matsugami A]]
-
[[Category: Sugiyama, R.]]
+
[[Category: Nagata T]]
-
[[Category: Takaku, H.]]
+
[[Category: Sugiyama R]]
-
[[Category: Yokoyama, S.]]
+
[[Category: Takaku H]]
-
[[Category: Antiviral defense]]
+
[[Category: Yokoyama S]]
-
[[Category: Apobec3g]]
+
-
[[Category: Cytidine deaminase]]
+
-
[[Category: Hiv]]
+
-
[[Category: Host-virus interaction]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Nucleus]]
+

Current revision

Structure, interaction, and real-time monitoring of the enzymatic reaction of wild type APOBEC3G

PDB ID 2kbo

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2kbo"
Personal tools