5w0u - Revision history

OCA at 14:04, 4 October 2023

2023-10-04T14:04:40Z

←Older revision		Revision as of 14:04, 4 October 2023
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	<StructureSection load='5w0u' size='340' side='right'caption='[[5w0u]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5w0u' size='340' side='right'caption='[[5w0u]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w0u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w0u]] is a 4 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=5W0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W0U FirstGlance]. <br>
-	</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=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 2.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w0r\|5w0r]], [[5w0z\|5w0z]]</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=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </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=5w0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0u OCA], [https://pdbe.org/5w0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w0u RCSB], [https://www.ebi.ac.uk/pdbsum/5w0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0u ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5w0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0u OCA], [~~http~~://pdbe.org/5w0u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w0u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w0u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0u ProSAT]</span></td></tr>	+
	</table>		</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 ==		== Function ==
-	[~~[http~~://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~~).	+	[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli O157:H7]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Single-stranded DNA cytosine deaminase]]~~	+	[[Category: Qiao Q]]
-	[[Category: Qiao, Q]]	+	[[Category: Wang L]]
-	[[Category: Wang, L]]	+	[[Category: Wu H]]
-	[[Category: Wu, H]]	+
-	~~[[Category: Class switch recombination]]~~	+
-	~~[[Category: Cytidine deaminase]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 08:46, 30 September 2020

2020-09-30T08:46:33Z

←Older revision		Revision as of 08:46, 30 September 2020
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	==Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP==		==Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP==
-	<StructureSection load='5w0u' size='340' side='right' caption='[[5w0u]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5w0u' size='340' side='right'caption='[[5w0u]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w0u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0U OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w0u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W0U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w0r\|5w0r]], [[5w0z\|5w0z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w0r\|5w0r]], [[5w0z\|5w0z]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </span></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=5w0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0u OCA], [http://pdbe.org/5w0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0u RCSB], [http://www.ebi.ac.uk/pdbsum/5w0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0u ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5w0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0u OCA], [http://pdbe.org/5w0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0u RCSB], [http://www.ebi.ac.uk/pdbsum/5w0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Single-stranded DNA cytosine deaminase]]		[[Category: Single-stranded DNA cytosine deaminase]]
	[[Category: Qiao, Q]]		[[Category: Qiao, Q]]

OCA: Protected "5w0u" [edit=sysop:move=sysop]

2017-08-17T06:07:05Z

Protected "5w0u" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:07, 17 August 2017

OCA: New page: ==Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP== == Structural highlights ==
<table><tr><td colspan='2'>[[5w0u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W0U FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5w0r|5w0r]], [[5w0z|5w0z]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </span></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=5w0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0u OCA], [http://pdbe.org/5w0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0u RCSB], [http://www.ebi.ac.uk/pdbsum/5w0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0u ProSAT]</span></td></tr>
</table>
== Function ==
[[http://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).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.

AID Recognizes Structured DNA for Class Switch Recombination.,Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H Mol Cell. 2017 Aug 3;67(3):361-373.e4. doi: 10.1016/j.molcel.2017.06.034. Epub, 2017 Jul 27. PMID:28757211<ref>PMID:28757211</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w0u" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Single-stranded DNA cytosine deaminase]]
[[Category: Qiao, Q]]
[[Category: Wang, L]]
[[Category: Wu, H]]
[[Category: Class switch recombination]]
[[Category: Cytidine deaminase]]
[[Category: Hydrolase-dna complex]]