2nyt

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{{Seed}}
 
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[[Image:2nyt.png|left|200px]]
 
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==The APOBEC2 Crystal Structure and Functional Implications for AID==
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The line below this paragraph, containing "STRUCTURE_2nyt", creates the "Structure Box" on the page.
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<StructureSection load='2nyt' size='340' side='right'caption='[[2nyt]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2nyt]] is a 4 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=2NYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NYT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<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>
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{{STRUCTURE_2nyt| PDB=2nyt | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nyt OCA], [https://pdbe.org/2nyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nyt RCSB], [https://www.ebi.ac.uk/pdbsum/2nyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nyt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ABEC2_HUMAN ABEC2_HUMAN] Probable C to U editing enzyme whose physiological substrate is not yet known. Does not display detectable apoB mRNA editing. Has a low intrinsic cytidine deaminase activity. May play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:21496894</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2nyt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2nyt ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long alpha-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.
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===The APOBEC2 Crystal Structure and Functional Implications for AID===
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The APOBEC-2 crystal structure and functional implications for the deaminase AID.,Prochnow C, Bransteitter R, Klein MG, Goodman MF, Chen XS Nature. 2007 Jan 25;445(7126):447-51. Epub 2006 Dec 24. PMID:17187054<ref>PMID:17187054</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17187054}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2nyt" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17187054 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17187054}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2NYT is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYT OCA].
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==Reference==
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<ref group="xtra">PMID:17187054</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Bransteitter, R.]]
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[[Category: Large Structures]]
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[[Category: Chen, X.]]
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[[Category: Bransteitter R]]
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[[Category: Goodman, M.]]
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[[Category: Chen X]]
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[[Category: Klein, M.]]
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[[Category: Goodman M]]
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[[Category: Prochnow, C.]]
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[[Category: Klein M]]
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[[Category: Apobec]]
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[[Category: Prochnow C]]
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[[Category: Cytidine deaminase]]
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[[Category: Zinc-ion binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:09:59 2009''
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Current revision

The APOBEC2 Crystal Structure and Functional Implications for AID

PDB ID 2nyt

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