View source for 5jj4


==Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein==
<StructureSection load='5jj4' size='340' side='right'caption='[[5jj4]], [[Resolution|resolution]] 2.81&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jj4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JJ4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.807&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900010:alpha-maltotetraose'>PRD_900010</scene>, <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=5jj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jj4 OCA], [https://pdbe.org/5jj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jj4 RCSB], [https://www.ebi.ac.uk/pdbsum/5jj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jj4 ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/AICDA_HUMAN AICDA_HUMAN] Hyper-IgM syndrome type 2. The disease is caused by mutations affecting the gene represented in this entry.
== Function ==
[https://www.uniprot.org/uniprot/AICDA_HUMAN AICDA_HUMAN] Single-stranded DNA-specific cytidine deaminase. Involved in somatic hypermutation (SHM), gene conversion, and class-switch recombination (CSR) in B-lymphocytes by deaminating C to U during transcription of Ig-variable (V) and Ig-switch (S) region DNA. Required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses (PubMed:18722174, PubMed:21385873, PubMed:21518874, PubMed:27716525). May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation (PubMed:21496894).<ref>PMID:18722174</ref> <ref>PMID:21385873</ref> <ref>PMID:21496894</ref> <ref>PMID:21518874</ref> <ref>PMID:27716525</ref> [https://www.uniprot.org/uniprot/MALE_ECO57 MALE_ECO57] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides (By similarity).
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== Publication Abstract from PubMed ==
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C--&gt;U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8A resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.

Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.,Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF DNA Repair (Amst). 2016 Jul;43:48-56. doi: 10.1016/j.dnarep.2016.05.029. Epub, 2016 May 13. PMID:27258794<ref>PMID:27258794</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5jj4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli O157:H7]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Afif SA]]
[[Category: Goodman MF]]
[[Category: Pedersen LC]]
[[Category: Pham P]]