5w09 - Revision history

OCA: Replacing page with 'REMOVED: The PDB entry 5w09 was removed.'

OCA — Wed, 07 Feb 2018 06:06:28 GMT

Replacing page with 'REMOVED: The PDB entry 5w09 was removed.'

←Older revision		Revision as of 06:06, 7 February 2018
Line 1:		Line 1:
-		+	REMOVED: The PDB entry 5w09 was removed.
-	~~==Crystal Structure of a twinned Human Activation-induced Cytidine Deaminase catalytic core (1-153) at 2.0A resolution==~~	+
-	~~<StructureSection load='5w09' size='340' side='right' caption='[[5w09]], [[Resolution\|resolution]] 2.00Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[5w09]] is a 1 chain structure. Full crystallographic information is available from [http~~:~~//oca.weizmann.ac.il/oca-bin/ocashort?id=5W09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W09 FirstGlance]. <br>~~	+
-	</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=5w09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w09 OCA], [http://pdbe.org/5w09 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w09 RCSB], [http://www.ebi.ac.uk/pdbsum/5w09 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w09 ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Disease ==~~	+
-	~~[[http://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 ==~~	+
-	[[http://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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1-153; AID(153)), an optimized in vitro folding procedure was ~~derived to obtain large amounts of AID(153), which led to crystals with good quality and to final structural determination~~. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis-to-trans proline isomerization, or vice versa, during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo. It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.	+
-		+
-	Hydrogen bonds are a primary driving force for de novo protein folding.,Lee S, Wang C, Liu H, Xiong J, Jiji R, Hong X, Yan X, Chen Z, Hammel M, Wang Y, Dai S, Wang J, Jiang C, Zhang G Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):955-969. doi:, 10.1107/S2059798317015303. Epub 2017 Nov 10. PMID:29199976<ref>PMID:29199976</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5w09" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Single-stranded DNA cytosine deaminase]]~~	+
-	~~[[Category: Dai, S]]~~	+
-	~~[[Category: Lee, S]]~~	+
-	~~[[Category: Wang, Y]]~~	+
-	~~[[Category: Zhang, G]]~~	+
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: B-cell]]~~	+
-	~~[[Category: Csr]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Shm]]~~	+

OCA at 06:17, 20 December 2017

OCA — Wed, 20 Dec 2017 06:17:18 GMT

←Older revision		Revision as of 06:17, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w09 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal Structure of a twinned Human Activation-induced Cytidine Deaminase catalytic core (1-153) at 2.0A resolution==
		+	<StructureSection load='5w09' size='340' side='right' caption='[[5w09]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5w09]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W09 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W09 FirstGlance]. <br>
		+	</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=5w09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w09 OCA], [http://pdbe.org/5w09 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w09 RCSB], [http://www.ebi.ac.uk/pdbsum/5w09 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w09 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://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 ==
		+	[[http://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;">
		+	== Publication Abstract from PubMed ==
		+	The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1-153; AID(153)), an optimized in vitro folding procedure was derived to obtain large amounts of AID(153), which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis-to-trans proline isomerization, or vice versa, during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo. It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.

-	~~Authors~~:	+	Hydrogen bonds are a primary driving force for de novo protein folding.,Lee S, Wang C, Liu H, Xiong J, Jiji R, Hong X, Yan X, Chen Z, Hammel M, Wang Y, Dai S, Wang J, Jiang C, Zhang G Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):955-969. doi:, 10.1107/S2059798317015303. Epub 2017 Nov 10. PMID:29199976<ref>PMID:29199976</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5w09" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Single-stranded DNA cytosine deaminase]]
		+	[[Category: Dai, S]]
		+	[[Category: Lee, S]]
		+	[[Category: Wang, Y]]
		+	[[Category: Zhang, G]]
		+	[[Category: Antibody]]
		+	[[Category: B-cell]]
		+	[[Category: Csr]]
		+	[[Category: Hydrolase]]
		+	[[Category: Shm]]

OCA: Protected "5w09" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:18:16 GMT

Protected "5w09" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:18, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w09 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 14:18:15 GMT

New page: '''Unreleased structure''' The entry 5w09 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5w09 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]